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122 results on '"Nitta, Kazuhiro R."'

3. Author Correction: Myt1l safeguards neuronal identity by actively repressing many non-neuronal fates

Author

Mall, Moritz, Kareta, Michael S., Chanda, Soham, Ahlenius, Henrik, Perotti, Nicholas, Zhou, Bo, Grieder, Sarah D., Ge, Xuecai, Drake, Sienna, Ang, Cheen Euong, Walker, Brandon M., Vierbuchen, Thomas, Fuentes, Daniel R., Brennecke, Philip, Nitta, Kazuhiro R., Jolma, Arttu, Steinmetz, Lars M., Taipale, Jussi, Südhof, Thomas C., and Wernig, Marius

Published
2024
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4. ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

Author

Brozovic, Matija, Dantec, Christelle, Dardaillon, Justine, Dauga, Delphine, Faure, Emmanuel, Gineste, Mathieu, Louis, Alexandra, Naville, Magali, Nitta, Kazuhiro R, Piette, Jacques, Reeves, Wendy, Scornavacca, Céline, Simion, Paul, Vincentelli, Renaud, Bellec, Maelle, Aicha, Sameh Ben, Fagotto, Marie, Guéroult-Bellone, Marion, Haeussler, Maximilian, Jacox, Edwin, Lowe, Elijah K, Mendez, Mickael, Roberge, Alexis, Stolfi, Alberto, Yokomori, Rui, Brown, C Titus, Cambillau, Christian, Christiaen, Lionel, Delsuc, Frédéric, Douzery, Emmanuel, Dumollard, Rémi, Kusakabe, Takehiro, Nakai, Kenta, Nishida, Hiroki, Satou, Yutaka, Swalla, Billie, Veeman, Michael, Volff, Jean-Nicolas, and Lemaire, Patrick

Subjects
Genetics, Bioengineering, Biotechnology, Human Genome, Animals, Biological Evolution, Ciona intestinalis, DNA, Data Mining, Databases, Genetic, Datasets as Topic, Evolution, Molecular, Gene Expression, Gene Ontology, Genome, Internet, Molecular Sequence Annotation, Phylogeny, Protein Binding, Species Specificity, Transcription Factors, Transcription, Genetic, Urochordata, Vertebrates, Web Browser, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Developmental Biology
Abstract

ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.

Published
2018

5. Fatal Perinatal Mitochondrial Cardiac Failure Caused by Recurrent De Novo Duplications in the ATAD3 Locus

Author

Frazier, Ann E., Compton, Alison G., Kishita, Yoshihito, Hock, Daniella H., Welch, AnneMarie E., Amarasekera, Sumudu S.C., Rius, Rocio, Formosa, Luke E., Imai-Okazaki, Atsuko, Francis, David, Wang, Min, Lake, Nicole J., Tregoning, Simone, Jabbari, Jafar S., Lucattini, Alexis, Nitta, Kazuhiro R., Ohtake, Akira, Murayama, Kei, Amor, David J., McGillivray, George, Wong, Flora Y., van der Knaap, Marjo S., Vermeulen, R. Jeroen, Wiltshire, Esko J., Fletcher, Janice M., Lewis, Barry, Baynam, Gareth, Ellaway, Carolyn, Balasubramaniam, Shanti, Bhattacharya, Kaustuv, Freckmann, Mary-Louise, Arbuckle, Susan, Rodriguez, Michael, Taft, Ryan J., Sadedin, Simon, Cowley, Mark J., Minoche, André E., Calvo, Sarah E., Mootha, Vamsi K., Ryan, Michael T., Okazaki, Yasushi, Stroud, David A., Simons, Cas, Christodoulou, John, and Thorburn, David R.

Published
2021
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9. Strategic validation of variants of uncertain significance inECHS1genetic testing

Author

Kishita, Yoshihito, primary, Sugiura, Ayumu, additional, Onuki, Takanori, additional, Ebihara, Tomohiro, additional, Matsuhashi, Tetsuro, additional, Shimura, Masaru, additional, Fushimi, Takuya, additional, Ichino, Noriko, additional, Nagatakidani, Yoshie, additional, Nishihata, Hitomi, additional, Nitta, Kazuhiro R, additional, Yatsuka, Yukiko, additional, Imai-Okazaki, Atsuko, additional, Wu, Yibo, additional, Osaka, Hitoshi, additional, Ohtake, Akira, additional, Murayama, Kei, additional, and Okazaki, Yasushi, additional

Published
2023
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11. Involvement of GLCCI1 in mouse spermatogenesis

Author

Takada, Masaru, primary, Fukuhara, Daisuke, additional, Takiura, Toshihiko, additional, Nishibori, Yukino, additional, Kotani, Masashi, additional, Kiuchi, Zentaro, additional, Kudo, Akihiko, additional, Beltcheva, Olga, additional, Ito‐Nitta, Noriko, additional, Nitta, Kazuhiro R., additional, Kimura, Toru, additional, Suehiro, Jun‐Ichi, additional, Katada, Tomohisa, additional, Takematsu, Hiromu, additional, and Yan, Kunimasa, additional

Published
2022
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12. Severe spinal cord hypoplasia due to a novel ATAD3A compound heterozygous deletion

Author

Ebihara, Tomohiro, primary, Nagatomo, Taro, additional, Sugiyama, Yohei, additional, Tsuruoka, Tomoko, additional, Osone, Yoshiteru, additional, Shimura, Masaru, additional, Tajika, Makiko, additional, Ichimoto, Keiko, additional, Naruke, Yuki, additional, Akiyama, Nana, additional, Lim, Sze Chern, additional, Yatsuka, Yukiko, additional, Nitta, Kazuhiro R., additional, Kishita, Yoshihito, additional, Fushimi, Takuya, additional, Okazaki, Atsuko, additional, Ohtake, Akira, additional, Okazaki, Yasushi, additional, and Murayama, Kei, additional

Published
2022
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13. Strategic validation of variants of uncertain significance inECHS1genetic testing

Author

Kishita, Yoshihito, primary, Sugiura, Ayumu, additional, Onuki, Takanori, additional, Ebihara, Tomohiro, additional, Matsuhashi, Tetsuro, additional, Shimura, Masaru, additional, Fushimi, Takuya, additional, Ichino, Noriko, additional, Nagatakidani, Yoshie, additional, Nishihata, Hitomi, additional, Nitta, Kazuhiro R, additional, Yatsuka, Yukiko, additional, Imai-Okazaki, Atsuko, additional, Wu, Yibo, additional, Osaka, Hitoshi, additional, Ohtake, Akira, additional, Murayama, Kei, additional, and Okazaki, Yasushi, additional

