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3. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project

Author

Dekker, Job, Alber, Frank, Aufmkolk, Sarah, Beliveau, Brian J, Bruneau, Benoit G, Belmont, Andrew S, Bintu, Lacramioara, Boettiger, Alistair, Calandrelli, Riccardo, Disteche, Christine M, Gilbert, David M, Gregor, Thomas, Hansen, Anders S, Huang, Bo, Huangfu, Danwei, Kalhor, Reza, Leslie, Christina S, Li, Wenbo, Li, Yun, Ma, Jian, Noble, William S, Park, Peter J, Phillips-Cremins, Jennifer E, Pollard, Katherine S, Rafelski, Susanne M, Ren, Bing, Ruan, Yijun, Shav-Tal, Yaron, Shen, Yin, Shendure, Jay, Shu, Xiaokun, Strambio-De-Castillia, Caterina, Vertii, Anastassiia, Zhang, Huaiying, and Zhong, Sheng

Subjects
Biological Sciences, Genetics, Human Genome, Bioengineering, 1.1 Normal biological development and functioning, Generic health relevance, Genome, Cell Nucleus, Chromatin, 4D nucleome, cell cycle, chromosome folding, development, disease model, genomics technologies, imaging technologies, modeling, nuclear organization, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

The four-dimensional nucleome (4DN) consortium studies the architecture of the genome and the nucleus in space and time. We summarize progress by the consortium and highlight the development of technologies for (1) mapping genome folding and identifying roles of nuclear components and bodies, proteins, and RNA, (2) characterizing nuclear organization with time or single-cell resolution, and (3) imaging of nuclear organization. With these tools, the consortium has provided over 2,000 public datasets. Integrative computational models based on these data are starting to reveal connections between genome structure and function. We then present a forward-looking perspective and outline current aims to (1) delineate dynamics of nuclear architecture at different timescales, from minutes to weeks as cells differentiate, in populations and in single cells, (2) characterize cis-determinants and trans-modulators of genome organization, (3) test functional consequences of changes in cis- and trans-regulators, and (4) develop predictive models of genome structure and function.

Published
2023

4. How Do Word Reading and Word Spelling Develop over Time? A Three-Year Longitudinal Study of Hong Kong Chinese-English Bilingual Children

Author

Ruan, Yijun, Ye, Yanyan, Lui, Kelvin Fai Hong, McBride, Catherine, and Ho, Connie Suk Han

Abstract

Word reading and word spelling are important processes of literacy acquisition for children. The longitudinal relationship between reading and spelling is still unclear, especially among bilinguals and biscriptals. In the present study, we compared the longitudinal word reading-spelling relationship in L1 (Chinese) and L2 (English), together with early cognitive-linguistic skills. Participants were 182 pairs of Chinese-English bilingual twins who were tested annually across 3 years on word reading and word spelling in both scripts. Chinese and English cognitive and linguistic skills were measured in the first year only (mean age = 7.38). Cross-lagged panel models were applied to analyze the longitudinal word reading-spelling relations. Predictors of word reading and word spelling differed between Chinese and English. Longitudinally, there were no bidirectional or unidirectional relationships between word reading and spelling in Chinese. In contrast, a reciprocal relationship between word reading and spelling was revealed in English. This study underscores similarities and differences in the development of literacy skills among biscriptal readers of L1 Chinese and L2 English.

Published
2023
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5. Multi-scale phase separation by explosive percolation with single-chromatin loop resolution

Author

Sengupta, Kaustav, Denkiewicz, Michał, Chiliński, Mateusz, Szczepińska, Teresa, Mollah, Ayatullah Faruk, Korsak, Sevastianos, D'Souza, Raissa, Ruan, Yijun, and Plewczynski, Dariusz

Subjects
Biochemistry and Cell Biology, Biological Sciences, Human Genome, Bioengineering, Genetics, 1.1 Normal biological development and functioning, Underpinning research, 3D genomics, Chromatin folding, Compartmentalisation, Loop extrusion, Networks, Percolation, Phase separation, Scalar parameter, Numerical and Computational Mathematics, Computation Theory and Mathematics, Biochemistry and cell biology, Applied computing
Abstract

