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232 results on '"Lajoie, Bryan R"'

1. Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight

Author

Tierney, Braden T., Kim, JangKeun, Overbey, Eliah G., Ryon, Krista A., Foox, Jonathan, Sierra, Maria A., Bhattacharya, Chandrima, Damle, Namita, Najjar, Deena, Park, Jiwoon, Garcia Medina, J. Sebastian, Houerbi, Nadia, Meydan, Cem, Wain Hirschberg, Jeremy, Qiu, Jake, Kleinman, Ashley S., Al-Ghalith, Gabriel A., MacKay, Matthew, Afshin, Evan E., Dhir, Raja, Borg, Joseph, Gatt, Christine, Brereton, Nicholas, Readhead, Benjamin P., Beyaz, Semir, Venkateswaran, Kasthuri J., Wiseman, Kelly, Moreno, Juan, Boddicker, Andrew M., Zhao, Junhua, Lajoie, Bryan R., Scott, Ryan T., Altomare, Andrew, Kruglyak, Semyon, Levy, Shawn, Church, George M., and Mason, Christopher E.

Published
2024
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2. Avidity sequencing of whole genomes from retinal degeneration pedigrees identifies causal variants

Author

Biswas, Pooja, Villanueva, Adda, Krajacich, Benjamin J, Moreno, Juan, Zhao, Junhua, Berry, Anne Marie, Lazaro, Danielle, Lajoie, Bryan R, Kruglyak, Semyon, and Ayyagari, Radha

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Neurosciences, Eye Disease and Disorders of Vision, Neurodegenerative, Rare Diseases, Human Genome, 2.1 Biological and endogenous factors, Eye, Good Health and Well Being, Humans, Retinal Degeneration, Pedigree, Whole Genome Sequencing, Male, Female, ATP-Binding Cassette Transporters, General Science & Technology
Abstract

Whole genome sequencing has been an effective tool in the discovery of variants that cause rare diseases. In this study, we determined the suitability of a novel avidity sequencing approach for rare disease applications. We built a sample to results workflow, combining this sequencing technology with standard library preparation kits, analysis workflows, and interpretation tools. We applied the workflow to ten pedigrees with inherited retinal degeneration (IRD) phenotype. Candidate variants of interest identified through whole genome sequencing were further evaluated using segregation analysis in the additional family members. Potentially causal variants in known IRD genes were detected in five of the ten cases. These high confidence variants were found in ABCA4, CERKL, MAK, PEX6 and RDH12 genes associated with retinal degeneration, that could be sufficient to cause pathology. Pending confirmatory clinical evaluation, we observed a 50% diagnostic yield, consistent with previously reported outcomes of IRD patient analysis. The study confirms that avidity sequencing is effective in detection of causal variants when used for whole genome sequencing in rare disease applications.