Published
2022
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14. Impact of measuring heteroplasmy of a pathogenic mitochondrial DNA variant at the single‐cell level in individuals with mitochondrial disease

Author

Imai‐Okazaki, Atsuko, primary, Nitta, Kazuhiro R., additional, Yatsuka, Yukiko, additional, Sugiura, Ayumu, additional, Arao, Masato, additional, Shimura, Masaru, additional, Ebihara, Tomohiro, additional, Onuki, Takanori, additional, Ichimoto, Keiko, additional, Ohtake, Akira, additional, Murayama, Kei, additional, and Okazaki, Yasushi, additional

Published
2022
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15. Novel ITPAvariants identified by whole genome sequencing and RNA sequencing

Author

Omichi, Nanako, Kishita, Yoshihito, Nakama, Mina, Sasai, Hideo, Terazawa, Atsushi, Kobayashi, Emiko, Fushimi, Takuya, Sugiyama, Yohei, Ichimoto, Keiko, Nitta, Kazuhiro R., Yatsuka, Yukiko, Ohtake, Akira, Murayama, Kei, and Okazaki, Yasushi

Abstract

Approximately 80% of rare diseases have a genetic cause, and an accurate genetic diagnosis is necessary for disease management, prognosis prediction, and genetic counseling. Whole-exome sequencing (WES) is a cost-effective approach for exploring the genetic cause, but several cases often remain undiagnosed. We combined whole genome sequencing (WGS) and RNA sequencing (RNA-seq) to identify the pathogenic variants in an unsolved case using WES. RNA-seq revealed aberrant exon 4 and exon 6 splicing of ITPA. WGS showed a previously unreported splicing donor variant, c.263+1G>A, and a novel heterozygous deletion, including exon 6. Detailed examination of the breakpoint indicated the deletion caused by recombination between Alu elements in different introns. The proband was found to have developmental and epileptic encephalopathies caused by variants in the ITPAgene. The combination of WGS and RNA-seq may be effective in diagnosing conditions in proband who could not be diagnosed using WES.

Published
2023
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16. Development of Leigh syndrome with a high probability of cardiac manifestations in infantile-onset patients with m.14453G > A

Author

Shimura, Masaru, primary, Onuki, Takanori, additional, Sugiyama, Yohei, additional, Matsuhashi, Tetsuro, additional, Ebihara, Tomohiro, additional, Fushimi, Takuya, additional, Tajika, Makiko, additional, Ichimoto, Keiko, additional, Matsunaga, Ayako, additional, Tsuruoka, Tomoko, additional, Nitta, Kazuhiro R, additional, Imai-Okazaki, Atsuko, additional, Yatsuka, Yukiko, additional, Kishita, Yoshihito, additional, Ohtake, Akira, additional, Okazaki, Yasushi, additional, and Murayama, Kei, additional

Published
2022
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17. Diverse Mechanisms of Resistance to Decitabine and Venetoclax Therapy in Newly Diagnosed and Relapsed/Refractory AML Inferred By Transcriptome Analysis

Author

Yamatani, Kotoko, primary, Tabe, Yoko, additional, Maiti, Abhishek, additional, Ai, Tomohiko, additional, Saito, Kaori, additional, Nitta, Kazuhiro R, additional, Kinjo, Sonoko, additional, Ikeo, Kazuho, additional, Miida, Takashi, additional, DiNardo, Courtney D., additional, Su, Xiaoping, additional, and Konopleva, Marina, additional

Published
2021
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18. Neonatal-onset mitochondrial disease: clinical features, molecular diagnosis and prognosis

Author

Ebihara, Tomohiro, primary, Nagatomo, Taro, additional, Sugiyama, Yohei, additional, Tsuruoka, Tomoko, additional, Osone, Yoshiteru, additional, Shimura, Masaru, additional, Tajika, Makiko, additional, Matsuhashi, Tetsuro, additional, Ichimoto, Keiko, additional, Matsunaga, Ayako, additional, Akiyama, Nana, additional, Ogawa-Tominaga, Minako, additional, Yatsuka, Yukiko, additional, Nitta, Kazuhiro R, additional, Kishita, Yoshihito, additional, Fushimi, Takuya, additional, Imai-Okazaki, Atsuko, additional, Ohtake, Akira, additional, Okazaki, Yasushi, additional, and Murayama, Kei, additional

Published
2021
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19. Long-term prognosis and genetic background of cardiomyopathy in 223 pediatric mitochondrial disease patients

Author

Imai-Okazaki, Atsuko, primary, Matsunaga, Ayako, additional, Yatsuka, Yukiko, additional, Nitta, Kazuhiro R., additional, Kishita, Yoshihito, additional, Sugiura, Ayumu, additional, Sugiyama, Yohei, additional, Fushimi, Takuya, additional, Shimura, Masaru, additional, Ichimoto, Keiko, additional, Tajika, Makiko, additional, Ogawa-Tominaga, Minako, additional, Ebihara, Tomohiro, additional, Matsuhashi, Tetsuro, additional, Tsuruoka, Tomoko, additional, Kohda, Masakazu, additional, Hirata, Tomoko, additional, Harashima, Hiroko, additional, Nojiri, Shuko, additional, Takeda, Atsuhito, additional, Nakaya, Akihiro, additional, Kogaki, Shigetoyo, additional, Sakata, Yasushi, additional, Ohtake, Akira, additional, Murayama, Kei, additional, and Okazaki, Yasushi, additional

Published
2021
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21. Genome sequencing and RNA‐seq analyses of mitochondrial complex I deficiency revealed Alu insertion‐mediated deletion in NDUFV2

Author

Kishita, Yoshihito, primary, Shimura, Masaru, additional, Kohda, Masakazu, additional, Fushimi, Takuya, additional, Nitta, Kazuhiro R., additional, Yatsuka, Yukiko, additional, Hirose, Shinichi, additional, Ideguchi, Hiroshi, additional, Ohtake, Akira, additional, Murayama, Kei, additional, and Okazaki, Yasushi, additional

Published
2021
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24. Strategic validation of variants of uncertain significance in ECHS1genetic testing

Author

Kishita, Yoshihito, Sugiura, Ayumu, Onuki, Takanori, Ebihara, Tomohiro, Matsuhashi, Tetsuro, Shimura, Masaru, Fushimi, Takuya, Ichino, Noriko, Nagatakidani, Yoshie, Nishihata, Hitomi, Nitta, Kazuhiro R, Yatsuka, Yukiko, Imai-Okazaki, Atsuko, Wu, Yibo, Osaka, Hitoshi, Ohtake, Akira, Murayama, Kei, and Okazaki, Yasushi