The 2 m-long human DNA is tightly intertwined into the cell nucleus of the size of 10 μm. The DNA packing is explained by folding of chromatin fiber. This folding leads to the formation of such hierarchical structures as: chromosomal territories, compartments; densely-packed genomic regions known as Topologically Associating Domains (TADs), or Chromatin Contact Domains (CCDs), and loops. We propose models of dynamical human genome folding into hierarchical components in human lymphoblastoid, stem cell, and fibroblast cell lines. Our models are based on explosive percolation theory. The chromosomes are modeled as graphs where CTCF chromatin loops are represented as edges. The folding trajectory is simulated by gradually introducing loops to the graph following various edge addition strategies that are based on topological network properties, chromatin loop frequencies, compartmentalization, or epigenomic features. Finally, we propose the genome folding model - a biophysical pseudo-time process guided by a single scalar order parameter. The parameter is calculated by Linear Discriminant Analysis of chromatin features. We also include dynamics of loop formation by using Loop Extrusion Model (LEM) while adding them to the system. The chromatin phase separation, where fiber folds in 3D space into topological domains and compartments, is observed when the critical number of contacts is reached. We also observe that at least 80% of the loops are needed for chromatin fiber to condense in 3D space, and this is constant through various cell lines. Overall, our in-silico model integrates the high-throughput 3D genome interaction experimental data with the novel theoretical concept of phase separation, which allows us to model event-based time dynamics of chromatin loop formation and folding trajectories.

Published
2022

8. Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma

Author

Wu, Yige, Terekhanova, Nadezhda V., Caravan, Wagma, Naser Al Deen, Nataly, Lal, Preet, Chen, Siqi, Mo, Chia-Kuei, Cao, Song, Li, Yize, Karpova, Alla, Liu, Ruiyang, Zhao, Yanyan, Shinkle, Andrew, Strunilin, Ilya, Weimholt, Cody, Sato, Kazuhito, Yao, Lijun, Serasanambati, Mamatha, Yang, Xiaolu, Wyczalkowski, Matthew, Zhu, Houxiang, Zhou, Daniel Cui, Jayasinghe, Reyka G., Mendez, Daniel, Wendl, Michael C., Clark, David, Newton, Chelsea, Ruan, Yijun, Reimers, Melissa A., Pachynski, Russell K., Kinsinger, Chris, Jewell, Scott, Chan, Daniel W., Zhang, Hui, Chaudhuri, Aadel A., Chheda, Milan G., Humphreys, Benjamin D., Mesri, Mehdi, Rodriguez, Henry, Hsieh, James J., Ding, Li, and Chen, Feng

Published
2023
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9. Author Correction: Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma

Author

Wu, Yige, Terekhanova, Nadezhda V., Caravan, Wagma, Naser Al Deen, Nataly, Lal, Preet, Chen, Siqi, Mo, Chia-Kuei, Cao, Song, Li, Yize, Karpova, Alla, Liu, Ruiyang, Zhao, Yanyan, Shinkle, Andrew, Strunilin, Ilya, Weimholt, Cody, Sato, Kazuhito, Yao, Lijun, Serasanambati, Mamatha, Yang, Xiaolu, Wyczalkowski, Matthew, Zhu, Houxiang, Zhou, Daniel Cui, Jayasinghe, Reyka G., Mendez, Daniel, Wendl, Michael C., Clark, David, Newton, Chelsea, Ruan, Yijun, Reimers, Melissa A., Pachynski, Russell K., Kinsinger, Chris, Jewell, Scott, Chan, Daniel W., Zhang, Hui, Chaudhuri, Aadel A., Chheda, Milan G., Humphreys, Benjamin D., Mesri, Mehdi, Rodriguez, Henry, Hsieh, James J., Ding, Li, and Chen, Feng

Published
2023
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10. Relations among Phonological Processing Skills and Mathematics in Children: A Meta-Analysis

Author

Yang, Xiujie, Yan, Mengge, Ruan, Yijun, Ku, Serena Yuk Yee, Lo, Jason Chor Ming, Peng, Peng, and McBride, Catherine