Published
2024

3. Sequencing by avidity enables high accuracy with low reagent consumption

Author

Arslan, Sinan, Garcia, Francisco J., Guo, Minghao, Kellinger, Matthew W., Kruglyak, Semyon, LeVieux, Jake A., Mah, Adeline H., Wang, Haosen, Zhao, Junhua, Zhou, Chunhong, Altomare, Andrew, Bailey, John, Byrne, Matthew B., Chang, Chiting, Chen, Steve X., Cho, Byungrae, Dennler, Claudia N., Dien, Vivian T., Fuller, Derek, Kelley, Ryan, Khandan, Omid, Klein, Michael G., Kim, Michael, Lajoie, Bryan R., Lin, Bill, Liu, Yu, Lopez, Tyler, Mains, Peter T., Price, Andrew D., Robertson, Samantha R., Taylor-Weiner, Hermes, Tippana, Ramreddy, Tomaney, Austin B., Zhang, Su, Abtahi, Minna, Ambroso, Mark R., Bajari, Rosita, Bellizzi, Ava M., Benitez, Chris B., Berard, Daniel R., Berti, Lorenzo, Blease, Kelly N., Blum, Angela P., Boddicker, Andrew M., Bondar, Leo, Brown, Chris, Bui, Chris A., Calleja-Aguirre, Juan, Cappa, Kevin, Chan, Joshua, Chang, Victor W., Charov, Katherine, Chen, Xiyi, Constandse, Rodger M., Damron, Weston, Dawood, Mariam, DeBuono, Nicole, Dimalanta, John D., Edoli, Laure, Elango, Keerthana, Faustino, Nikka, Feng, Chao, Ferrari, Matthew, Frankie, Keith, Fries, Adam, Galloway, Anne, Gavrila, Vlad, Gemmen, Gregory J., Ghadiali, James, Ghorbani, Arash, Goddard, Logan A., Guetter, Adriana Roginski, Hendricks, Garren L., Hentschel, Jendrik, Honigfort, Daniel J., Hsieh, Yun-Ting, Hwang Fu, Yu-Hsien, Im, Scott K., Jin, Chaoyi, Kabu, Shradha, Kincade, Daniel E., Levy, Shawn, Li, Yu, Liang, Vincent K., Light, William H., Lipsher, Jonathan B., Liu, Tsung-li, Long, Grace, Ma, Rui, Mailloux, John M., Mandla, Kyle A., Martinez, Anyssa R., Mass, Max, McKean, Daniel T., Meron, Michael, Miller, Edmund A., Moh, Celyne S., Moore, Rachel K., Moreno, Juan, Neysmith, Jordan M., Niman, Cassandra S., Nunez, Jesus M., Ojeda, Micah T., Ortiz, Sara Espinosa, Owens, Jenna, Piland, Geoffrey, Proctor, Daniel J., Purba, Josua B., Ray, Michael, Rong, Daisong, Saade, Virginia M., Saha, Sanchari, Tomas, Gustav Santo, Scheidler, Nicholas, Sirajudeen, Luqmanal H., Snow, Samantha, Stengel, Gudrun, Stinson, Ryan, Stone, Michael J., Sundseth, Keoni J., Thai, Eileen, Thompson, Connor J., Tjioe, Marco, Trejo, Christy L., Trieger, Greg, Truong, Diane Ni, Tse, Ben, Voiles, Benjamin, Vuong, Henry, Wong, Jennifer C., Wu, Chiung-Ting, Yu, Hua, Yu, Yingxian, Yu, Ming, Zhang, Xi, Zhao, Da, Zheng, Genhua, He, Molly, and Previte, Michael

Published
2024
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4. An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases

Author

Owen, Mallory J, Lefebvre, Sebastien, Hansen, Christian, Kunard, Chris M, Dimmock, David P, Smith, Laurie D, Scharer, Gunter, Mardach, Rebecca, Willis, Mary J, Feigenbaum, Annette, Niemi, Anna-Kaisa, Ding, Yan, Van Der Kraan, Luca, Ellsworth, Katarzyna, Guidugli, Lucia, Lajoie, Bryan R, McPhail, Timothy K, Mehtalia, Shyamal S, Chau, Kevin K, Kwon, Yong H, Zhu, Zhanyang, Batalov, Sergey, Chowdhury, Shimul, Rego, Seema, Perry, James, Speziale, Mark, Nespeca, Mark, Wright, Meredith S, Reese, Martin G, De La Vega, Francisco M, Azure, Joe, Frise, Erwin, Rigby, Charlene Son, White, Sandy, Hobbs, Charlotte A, Gilmer, Sheldon, Knight, Gail, Oriol, Albert, Lenberg, Jerica, Nahas, Shareef A, Perofsky, Kate, Kim, Kyu, Carroll, Jeanne, Coufal, Nicole G, Sanford, Erica, Wigby, Kristen, Weir, Jacqueline, Thomson, Vicki S, Fraser, Louise, Lazare, Seka S, Shin, Yoon H, Grunenwald, Haiying, Lee, Richard, Jones, David, Tran, Duke, Gross, Andrew, Daigle, Patrick, Case, Anne, Lue, Marisa, Richardson, James A, Reynders, John, Defay, Thomas, Hall, Kevin P, Veeraraghavan, Narayanan, and Kingsmore, Stephen F

Subjects
Human Genome, Pediatric, Genetics, Biotechnology, Pediatric Research Initiative, Good Health and Well Being, Child, DNA Copy Number Variations, Humans, Infant, Retrospective Studies, Whole Genome Sequencing
Abstract

While many genetic diseases have effective treatments, they frequently progress rapidly to severe morbidity or mortality if those treatments are not implemented immediately. Since front-line physicians frequently lack familiarity with these diseases, timely molecular diagnosis may not improve outcomes. Herein we describe Genome-to-Treatment, an automated, virtual system for genetic disease diagnosis and acute management guidance. Diagnosis is achieved in 13.5 h by expedited whole genome sequencing, with superior analytic performance for structural and copy number variants. An expert panel adjudicated the indications, contraindications, efficacy, and evidence-of-efficacy of 9911 drug, device, dietary, and surgical interventions for 563 severe, childhood, genetic diseases. The 421 (75%) diseases and 1527 (15%) effective interventions retained are integrated with 13 genetic disease information resources and appended to diagnostic reports ( https://gtrx.radygenomiclab.com ). This system provided correct diagnoses in four retrospectively and two prospectively tested infants. The Genome-to-Treatment system facilitates optimal outcomes in children with rapidly progressive genetic diseases.