Abstract

BackgroundEnoyl-CoA hydratase short-chain 1 (ECHS1) is an enzyme involved in the metabolism of branched chain amino acids and fatty acids. Mutations in the ECHS1gene lead to mitochondrial short-chain enoyl-CoA hydratase 1 deficiency, resulting in the accumulation of intermediates of valine. This is one of the most common causative genes in mitochondrial diseases. While genetic analysis studies have diagnosed numerous cases with ECHS1variants, the increasing number of variants of uncertain significance (VUS) in genetic diagnosis is a major problem.MethodsHere, we constructed an assay system to verify VUS function for ECHS1gene. A high-throughput assay using ECHS1knockout cells was performed to index these phenotypes by expressing cDNAs containing VUS. In parallel with the VUS validation system, a genetic analysis of samples from patients with mitochondrial disease was performed. The effect on gene expression in cases was verified by RNA-seq and proteome analysis.ResultsThe functional validation of VUS identified novel variants causing loss of ECHS1function. The VUS validation system also revealed the effect of the VUS in the compound heterozygous state and provided a new methodology for variant interpretation. Moreover, we performed multiomics analysis and identified a synonymous substitution p.P163= that results in splicing abnormality. The multiomics analysis complemented the diagnosis of some cases that could not be diagnosed by the VUS validation system.ConclusionsIn summary, this study uncovered new ECHS1cases based on VUS validation and omics analysis; these analyses are applicable to the functional evaluation of other genes associated with mitochondrial disease.

Published
2023
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25. Functional annotation of human long noncoding RNAs via molecular phenotyping

Author

Ramilowski, Jordan A., Yip, Chi Wai, Agrawal, Saumya, Chang, Jen-Chien, Ciani, Yari, Kulakovskiy, Ivan V., Mendez, Mickaël, Ooi, Jasmine Li Ching, Ouyang, John F., Parkinson, Nicholas J., Petri, Andreas, Roos, Leonie, Severin, Jessica, Yasuzawa, Kayoko, Abugessaisa, Imad, Akalin, Altuna, Antonov, Ivan V., Arner, Erik, Bonetti, Alessandro, Bono, Hidemasa, Borsari, Beatrice, Brombacher, Frank, Cameron, Christopher J.F., Cannistraci, Carlo V., Cardenas, Ryan, Cardon, Melissa, Chang, Howard, Dostie, Josée, Ducoli, Luca, Favorov, Alexander V., Fort, Alexandre, Garrido, Diego, Gil, Noa, Gimenez, Juliette, Guler, Reto, Handoko, Lusy, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Kosuke, Hayatsu, Norihito, Heutink, Peter, Hirose, Tetsuro, Imada, Eddie L., Itoh, Masayoshi, Kaczkowski, Bogumil, Kanhere, Aditi S., Kawabata, Emily, Kawaji, Hideya, Kawashima, Tsugumi, Kelly, S. Thomas, Kojima, Miki, Kondo, Naoto, Koseki, Haruhiko, Kouno, Tsukasa, Kratz, Anton, Kurowska-Stolarska, Mariola S., Kwon, Andrew Tae Jun, Leek, Jeffrey T., Lennartsson, Andreas, Lizio, Marina, López-Redondo, Fernando, Luginbühl, Joachim, Maeda, Shiori, Makeev, Vsevolod, Marchionni, Luigi, Medvedeva, Yulia A., Minoda, Aki, Müller, Ferenc, Muñoz-Aguirre, Manuel, Murata, Mitsuyoshi, Nishiyori, Hiromi, Nitta, Kazuhiro R., Noguchi, Shuhei, Noro, Yukihiko, Nurtdinov, Ramil N., Okazaki, Yasushi, Orlando, Valerio, Paquette, Denis, Parr, Callum J.C., Rackham, Owen J.L., Rizzu, Patrizia, Sánchez Martinez, Diego Fernando, Sandelin, Albin, Sanjana, Pillay, Semple, Colin A.M., Shibayama, Youtaro, Sivaraman, Divya M., Szumowski, Suzannah C., Tagami, Michihira, Taylor, Martin S., Terao, Chikashi, Thodberg, Malte, Thongjuea, Supat, Tripathi, Vidisha, Ulitsky, Igor, Verardo, Roberto, Vorontsov, Ilya E., Yamamoto, Chinatsu, Baillie, J. Kenneth, Forrest, Alistair R.R., Guigó, Roderic, Hoffman, Michael, Hon, Chungchau, Kasukawa, Takeya, Kauppinen, Sakari, Kere, Jura, Lenhard, Boris, Schneider, Claudio, Suzuki, Harukazu, Yagi, Ken, de Hoon, Michiel J.L., Shin, Jay W., and Carninci, Piero

Abstract

Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2., Genome Research, 30 (7), ISSN:1088-9051, ISSN:1549-5469

Published
2020

26. XSIP1 is essential for early neural gene expression and neural differentiation by suppression of BMP signaling

Author

Nitta, Kazuhiro R., Tanegashima, Kousuke, Takahashi, Shuji, and Asashima, Makoto

Subjects
Gene expression -- Observations, Developmental neurology -- Observations, Neurogenetics -- Observations, Biological sciences
Abstract

Neural differentiation is induced by inhibition of BMP signaling. Secreted inhibitors of BMP such as Chordin from the Spemann organizer contribute to the initial step of neural induction. Xenopus Smad-interacting protein-1 gene (XSIP1) is expressed in neuroectoderm from the early gastrula stage through to the neurula stage. XSIPI is able to inhibit BMP signaling and overexpression of XS1PI induces neural differentiation. To clarify the function of XSIP1 in neural differentiation, we performed a loss-of-function study of XSIP1. Knockdown of XSIP1 inhibited SoxD expression and neural differentiation. These results indicate that XS1P1 is essential for neural induction. Furthermore, loss-of-function experiments showed that SoxD is essential for XSIP1 transcription and for neural differentiation. However, inhibition of XSIP1 translation prevented neural differentiation induced by SoxD; thus, SoxD was not sufficient to mediate neural differentiation. Expression of XSIPI was also required for inhibition of BMP signaling. Together, these results suggest that XSIP1 and SoxD interdependently function to maintain neural differentiation. Keywords: XSIP1; Xenopus; Neural induction; [delta]EF1/ZFH family; SoxD; BMP; Zinc finger