Abstract

The present study presents a meta-analysis of the relations between phonological processing abilities and different mathematics subskills. Using a random-effects model with 94 studies (135 unique samples, 826 effect sizes), the present meta-analysis revealed a significant general association between phonological processing and mathematics (average r = 0.33, p < 0.001, 95% CI [0.30, 0.36]). Phonological awareness (PA) and rapid automatized naming (RAN) showed stronger correlations with mathematics than phonological memory (PM) did. The correlations among phonological processing abilities and mathematics skills were generally stronger among younger children than among older children. PA and PM manifested larger effect sizes when correlated with mathematics accuracy than with mathematics fluency, whereas RAN yielded larger effect sizes when associated with mathematics fluency than with mathematics accuracy. Metastructural equation modeling results revealed that, after statistically controlling for domain-general abilities (i.e., vocabulary knowledge, executive functioning, and nonverbal intelligence), phonological processing still made a unique contribution to different mathematics subskills ([beta]s = 0.20 [approximately] 0.54). These results suggest that children may use phonological processing abilities as one mechanism through which to represent, manipulate, and retrieve mathematics knowledge.

Published
2022
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11. Exploring the Underpinnings and Longitudinal Associations of Word Reading and Word Spelling: A 2-Year Longitudinal Study of Hong Kong Chinese Children Transitioning to Primary School

Author

Ye, Yanyan, Yan, Mengge, Ruan, Yijun, McBride, Catherine, Zheng, Mo, and Yin, Li

Abstract

We investigated the correlates of word reading and spelling as well as the relations of word reading and spelling in Hong Kong Chinese children. A set of literacy-related skills and delayed copying were administered in kindergarten, and Chinese word reading and dictation were tested at kindergarten as well as in first and second grade. The final preferred model in cross-lagged analysis showed that reading performance at kindergarten and first grade predicted spelling performance at first grade and second grade, respectively. However, the relations were not bidirectional. This study underscores the critical roles of morphological awareness, RAN, and delayed copying for early literacy performance in Chinese. In addition, it demonstrates that earlier reading performance predicts later spelling performance in Chinese, but early spelling does not predict subsequent reading in Chinese in the early grades.

Published
2022
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12. Multidimensional single-cell analysis of human peripheral blood reveals characteristic features of the immune system landscape in aging and frailty

Author

Luo, Oscar Junhong, Lei, Wen, Zhu, Guodong, Ren, Zhiyao, Xu, Yudai, Xiao, Chanchan, Zhang, Hongyi, Cai, Junxiang, Luo, Zhiping, Gao, Lijuan, Su, Jun, Tang, Lei, Guo, Wei, Su, Huanxing, Zhang, Zhang-Jin, Fang, Evandro Fei, Ruan, Yijun, Leng, Sean Xiao, Ju, Zhenyu, Lou, Huiling, Gao, Junling, Peng, Nan, Chen, Jie, Bao, Zhijun, Liu, Feng, and Chen, Guobing

Published
2022
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19. Kdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons

Author

Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Ministry of Science and Higher Education (Poland), European Commission, Fundació La Marató de TV3, Generalitat Valenciana, Fundación la Caixa, National Institutes of Health (US), Human Frontier Science Program, Consejo Superior de Investigaciones Científicas (España), Blanco, Beatriz del, Niñerola, Sergio, Martín-Gonzalez, Ana M., Paraíso-Luna, Juan, Kim, Minji, Muñoz-Viana, Rafael, Racovac, Carina, Sánchez-Mut, José Vicente, Ruan, Yijun, Barco, Ángel, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Ministry of Science and Higher Education (Poland), European Commission, Fundació La Marató de TV3, Generalitat Valenciana, Fundación la Caixa, National Institutes of Health (US), Human Frontier Science Program, Consejo Superior de Investigaciones Científicas (España), Blanco, Beatriz del, Niñerola, Sergio, Martín-Gonzalez, Ana M., Paraíso-Luna, Juan, Kim, Minji, Muñoz-Viana, Rafael, Racovac, Carina, Sánchez-Mut, José Vicente, Ruan, Yijun, and Barco, Ángel