Published
2004

27. Neonatal-onset mitochondrial disease: clinical features, molecular diagnosis and prognosis.

Author

Tomohiro Ebihara, Taro Nagatomo, Yohei Sugiyama, Tomoko Tsuruoka, Yoshiteru Osone, Masaru Shimura, Makiko Tajika, Tetsuro Matsuhashi, Keiko Ichimoto, Ayako Matsunaga, Nana Akiyama, Minako Ogawa-Tominaga, Yukiko Yatsuka, Nitta, Kazuhiro R., Yoshihito Kishita, Takuya Fushimi, Atsuko Imai-Okazaki, Akira Ohtake, Yasushi Okazaki, and Kei Murayama

Subjects
DNA, GENETIC mutation, MITOCHONDRIAL pathology, PROGNOSIS, LEIGH disease
Abstract

Objective: Neonatal-onset mitochondrial disease has not been fully characterised owing to its heterogeneity. We analysed neonatal-onset mitochondrial disease in Japan to clarify its clinical features, molecular diagnosis and prognosis.Design: Retrospective observational study from January 2004 to March 2020.Setting: Population based.Patients: Patients (281) with neonatal-onset mitochondrial disease diagnosed by biochemical and genetic approaches.Interventions: None.Main Outcome Measures: Disease types, initial symptoms, biochemical findings, molecular diagnosis and prognosis.Results: Of the 281 patients, multisystem mitochondrial disease was found in 194, Leigh syndrome in 26, cardiomyopathy in 38 and hepatopathy in 23 patients. Of the 321 initial symptoms, 236 occurred within 2 days of birth. Using biochemical approaches, 182 patients were diagnosed by mitochondrial respiratory chain enzyme activity rate and 89 by oxygen consumption rate. The remaining 10 patients were diagnosed using a genetic approach. Genetic analysis revealed 69 patients had nuclear DNA variants in 36 genes, 11 of 15 patients had mitochondrial DNA variants in five genes and four patients had single large deletion. The Cox proportional hazards regression analysis showed the effects of Leigh syndrome (HR=0.15, 95% CI 0.04 to 0.63, p=0.010) and molecular diagnosis (HR=1.87, 95% CI 1.18 to 2.96, p=0.008) on survival.Conclusions: Neonatal-onset mitochondrial disease has a heterogenous aetiology. The number of diagnoses can be increased, and clarity regarding prognosis can be achieved by comprehensive biochemical and molecular analyses using appropriate tissue samples. [ABSTRACT FROM AUTHOR]

Published
2022
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28. Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping

Author

Ramilowski, Jordan A., primary, Yip, Chi Wai, additional, Agrawal, Saumya, additional, Chang, Jen-Chien, additional, Ciani, Yari, additional, Kulakovskiy, Ivan V., additional, Mendez, Mickaël, additional, Ooi, Jasmine Li Ching, additional, Ouyang, John F., additional, Parkinson, Nick, additional, Petri, Andreas, additional, Roos, Leonie, additional, Severin, Jessica, additional, Yasuzawa, Kayoko, additional, Abugessaisa, Imad, additional, Akalin, Altuna, additional, Antonov, Ivan V., additional, Arner, Erik, additional, Bonetti, Alessandro, additional, Bono, Hidemasa, additional, Borsari, Beatrice, additional, Brombacher, Frank, additional, Cameron, Christopher J.F., additional, Cannistraci, Carlo Vittorio, additional, Cardenas, Ryan, additional, Cardon, Melissa, additional, Chang, Howard, additional, Dostie, Josée, additional, Ducoli, Luca, additional, Favorov, Alexander, additional, Fort, Alexandre, additional, Garrido, Diego, additional, Gil, Noa, additional, Gimenez, Juliette, additional, Guler, Reto, additional, Handoko, Lusy, additional, Harshbarger, Jayson, additional, Hasegawa, Akira, additional, Hasegawa, Yuki, additional, Hashimoto, Kosuke, additional, Hayatsu, Norihito, additional, Heutink, Peter, additional, Hirose, Tetsuro, additional, Imada, Eddie L., additional, Itoh, Masayoshi, additional, Kaczkowski, Bogumil, additional, Kanhere, Aditi, additional, Kawabata, Emily, additional, Kawaji, Hideya, additional, Kawashima, Tsugumi, additional, Kelly, S. Thomas, additional, Kojima, Miki, additional, Kondo, Naoto, additional, Koseki, Haruhiko, additional, Kouno, Tsukasa, additional, Kratz, Anton, additional, Kurowska-Stolarska, Mariola, additional, Kwon, Andrew Tae Jun, additional, Leek, Jeffrey, additional, Lennartsson, Andreas, additional, Lizio, Marina, additional, López-Redondo, Fernando, additional, Luginbühl, Joachim, additional, Maeda, Shiori, additional, Makeev, Vsevolod J., additional, Marchionni, Luigi, additional, Medvedeva, Yulia A., additional, Minoda, Aki, additional, Müller, Ferenc, additional, Muñoz-Aguirre, Manuel, additional, Murata, Mitsuyoshi, additional, Nishiyori, Hiromi, additional, Nitta, Kazuhiro R., additional, Noguchi, Shuhei, additional, Noro, Yukihiko, additional, Nurtdinov, Ramil, additional, Okazaki, Yasushi, additional, Orlando, Valerio, additional, Paquette, Denis, additional, Parr, Callum J.C., additional, Rackham, Owen J.L., additional, Rizzu, Patrizia, additional, Martinez, Diego Fernando Sánchez, additional, Sandelin, Albin, additional, Sanjana, Pillay, additional, Semple, Colin A.M., additional, Shibayama, Youtaro, additional, Sivaraman, Divya M., additional, Suzuki, Takahiro, additional, Szumowski, Suzannah C., additional, Tagami, Michihira, additional, Taylor, Martin S., additional, Terao, Chikashi, additional, Thodberg, Malte, additional, Thongjuea, Supat, additional, Tripathi, Vidisha, additional, Ulitsky, Igor, additional, Verardo, Roberto, additional, Vorontsov, Ilya E., additional, Yamamoto, Chinatsu, additional, Young, Robert S., additional, Baillie, J. Kenneth, additional, Forrest, Alistair R.R., additional, Guigó, Roderic, additional, Hoffman, Michael M., additional, Hon, Chung Chau, additional, Kasukawa, Takeya, additional, Kauppinen, Sakari, additional, Kere, Juha, additional, Lenhard, Boris, additional, Schneider, Claudio, additional, Suzuki, Harukazu, additional, Yagi, Ken, additional, de Hoon, Michiel J.L., additional, Shin, Jay W., additional, and Carninci, Piero, additional