Abstract

Kdm1a is a histone demethylase linked to intellectual disability with essential roles during gastrulation and the terminal differentiation of specialized cell types, including neurons, that remains highly expressed in the adult brain. To explore Kdm1a’s function in adult neurons, we develop inducible and forebrain-restricted Kdm1a knockouts. By applying multi-omic transcriptome, epigenome and chromatin conformation data, combined with super-resolution microscopy, we find that Kdm1a elimination causes the neuronal activation of nonneuronal genes that are silenced by the polycomb repressor complex and interspersed with active genes. Functional assays demonstrate that the N-terminus of Kdm1a contains an intrinsically disordered region that is essential to segregate Kdm1a-repressed genes from the neighboring active chromatin environment. Finally, we show that the segregation of Kdm1a-target genes is weakened in neurons during natural aging, underscoring the role of Kdm1a safeguarding neuronal genome organization and gene silencing throughout life.

Published
2024

21. Multifaceted roles of cohesin in regulating transcriptional loops

Author

Kim, Minji, primary, Wang, Ping, additional, Clow, Patricia, additional, Chien, I, additional, Wang, Xiaotao, additional, Peng, Jianhao, additional, Chai, Haoxi, additional, Liu, Xiyuan, additional, Lee, Byoungkoo, additional, Ngan, Chew Yee, additional, Yue, Feng, additional, Milenkovic, Olgica, additional, Chuang, Jeffrey H, additional, Wei, Chia-Lin, additional, Casellas, Rafael, additional, Cheng, Albert, additional, and Ruan, Yijun, additional

Published
2024
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23. Nuclear pore protein NUP210 depletion suppresses metastasis through heterochromatin-mediated disruption of tumor cell mechanical response

Author

Amin, Ruhul, Shukla, Anjali, Zhu, Jacqueline Jufen, Kim, Sohyoung, Wang, Ping, Tian, Simon Zhongyuan, Tran, Andy D., Paul, Debasish, Cappell, Steven D., Burkett, Sandra, Liu, Huaitian, Lee, Maxwell P., Kruhlak, Michael J., Dwyer, Jennifer E., Simpson, R. Mark, Hager, Gordon L., Ruan, Yijun, and Hunter, Kent W.

Published
2021
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26. Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic β Cell Identity and Function

Author

Lawlor, Nathan, Márquez, Eladio J., Orchard, Peter, Narisu, Narisu, Shamim, Muhammad Saad, Thibodeau, Asa, Varshney, Arushi, Kursawe, Romy, Erdos, Michael R., Kanke, Matt, Gu, Huiya, Pak, Evgenia, Dutra, Amalia, Russell, Sheikh, Li, Xingwang, Piecuch, Emaly, Luo, Oscar, Chines, Peter S., Fuchbserger, Christian, Sethupathy, Praveen, Aiden, Aviva Presser, Ruan, Yijun, Aiden, Erez Lieberman, Collins, Francis S., Ucar, Duygu, Parker, Stephen C.J., and Stitzel, Michael L.

Published
2019
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28. The Energetics and Physiological Impact of Cohesin Extrusion

Author

Vian, Laura, Pękowska, Aleksandra, Rao, Suhas S.P., Kieffer-Kwon, Kyong-Rim, Jung, Seolkyoung, Baranello, Laura, Huang, Su-Chen, El Khattabi, Laila, Dose, Marei, Pruett, Nathanael, Sanborn, Adrian L., Canela, Andres, Maman, Yaakov, Oksanen, Anna, Resch, Wolfgang, Li, Xingwang, Lee, Byoungkoo, Kovalchuk, Alexander L., Tang, Zhonghui, Nelson, Steevenson, Di Pierro, Michele, Cheng, Ryan R., Machol, Ido, St Hilaire, Brian Glenn, Durand, Neva C., Shamim, Muhammad S., Stamenova, Elena K., Onuchic, José N., Ruan, Yijun, Nussenzweig, Andre, Levens, David, Aiden, Erez Lieberman, and Casellas, Rafael

Published
2018
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29. Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

Author

Zhang, Yubo, Wong, Chee-Hong, Birnbaum, Ramon Y, Li, Guoliang, Favaro, Rebecca, Ngan, Chew Yee, Lim, Joanne, Tai, Eunice, Poh, Huay Mei, Wong, Eleanor, Mulawadi, Fabianus Hendriyan, Sung, Wing-Kin, Nicolis, Silvia, Ahituv, Nadav, Ruan, Yijun, and Wei, Chia-Lin

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Ecology, Genetics, Stem Cell Research, Animals, Cell Line, Cell Lineage, Chromatin, Embryonic Stem Cells, Enhancer Elements, Genetic, Gene Expression Regulation, In Situ Hybridization, Fluorescence, Mice, Neural Stem Cells, Promoter Regions, Genetic, RNA Polymerase II, Transcription, Genetic, Zebrafish, General Science & Technology
Abstract

In multicellular organisms, transcription regulation is one of the central mechanisms modelling lineage differentiation and cell-fate determination. Transcription requires dynamic chromatin configurations between promoters and their corresponding distal regulatory elements. It is believed that their communication occurs within large discrete foci of aggregated RNA polymerases termed transcription factories in three-dimensional nuclear space. However, the dynamic nature of chromatin connectivity has not been characterized at the genome-wide level. Here, through a chromatin interaction analysis with paired-end tagging approach using an antibody that primarily recognizes the pre-initiation complexes of RNA polymerase II, we explore the transcriptional interactomes of three mouse cells of progressive lineage commitment, including pluripotent embryonic stem cells, neural stem cells and neurosphere stem/progenitor cells. Our global chromatin connectivity maps reveal approximately 40,000 long-range interactions, suggest precise enhancer-promoter associations and delineate cell-type-specific chromatin structures. Analysis of the complex regulatory repertoire shows that there are extensive colocalizations among promoters and distal-acting enhancers. Most of the enhancers associate with promoters located beyond their nearest active genes, indicating that the linear juxtaposition is not the only guiding principle driving enhancer target selection. Although promoter-enhancer interactions exhibit high cell-type specificity, promoters involved in interactions are found to be generally common and mostly active among different cells. Chromatin connectivity networks reveal that the pivotal genes of reprogramming functions are transcribed within physical proximity to each other in embryonic stem cells, linking chromatin architecture to coordinated gene expression. Our study sets the stage for the full-scale dissection of spatial and temporal genome structures and their roles in orchestrating development.

Published
2013

31. Landscape of transcription in human cells

Author

Djebali, Sarah, Davis, Carrie A, Merkel, Angelika, Dobin, Alex, Lassmann, Timo, Mortazavi, Ali, Tanzer, Andrea, Lagarde, Julien, Lin, Wei, Schlesinger, Felix, Xue, Chenghai, Marinov, Georgi K, Khatun, Jainab, Williams, Brian A, Zaleski, Chris, Rozowsky, Joel, Röder, Maik, Kokocinski, Felix, Abdelhamid, Rehab F, Alioto, Tyler, Antoshechkin, Igor, Baer, Michael T, Bar, Nadav S, Batut, Philippe, Bell, Kimberly, Bell, Ian, Chakrabortty, Sudipto, Chen, Xian, Chrast, Jacqueline, Curado, Joao, Derrien, Thomas, Drenkow, Jorg, Dumais, Erica, Dumais, Jacqueline, Duttagupta, Radha, Falconnet, Emilie, Fastuca, Meagan, Fejes-Toth, Kata, Ferreira, Pedro, Foissac, Sylvain, Fullwood, Melissa J, Gao, Hui, Gonzalez, David, Gordon, Assaf, Gunawardena, Harsha, Howald, Cedric, Jha, Sonali, Johnson, Rory, Kapranov, Philipp, King, Brandon, Kingswood, Colin, Luo, Oscar J, Park, Eddie, Persaud, Kimberly, Preall, Jonathan B, Ribeca, Paolo, Risk, Brian, Robyr, Daniel, Sammeth, Michael, Schaffer, Lorian, See, Lei-Hoon, Shahab, Atif, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Trout, Diane, Walters, Nathalie, Wang, Huaien, Wrobel, John, Yu, Yanbao, Ruan, Xiaoan, Hayashizaki, Yoshihide, Harrow, Jennifer, Gerstein, Mark, Hubbard, Tim, Reymond, Alexandre, Antonarakis, Stylianos E, Hannon, Gregory, Giddings, Morgan C, Ruan, Yijun, Wold, Barbara, Carninci, Piero, Guigó, Roderic, and Gingeras, Thomas R