Published
2020
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29. A homozygous variant inNDUFA8is associated with developmental delay, microcephaly, and epilepsy due to mitochondrial complex I deficiency

Author

Yatsuka, Yukiko, primary, Kishita, Yoshihito, additional, Formosa, Luke E., additional, Shimura, Masaru, additional, Nozaki, Fumihito, additional, Fujii, Tatsuya, additional, Nitta, Kazuhiro R., additional, Ohtake, Akira, additional, Murayama, Kei, additional, Ryan, Michael T., additional, and Okazaki, Yasushi, additional

Published
2020
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30. ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates

Author

Dardaillon, Justine, primary, Dauga, Delphine, additional, Simion, Paul, additional, Faure, Emmanuel, additional, Onuma, Takeshi A, additional, DeBiasse, Melissa B, additional, Louis, Alexandra, additional, Nitta, Kazuhiro R, additional, Naville, Magali, additional, Besnardeau, Lydia, additional, Reeves, Wendy, additional, Wang, Kai, additional, Fagotto, Marie, additional, Guéroult-Bellone, Marion, additional, Fujiwara, Shigeki, additional, Dumollard, Rémi, additional, Veeman, Michael, additional, Volff, Jean-Nicolas, additional, Roest Crollius, Hugues, additional, Douzery, Emmanuel, additional, Ryan, Joseph F, additional, Davidson, Bradley, additional, Nishida, Hiroki, additional, Dantec, Christelle, additional, and Lemaire, Patrick, additional

Published
2019
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31. Neonatal-onset mitochondrial disease: clinical features, molecular diagnosis and prognosis

Author

Ebihara, Tomohiro, Nagatomo, Taro, Sugiyama, Yohei, Tsuruoka, Tomoko, Osone, Yoshiteru, Shimura, Masaru, Tajika, Makiko, Matsuhashi, Tetsuro, Ichimoto, Keiko, Matsunaga, Ayako, Akiyama, Nana, Ogawa-Tominaga, Minako, Yatsuka, Yukiko, Nitta, Kazuhiro R, Kishita, Yoshihito, Fushimi, Takuya, Imai-Okazaki, Atsuko, Ohtake, Akira, Okazaki, Yasushi, and Murayama, Kei

Abstract

ObjectiveNeonatal-onset mitochondrial disease has not been fully characterised owing to its heterogeneity. We analysed neonatal-onset mitochondrial disease in Japan to clarify its clinical features, molecular diagnosis and prognosis.DesignRetrospective observational study from January 2004 to March 2020.SettingPopulation based.PatientsPatients (281) with neonatal-onset mitochondrial disease diagnosed by biochemical and genetic approaches.InterventionsNone.Main outcome measuresDisease types, initial symptoms, biochemical findings, molecular diagnosis and prognosis.ResultsOf the 281 patients, multisystem mitochondrial disease was found in 194, Leigh syndrome in 26, cardiomyopathy in 38 and hepatopathy in 23 patients. Of the 321 initial symptoms, 236 occurred within 2 days of birth. Using biochemical approaches, 182 patients were diagnosed by mitochondrial respiratory chain enzyme activity rate and 89 by oxygen consumption rate. The remaining 10 patients were diagnosed using a genetic approach. Genetic analysis revealed 69 patients had nuclear DNA variants in 36 genes, 11 of 15 patients had mitochondrial DNA variants in five genes and four patients had single large deletion. The Cox proportional hazards regression analysis showed the effects of Leigh syndrome (HR=0.15, 95% CI 0.04 to 0.63, p=0.010) and molecular diagnosis (HR=1.87, 95% CI 1.18 to 2.96, p=0.008) on survival.ConclusionsNeonatal-onset mitochondrial disease has a heterogenous aetiology. The number of diagnoses can be increased, and clarity regarding prognosis can be achieved by comprehensive biochemical and molecular analyses using appropriate tissue samples.

Published
2022
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32. ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

Author

40314174, Brozovic, Matija, Dantec, Christelle, Dardaillon, Justine, Dauga, Delphine, Faure, Emmanuel, Gineste, Mathieu, Louis, Alexandra, Naville, Magali, Nitta, Kazuhiro R, Piette, Jacques, Reeves, Wendy, Scornavacca, Céline, Simion, Paul, Vincentelli, Renaud, Bellec, Maelle, Aicha, Sameh Ben, Fagotto, Marie, Guéroult-Bellone, Marion, Haeussler, Maximilian, Jacox, Edwin, Lowe, Elijah K, Mendez, Mickael, Roberge, Alexis, Stolfi, Alberto, Yokomori, Rui, Brown, C Titus, Cambillau, Christian, Christiaen, Lionel, Delsuc, Frédéric, Douzery, Emmanuel, Dumollard, Rémi, Kusakabe, Takehiro, Nakai, Kenta, Nishida, Hiroki, Satou, Yutaka, Swalla, Billie, Veeman, Michael, Volff, Jean-Nicolas, Lemaire, Patrick, 40314174, Brozovic, Matija, Dantec, Christelle, Dardaillon, Justine, Dauga, Delphine, Faure, Emmanuel, Gineste, Mathieu, Louis, Alexandra, Naville, Magali, Nitta, Kazuhiro R, Piette, Jacques, Reeves, Wendy, Scornavacca, Céline, Simion, Paul, Vincentelli, Renaud, Bellec, Maelle, Aicha, Sameh Ben, Fagotto, Marie, Guéroult-Bellone, Marion, Haeussler, Maximilian, Jacox, Edwin, Lowe, Elijah K, Mendez, Mickael, Roberge, Alexis, Stolfi, Alberto, Yokomori, Rui, Brown, C Titus, Cambillau, Christian, Christiaen, Lionel, Delsuc, Frédéric, Douzery, Emmanuel, Dumollard, Rémi, Kusakabe, Takehiro, Nakai, Kenta, Nishida, Hiroki, Satou, Yutaka, Swalla, Billie, Veeman, Michael, Volff, Jean-Nicolas, and Lemaire, Patrick

Abstract

ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.