Subjects
Genetics, Human Genome, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Alleles, Cell Line, DNA, DNA, Intergenic, Encyclopedias as Topic, Enhancer Elements, Genetic, Exons, Gene Expression Profiling, Genes, Genome, Human, Genomics, Humans, Molecular Sequence Annotation, Polyadenylation, Protein Isoforms, RNA, RNA Editing, RNA Splicing, Regulatory Sequences, Nucleic Acid, Repetitive Sequences, Nucleic Acid, Sequence Analysis, RNA, Transcription, Genetic, Transcriptome, General Science & Technology
Abstract

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.

Published
2012

32. International network of cancer genome projects

Author

Hudson (Chairperson), Thomas J, Anderson, Warwick, Aretz, Axel, Barker, Anna D, Bell, Cindy, Bernabé, Rosa R, Bhan, MK, Calvo, Fabien, Eerola, Iiro, Gerhard, Daniela S, Guttmacher, Alan, Guyer, Mark, Hemsley, Fiona M, Jennings, Jennifer L, Kerr, David, Klatt, Peter, Kolar, Patrik, Kusuda, Jun, Lane, David P, Laplace, Frank, Lu, Youyong, Nettekoven, Gerd, Ozenberger, Brad, Peterson, Jane, Rao, TS, Remacle, Jacques, Schafer, Alan J, Shibata, Tatsuhiro, Stratton, Michael R, Vockley, Joseph G, Watanabe, Koichi, Yang, Huanming, Yuen, Matthew MF, Knoppers (Leader), Bartha M, Bobrow, Martin, Cambon-Thomsen, Anne, Dressler, Lynn G, Dyke, Stephanie OM, Joly, Yann, Kato, Kazuto, Kennedy, Karen L, Nicolás, Pilar, Parker, Michael J, Rial-Sebbag, Emmanuelle, Romeo-Casabona, Carlos M, Shaw, Kenna M, Wallace, Susan, Wiesner, Georgia L, Zeps, Nikolajs, Lichter (Leader), Peter, Biankin, Andrew V, Chabannon, Christian, Chin, Lynda, Clément, Bruno, de Alava, Enrique, Degos, Françoise, Ferguson, Martin L, Geary, Peter, Hayes, D Neil, Hudson, Thomas J, Johns, Amber L, Kasprzyk, Arek, Nakagawa, Hidewaki, Penny, Robert, Piris, Miguel A, Sarin, Rajiv, Scarpa, Aldo, van de Vijver, Marc, Futreal (Leader), P Andrew, Aburatani, Hiroyuki, Bayés, Mónica, Bowtell, David DL, Campbell, Peter J, Estivill, Xavier, Grimmond, Sean M, Gut, Ivo, Hirst, Martin, López-Otín, Carlos, Majumder, Partha, Marra, Marco, McPherson, John D, Ning, Zemin, Puente, Xose S, Ruan, Yijun, Stunnenberg, Hendrik G, Swerdlow, Harold, Velculescu, Victor E, Wilson, Richard K, Xue, Hong H, Yang, Liu, Spellman (Leader), Paul T, Bader, Gary D, Boutros, Paul C, and Flicek, Paul

Subjects
Cancer, Genetics, Human Genome, DNA Methylation, DNA Mutational Analysis, Databases, Genetic, Genes, Neoplasm, Genetics, Medical, Genome, Human, Genomics, Humans, Intellectual Property, International Cooperation, Mutation, Neoplasms, International Cancer Genome Consortium, General Science & Technology
Abstract

The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.