Published
2018

33. ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

Author

Brozovic, Matija, Dantec, Christelle, Dardaillon, Justine, Dauga, Delphine, Faure, Emmanuel, Gineste, Mathieu, Louis, Alexandra, Naville, Magali, Nitta, Kazuhiro R, Piette, Jacques, Reeves, Wendy, Scornavacca, Céline, Simion, Paul, Vincentelli, Renaud, Bellec, Maelle, Aicha, Sameh Ben, Fagotto, Marie, Guéroult-Bellone, Marion, Haeussler, Maximilian, Jacox, Edwin, Lowe, Elijah K, Mendez, Mickael, Roberge, Alexis, Stolfi, Alberto, Yokomori, Rui, Brown, CTitus, Cambillau, Christian, Christiaen, Lionel, Delsuc, Frédéric, Douzery, Emmanuel, Dumollard, Rémi, Kusakabe, Takehiro, Nakai, Kenta, Nishida, Hiroki, Satou, Yutaka, Swalla, Billie, Veeman, Michael, Volff, Jean-Nicolas, Lemaire, Patrick, Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Bioself Communication [Marseille], Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Visual Objects from Reality To Expression (VORTEX), Institut de recherche en informatique de Toulouse (IRIT), Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF)-Centre National de la Recherche Scientifique (CNRS), Kansas State University, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Santa Cruz Genomics Institute, University of California [Santa Cruz] (UCSC), University of California-University of California, Michigan State University [East Lansing], Michigan State University System, School of Biology [Atlanta], Georgia Institute of Technology [Atlanta], The University of Tokyo, New York University [New York] (NYU), NYU System (NYU), Konan University [Kobe, Japan], Osaka University [Osaka], Kyoto University [Kyoto], Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Centre de recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Real Expression Artificial Life (IRIT-REVA), Université Toulouse Capitole (UT Capitole), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Toulouse Mind & Brain Institut (TMBI), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse Capitole (UT Capitole), Institut de biologie de l'ENS Paris (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC)-University of California (UC), The University of Tokyo (UTokyo), Kyoto University, Godin, Christophe, Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse 1 Capitole (UT1), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Toulouse Mind & Brain Institut (TMBI), Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), ANR-16-CE92-0019,EVOBOOSTER,Impact des éléments transposables sur les réseaux de régulation génique : application aux voies biologiques à évolution rapide chez les poissons(2016), and Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)

Subjects
Transcription, Genetic, Evolution, Datasets as Topic, Gene Expression, Bioengineering, Web Browser, Evolution, Molecular, Databases, Genetic, Species Specificity, Information and Computing Sciences, Databases, Genetic, Genetics, Animals, Data Mining, Database Issue, natural sciences, Urochordata, Phylogeny, Internet, Genome, Human Genome, Molecular, Molecular Sequence Annotation, DNA, Biological Sciences, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Biological Evolution, Ciona intestinalis, Gene Ontology, Vertebrates, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, Transcription, Environmental Sciences, Biotechnology, Developmental Biology, Protein Binding, Transcription Factors
Abstract

International audience; ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.

Published
2017
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34. A homozygous variant in NDUFA8 is associated with developmental delay, microcephaly, and epilepsy due to mitochondrial complex I deficiency.

Author

Yatsuka, Yukiko, Kishita, Yoshihito, Formosa, Luke E., Shimura, Masaru, Nozaki, Fumihito, Fujii, Tatsuya, Nitta, Kazuhiro R., Ohtake, Akira, Murayama, Kei, Ryan, Michael T., and Okazaki, Yasushi

Subjects
DEVELOPMENTAL delay, ZIKA virus infections, EPILEPSY, MULTIENZYME complexes, HUMAN abnormalities, OXYGEN consumption
Abstract

Mitochondrial complex I deficiency is caused by pathogenic variants in mitochondrial and nuclear genes associated with complex I structure and assembly. We report the case of a patient with NDUFA8‐related mitochondrial disease. The patient presented with developmental delay, microcephaly, and epilepsy. His fibroblasts showed apparent biochemical defects in mitochondrial complex I. Whole‐exome sequencing revealed that the patient carried a homozygous variant in NDUFA8. His fibroblasts showed a reduction in the protein expression level of not only NDUFA8, but also the other complex I subunits, consistent with assembly defects. The enzyme activity of complex I and oxygen consumption rate were restored by reintroducing wild‐typeNDUFA8 cDNA into patient fibroblasts. The functional properties of the variant in NDUFA8 were also investigated using NDUFA8 knockout cells expressing wild‐type or mutated NDUFA8 cDNA. These experiments further supported the pathogenicity of the variant in complex I assembly. This is the first report describing that the loss of NDUFA8, which has not previously been associated with mitochondrial disease, causes severe defect in the assembly of mitochondrial complex I, leading to progressive neurological and developmental abnormalities. [ABSTRACT FROM AUTHOR]

Published
2020
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35. ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates.

Author

Dardaillon, Justine, Dauga, Delphine, Simion, Paul, Faure, Emmanuel, Onuma, Takeshi A, DeBiasse, Melissa B, Louis, Alexandra, Nitta, Kazuhiro R, Naville, Magali, Besnardeau, Lydia, Reeves, Wendy, Wang, Kai, Fagotto, Marie, Guéroult-Bellone, Marion, Fujiwara, Shigeki, Dumollard, Rémi, Veeman, Michael, Volff, Jean-Nicolas, Roest Crollius, Hugues, and Douzery, Emmanuel

Published
2020
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36. Myt1l safeguards neuronal identity by actively repressing many non-neuronal fates

Author

University of Helsinki, Medicum, Mall, Moritz, Kareta, Michael S., Chanda, Soham, Ahlenius, Henrik, Perotti, Nicholas, Zhou, Bo, Grieder, Sarah D., Ge, Xuecai, Drake, Sienna, Ang, Cheen Euong, Walker, Brandon M., Vierbuchen, Thomas, Fuentes, Daniel R., Brennecke, Philip, Nitta, Kazuhiro R., Jolma, Arttu, Steinmetz, Lars M., Taipale, Jussi, Sudhof, Thomas C., Wernig, Marius, University of Helsinki, Medicum, Mall, Moritz, Kareta, Michael S., Chanda, Soham, Ahlenius, Henrik, Perotti, Nicholas, Zhou, Bo, Grieder, Sarah D., Ge, Xuecai, Drake, Sienna, Ang, Cheen Euong, Walker, Brandon M., Vierbuchen, Thomas, Fuentes, Daniel R., Brennecke, Philip, Nitta, Kazuhiro R., Jolma, Arttu, Steinmetz, Lars M., Taipale, Jussi, Sudhof, Thomas C., and Wernig, Marius