Published
2010

33. International network of cancer genome projects.

Author

International Cancer Genome Consortium, Hudson, Thomas J, Anderson, Warwick, Artez, Axel, Barker, Anna D, Bell, Cindy, Bernabé, Rosa R, Bhan, MK, Calvo, Fabien, Eerola, Iiro, Gerhard, Daniela S, Guttmacher, Alan, Guyer, Mark, Hemsley, Fiona M, Jennings, Jennifer L, Kerr, David, Klatt, Peter, Kolar, Patrik, Kusada, Jun, Lane, David P, Laplace, Frank, Youyong, Lu, Nettekoven, Gerd, Ozenberger, Brad, Peterson, Jane, Rao, TS, Remacle, Jacques, Schafer, Alan J, Shibata, Tatsuhiro, Stratton, Michael R, Vockley, Joseph G, Watanabe, Koichi, Yang, Huanming, Yuen, Matthew MF, Knoppers, Bartha M, Bobrow, Martin, Cambon-Thomsen, Anne, Dressler, Lynn G, Dyke, Stephanie OM, Joly, Yann, Kato, Kazuto, Kennedy, Karen L, Nicolás, Pilar, Parker, Michael J, Rial-Sebbag, Emmanuelle, Romeo-Casabona, Carlos M, Shaw, Kenna M, Wallace, Susan, Wiesner, Georgia L, Zeps, Nikolajs, Lichter, Peter, Biankin, Andrew V, Chabannon, Christian, Chin, Lynda, Clément, Bruno, de Alava, Enrique, Degos, Françoise, Ferguson, Martin L, Geary, Peter, Hayes, D Neil, Johns, Amber L, Kasprzyk, Arek, Nakagawa, Hidewaki, Penny, Robert, Piris, Miguel A, Sarin, Rajiv, Scarpa, Aldo, van de Vijver, Marc, Futreal, P Andrew, Aburatani, Hiroyuki, Bayés, Mónica, Botwell, David DL, Campbell, Peter J, Estivill, Xavier, Grimmond, Sean M, Gut, Ivo, Hirst, Martin, López-Otín, Carlos, Majumder, Partha, Marra, Marco, McPherson, John D, Ning, Zemin, Puente, Xose S, Ruan, Yijun, Stunnenberg, Hendrik G, Swerdlow, Harold, Velculescu, Victor E, Wilson, Richard K, Xue, Hong H, Yang, Liu, Spellman, Paul T, Bader, Gary D, and Boutros, Paul C

Subjects
International Cancer Genome Consortium, Humans, Neoplasms, DNA Mutational Analysis, Genetics, Medical, Genomics, DNA Methylation, Mutation, Genome, Human, International Cooperation, Intellectual Property, Databases, Genetic, Genes, Neoplasm, Genetics, Medical, Genome, Human, Databases, Genetic, Genes, Neoplasm, General Science & Technology
Abstract

The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.

Published
2010

39. Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization

Author

Trzaskoma, Paweł, Ruszczycki, Błażej, Lee, Byoungkoo, Pels, Katarzyna K., Krawczyk, Katarzyna, Bokota, Grzegorz, Szczepankiewicz, Andrzej A., Aaron, Jesse, Walczak, Agnieszka, Śliwińska, Małgorzata A., Magalska, Adriana, Kadlof, Michal, Wolny, Artur, Parteka, Zofia, Arabasz, Sebastian, Kiss-Arabasz, Magdalena, Plewczyński, Dariusz, Ruan, Yijun, and Wilczyński, Grzegorz M.

Published
2020
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40. Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells

Author

Higashijima, Yoshiki, Matsui, Yusuke, Shimamura, Teppei, Nakaki, Ryo, Nagai, Nao, Tsutsumi, Shuichi, Abe, Yohei, Link, Verena M, Osaka, Mizuko, Yoshida, Masayuki, Watanabe, Ryo, Tanaka, Toshihiro, Taguchi, Akashi, Miura, Mai, Ruan, Xiaoan, Li, Guoliang, Inoue, Tsuyoshi, Nangaku, Masaomi, Kimura, Hiroshi, Furukawa, Tetsushi, Aburatani, Hiroyuki, Wada, Youichiro, Ruan, Yijun, Glass, Christopher K, and Kanki, Yasuharu

Published
2020
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44. An expansion of the non-coding genome and its regulatory potential underlies vertebrate neuronal diversity