Abstract

Normal differentiation and induced reprogramming require the activation of target cell programs and silencing of donor cell programs(1,2). In reprogramming, the same factors are often used to reprogram many different donor cell types3. As most developmental repressors, such as RE1-silencing transcription factor (REST) and Groucho (also known as TLE), are considered lineage-specific repressors(4,5), it remains unclear how identical combinations of transcription factors can silence so many different donor programs. Distinct lineage repressors would have to be induced in different donor cell types. Here, by studying the reprogramming of mouse fibroblasts to neurons, we found that the pan neuron-specific transcription factor Myt1-like (Myt1l)(6) exerts its pro-neuronal function by direct repression of many different somatic lineage programs except the neuronal program. The repressive function of Myt1l is mediated via recruitment of a complex containing Sin3b by binding to a previously uncharacterized N-terminal domain. In agreement with its repressive function, the genomic binding sites of Myt1l are similar in neurons and fibroblasts and are preferentially in an open chromatin configuration. The Notch signalling pathway is repressed by Myt1l through silencing of several members, including Hes1. Acute knockdown of Myt1l in the developing mouse brain mimicked a Notch gain-of-function phenotype, suggesting that Myt1l allows newborn neurons to escape Notch activation during normal development. Depletion of Myt1l in primary postmitotic neurons de-repressed non-neuronal programs and impaired neuronal gene expression and function, indicating that many somatic lineage programs are actively and persistently repressed by Myt1l to maintain neuronal identity. It is now tempting to speculate that similar 'many-but-one' lineage repressors exist for other cell fates; such repressors, in combination with lineage-specific activators, would be prime candidates for use in reprogramming ad

Published
2017

37. Spacer sequences separating transcription factor binding motifs set enhancer quality and strength

Author

Guéroult-Bellone, Marion, primary, Nitta, Kazuhiro R., additional, Kari, Willi, additional, Jacox, Edwin, additional, Beulé Dauzat, Rémy, additional, Vincentelli, Renaud, additional, Diarra, Carine, additional, Rothbächer, Ute, additional, Dantec, Christelle, additional, Cambillau, Christian, additional, Piette, Jacques, additional, and Lemaire, Patrick, additional

Published
2017
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41. Involvement of GLCCI1 in mouse spermatogenesis.

Author

Masaru Takada, Daisuke Fukuhara, Toshihiko Takiura, Yukino Nishibori, Masashi Kotani, Zentaro Kiuchi, Akihiko Kudo, Beltcheva, Olga, Noriko Ito-Nitta, Nitta, Kazuhiro R., Toru Kimura, Jun-Ichi Suehiro, Tomohisa Katada, Hiromu Takematsu, and Kunimasa Yan

Published
2023
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42. DNA-Binding Specificities of Human Transcription Factors

Author

Jolma, Arttu, primary, Yan, Jian, additional, Whitington, Thomas, additional, Toivonen, Jarkko, additional, Nitta, Kazuhiro R., additional, Rastas, Pasi, additional, Morgunova, Ekaterina, additional, Enge, Martin, additional, Taipale, Mikko, additional, Wei, Gonghong, additional, Palin, Kimmo, additional, Vaquerizas, Juan M., additional, Vincentelli, Renaud, additional, Luscombe, Nicholas M., additional, Hughes, Timothy R., additional, Lemaire, Patrick, additional, Ukkonen, Esko, additional, Kivioja, Teemu, additional, and Taipale, Jussi, additional

Published
2013
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44. Conservation of transcription factor binding specificities across 600 million years of bilateria evolution.

Author

Furlong, Eileen E. M., Taipale, Jussi, Nitta, Kazuhiro R., Yimeng Yin, Morgunova, Ekaterina, Jolma, Arttu, Deplancke, Bart, Kivioja, Teemu, Akhtar, Junaid, Toivonen, Jarkko, and Hens, Korneel

Subjects
TRANSCRIPTION factors, CARRIER proteins, DROSOPHILA, BILATERIA, DINUCLEOTIDES
Abstract

The article presents a study related to divergence morphology, conducted on Drosophila. This study determines the binding specificities of 242 Drosophila transcription factors (TFs), and compares them to human and mouse data. Discussing dinucleotide binding preferences and orthologous TFs, it is inferred that evolution of TF specificities contributes to emergence of novel types of differentiated cells.

Published
2015
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46. Hem R is an Omp R/ Pho B-like response regulator from L eptospira, which simultaneously effects transcriptional activation and repression of key haem metabolism genes.

Author

Morero, Natalia R., Botti, Horacio, Nitta, Kazuhiro R., Carrión, Federico, Obal, Gonzalo, Picardeau, Mathieu, and Buschiazzo, Alejandro

Subjects
LEPTOSPIRA, LEPTOSPIROSIS, GENETIC transcription, CELLULAR signal transduction, CRYSTAL structure
Abstract

Several L eptospira species cause leptospirosis, the most extended zoonosis worldwide. In bacteria, two-component systems constitute key signalling pathways, some of which are involved in pathogenesis. The physiological roles of two-component systems in L eptospira are largely unknown, despite identifying several dozens within their genomes. Biochemical confirmation of an operative phosphorelaying two-component system has been obtained so far only for the Hklep/ Rrlep pair. It is known that hklep / rrlep knockout strains of L eptospira biflexa result in haem auxotrophy, although their de novo biosynthesis machinery remains fully functional. Haem is essential for L eptospira, but information about Hklep/ Rrlep effector function(s) and target(s) is still lacking. We are now reporting a thorough molecular characterization of this system, which we rename Hem K/ Hem R. The DNA Hem R-binding motif was determined, and found within the genomes of saprophyte and pathogenic L eptospira. In this way, putative Hem R-regulated genes were pinpointed, including haem catabolism-related ( hmuO - haem oxygenase) and biosynthesis-related (the hemA/C/D/B/L/E/N/G operon). Specific HemR binding to these two promoters was quantified, and a dual function was observed in vivo, inversely repressing the hmuO, while activating the hemA operon transcription. The crystal structure of Hem R receiver domain was determined, leading to a mechanistic model for its dual regulatory role. [ABSTRACT FROM AUTHOR]

Published
2014
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47. Fatal Perinatal Mitochondrial Cardiac Failure Caused by Recurrent De NovoDuplications in the ATAD3Locus

Author

Frazier, Ann E., Compton, Alison G., Kishita, Yoshihito, Hock, Daniella H., Welch, AnneMarie E., Amarasekera, Sumudu S.C., Rius, Rocio, Formosa, Luke E., Imai-Okazaki, Atsuko, Francis, David, Wang, Min, Lake, Nicole J., Tregoning, Simone, Jabbari, Jafar S., Lucattini, Alexis, Nitta, Kazuhiro R., Ohtake, Akira, Murayama, Kei, Amor, David J., McGillivray, George, Wong, Flora Y., van der Knaap, Marjo S., Vermeulen, R. Jeroen, Wiltshire, Esko J., Fletcher, Janice M., Lewis, Barry, Baynam, Gareth, Ellaway, Carolyn, Balasubramaniam, Shanti, Bhattacharya, Kaustuv, Freckmann, Mary-Louise, Arbuckle, Susan, Rodriguez, Michael, Taft, Ryan J., Sadedin, Simon, Cowley, Mark J., Minoche, André E., Calvo, Sarah E., Mootha, Vamsi K., Ryan, Michael T., Okazaki, Yasushi, Stroud, David A., Simons, Cas, Christodoulou, John, and Thorburn, David R.