Author

Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Closser, Michael, Guo, Yuchun, Wang, Ping, Patel, Tulsi, Jang, Sumin, Hammelman, Jennifer, De Nooij, Joriene C, Kopunova, Rachel, Mazzoni, Esteban O, Ruan, Yijun, Gifford, David K, Wichterle, Hynek, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Closser, Michael, Guo, Yuchun, Wang, Ping, Patel, Tulsi, Jang, Sumin, Hammelman, Jennifer, De Nooij, Joriene C, Kopunova, Rachel, Mazzoni, Esteban O, Ruan, Yijun, Gifford, David K, and Wichterle, Hynek

Abstract

Proper assembly and function of the nervous system requires the generation of a uniquely diverse population of neurons expressing a cell-type-specific combination of effector genes that collectively define neuronal morphology, connectivity, and function. How countless partially overlapping but cell-type-specific patterns of gene expression are controlled at the genomic level remains poorly understood. Here we show that neuronal genes are associated with highly complex gene regulatory systems composed of independent cell-type- and cell-stage-specific regulatory elements that reside in expanded non-coding genomic domains. Mapping enhancer-promoter interactions revealed that motor neuron enhancers are broadly distributed across the large chromatin domains. This distributed regulatory architecture is not a unique property of motor neurons but is employed throughout the nervous system. The number of regulatory elements increased dramatically during the transition from invertebrates to vertebrates, suggesting that acquisition of new enhancers might be a fundamental process underlying the evolutionary increase in cellular complexity.

Published
2023

45. Refined mapping of autoimmune disease associated genetic variants with gene expression suggests an important role for non-coding RNAs

Author

Heijmans, Bastiaan T., 't Hoen, Peter A.C., van Meurs, Joyce, Isaacs, Aaron, Jansen, Rick, Franke, Lude, Boomsma, Dorret I., Pool, René, van Dongen, Jenny, Hottenga, Jouke J., van Greevenbroek, Marleen M.J., Stehouwer, Coen D.A., van der Kallen, Carla J.H., Schalkwijk, Casper G., Wijmenga, Cisca, Zhernakova, Alexandra, Tigchelaar, Ettje F., Slagboom, P. Eline, Beekman, Marian, Deelen, Joris, van Heemst, Diana, Veldink, Jan H., van den Berg, Leonard H., van Duijn, Cornelia M., Hofman, Bert A., Uitterlinden, André G., Jhamai, P. Mila, Verbiest, Michael, Suchiman, H. Eka D., Verkerk, Marijn, van der Breggen, Ruud, van Rooij, Jeroen, Lakenberg, Nico, Mei, Hailiang, van Iterson, Maarten, van Galen, Michiel, Bot, Jan, Hof, Peter van 't, Deelen, Patrick, Nooren, Irene, Moed, Matthijs, Vermaat, Martijn, Zhernakova, Daria V., Luijk, René, Bonder, Marc Jan, van Dijk, Freerk, Arindrarto, Wibowo, Kielbasa, Szymon M., Swertz, Morris A., van Zwet, Erik W., Ricaño-Ponce, Isis, Luo, Oscar, Li, Xingwang, Karjalainen, Juha, Di Tommaso, Jennifer, Borek, Zuzanna Agnieszka, Zorro, Maria M., Gutierrez-Achury, Javier, Uitterlinden, Andre G., Hofman, Albert, Netea, Mihai G., Jonkers, Iris H., Withoff, Sebo, Li, Yang, Ruan, Yijun, and Kumar, Vinod

Published
2016
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50. CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

Author

Tang, Zhonghui, Luo, Oscar Junhong, Li, Xingwang, Zheng, Meizhen, Zhu, Jacqueline Jufen, Szalaj, Przemyslaw, Trzaskoma, Pawel, Magalska, Adriana, Wlodarczyk, Jakub, Ruszczycki, Blazej, Michalski, Paul, Piecuch, Emaly, Wang, Ping, Wang, Danjuan, Tian, Simon Zhongyuan, Penrad-Mobayed, May, Sachs, Laurent M., Ruan, Xiaoan, Wei, Chia-Lin, Liu, Edison T., Wilczynski, Grzegorz M., Plewczynski, Dariusz, Li, Guoliang, and Ruan, Yijun

Published
2015
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