Abstract

In about half of all patients with a suspected monogenic disease, genomic investigations fail to identify the diagnosis. A contributing factor is the difficulty with repetitive regions of the genome, such as those generated by segmental duplications. The ATAD3locus is one such region in which recessive deletions and dominant duplications have recently been reported to cause lethal perinatal mitochondrial diseases characterized by pontocerebellar hypoplasia or cardiomyopathy, respectively.

Published
2021
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48. Strategic validation of variants of uncertain significance in ECHS1 genetic testing.

Author

Kishita Y, Sugiura A, Onuki T, Ebihara T, Matsuhashi T, Shimura M, Fushimi T, Ichino N, Nagatakidani Y, Nishihata H, Nitta KR, Yatsuka Y, Imai-Okazaki A, Wu Y, Osaka H, Ohtake A, Murayama K, and Okazaki Y

Subjects
Humans, Phenotype, Mutation genetics, Enoyl-CoA Hydratase genetics, Enoyl-CoA Hydratase metabolism, Genetic Testing, Mitochondrial Diseases diagnosis, Mitochondrial Diseases genetics
Abstract

Background: Enoyl-CoA hydratase short-chain 1 (ECHS1) is an enzyme involved in the metabolism of branched chain amino acids and fatty acids. Mutations in the ECHS1 gene lead to mitochondrial short-chain enoyl-CoA hydratase 1 deficiency, resulting in the accumulation of intermediates of valine. This is one of the most common causative genes in mitochondrial diseases. While genetic analysis studies have diagnosed numerous cases with ECHS1 variants, the increasing number of variants of uncertain significance (VUS) in genetic diagnosis is a major problem., Methods: Here, we constructed an assay system to verify VUS function for ECHS1 gene. A high-throughput assay using ECHS1 knockout cells was performed to index these phenotypes by expressing cDNAs containing VUS. In parallel with the VUS validation system, a genetic analysis of samples from patients with mitochondrial disease was performed. The effect on gene expression in cases was verified by RNA-seq and proteome analysis., Results: The functional validation of VUS identified novel variants causing loss of ECHS1 function. The VUS validation system also revealed the effect of the VUS in the compound heterozygous state and provided a new methodology for variant interpretation. Moreover, we performed multiomics analysis and identified a synonymous substitution p.P163= that results in splicing abnormality. The multiomics analysis complemented the diagnosis of some cases that could not be diagnosed by the VUS validation system., Conclusions: In summary, this study uncovered new ECHS1 cases based on VUS validation and omics analysis; these analyses are applicable to the functional evaluation of other genes associated with mitochondrial disease., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2023. No commercial re-use. See rights and permissions. Published by BMJ.)

Published
2023
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49. Involvement of GLCCI1 in mouse spermatogenesis.

Author

Takada M, Fukuhara D, Takiura T, Nishibori Y, Kotani M, Kiuchi Z, Kudo A, Beltcheva O, Ito-Nitta N, Nitta KR, Kimura T, Suehiro JI, Katada T, Takematsu H, and Yan K

Subjects
Male, Mice, Animals, Spermatogenesis, Spermatids, Estrogens, Glucocorticoids, Semen
Abstract

Spermatid production is a complex regulatory process in which coordination between hormonal control and apoptosis plays a pivotal role in maintaining a balanced number of sperm cells. Apoptosis in spermatogenesis is controlled by pro-apoptotic and anti-apoptotic molecules. Hormones involved in the apoptotic process during spermatogenesis include gonadotrophins, sex hormones, and glucocorticoid (GC). GC acts broadly as an apoptosis inducer by binding to its receptor (glucocorticoid receptor: GR) during organ development processes, such as spermatogenesis. However, the downstream pathway induced in GC-GR signaling and the apoptotic process during spermatogenesis remains poorly understood. We reported previously that GC induces full-length glucocorticoid-induced transcript 1 (GLCCI1-long), which functions as an anti-apoptotic mediator in thymic T cell development. Here, we demonstrate that mature murine testis expresses a novel isoform of GLCCI1 protein (GLCCI1-short) in addition to GLCCI1-long. We demonstrate that GLCCI1-long is expressed in spermatocytes along with GR. In contrast, GLCCI1-short is primarily expressed in spermatids where GR is absent; instead, the estrogen receptor is expressed. GLCCI1-short also binds to LC8, which is a known mediator of the anti-apoptotic effect of GLCCI1-long. A luciferase reporter assay revealed that β-estradiol treatment synergistically increased Glcci1-short promotor-driven luciferase activity in Erα-overexpressing cells. Together with the evidence that the conversion of testosterone to estrogen is preceded by aromatase expression in spermatids, we hypothesize that estrogen induces GLCCI1-short, which, in turn, may function as a novel anti-apoptotic mediator in mature murine testis., (© 2022 Federation of American Societies for Experimental Biology.)

Published
2023
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50. Functional annotation of human long noncoding RNAs via molecular phenotyping.

Author

Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJ, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJC, Rackham OJL, Rizzu P, Sánchez Martinez DF, Sandelin A, Sanjana P, Semple CAM, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest ARR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJL, Shin JW, and Carninci P

Subjects
Cell Growth Processes genetics, Cell Movement genetics, Fibroblasts cytology, Fibroblasts metabolism, Humans, KCNQ Potassium Channels metabolism, Molecular Sequence Annotation, Oligonucleotides, Antisense, RNA, Long Noncoding antagonists & inhibitors, RNA, Long Noncoding metabolism, RNA, Small Interfering, RNA, Long Noncoding physiology
Abstract

Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2 ., (© 2020 Ramilowski et al.; Published by Cold Spring Harbor Laboratory Press.)

Published
2020
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