Published
2022

6. Condensin-driven remodelling of X chromosome topology during dosage compensation

Author

Crane, Emily, Bian, Qian, McCord, Rachel Patton, Lajoie, Bryan R, Wheeler, Bayly S, Ralston, Edward J, Uzawa, Satoru, Dekker, Job, and Meyer, Barbara J

Subjects
Biological Sciences, Genetics, Human Genome, Underpinning research, 1.1 Normal biological development and functioning, Adenosine Triphosphatases, Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, DNA-Binding Proteins, Dosage Compensation, Genetic, Female, Gene Expression Regulation, In Situ Hybridization, Fluorescence, Male, Multiprotein Complexes, Protein Binding, Sequence Analysis, RNA, X Chromosome, General Science & Technology
Abstract

The three-dimensional organization of a genome plays a critical role in regulating gene expression, yet little is known about the machinery and mechanisms that determine higher-order chromosome structure. Here we perform genome-wide chromosome conformation capture analysis, fluorescent in situ hybridization (FISH), and RNA-seq to obtain comprehensive three-dimensional (3D) maps of the Caenorhabditis elegans genome and to dissect X chromosome dosage compensation, which balances gene expression between XX hermaphrodites and XO males. The dosage compensation complex (DCC), a condensin complex, binds to both hermaphrodite X chromosomes via sequence-specific recruitment elements on X (rex sites) to reduce chromosome-wide gene expression by half. Most DCC condensin subunits also act in other condensin complexes to control the compaction and resolution of all mitotic and meiotic chromosomes. By comparing chromosome structure in wild-type and DCC-defective embryos, we show that the DCC remodels hermaphrodite X chromosomes into a sex-specific spatial conformation distinct from autosomes. Dosage-compensated X chromosomes consist of self-interacting domains (∼1 Mb) resembling mammalian topologically associating domains (TADs). TADs on X chromosomes have stronger boundaries and more regular spacing than on autosomes. Many TAD boundaries on X chromosomes coincide with the highest-affinity rex sites and become diminished or lost in DCC-defective mutants, thereby converting the topology of X to a conformation resembling autosomes. rex sites engage in DCC-dependent long-range interactions, with the most frequent interactions occurring between rex sites at DCC-dependent TAD boundaries. These results imply that the DCC reshapes the topology of X chromosomes by forming new TAD boundaries and reinforcing weak boundaries through interactions between its highest-affinity binding sites. As this model predicts, deletion of an endogenous rex site at a DCC-dependent TAD boundary using CRISPR/Cas9 greatly diminished the boundary. Thus, the DCC imposes a distinct higher-order structure onto X chromosomes while regulating gene expression chromosome-wide.

Published
2015

9. Heterochromatin drives compartmentalization of inverted and conventional nuclei

Author

Falk, Martin, Feodorova, Yana, Naumova, Natalia, Imakaev, Maxim, Lajoie, Bryan R., Leonhardt, Heinrich, and Joffe, Boris

Subjects
Chromatin -- Research, Cell research, Cell nuclei -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The nucleus of mammalian cells displays a distinct spatial segregation of active euchromatic and inactive heterochromatic regions of the genome.sup.1,2. In conventional nuclei, microscopy shows that euchromatin is localized in the nuclear interior and heterochromatin at the nuclear periphery.sup.1,2. Genome-wide chromosome conformation capture (Hi-C) analyses show this segregation as a plaid pattern of contact enrichment within euchromatin and heterochromatin compartments.sup.3, and depletion between them. Many mechanisms for the formation of compartments have been proposed, such as attraction of heterochromatin to the nuclear lamina.sup.2,4, preferential attraction of similar chromatin to each other.sup.1,4-12, higher levels of chromatin mobility in active chromatin.sup.13-15 and transcription-related clustering of euchromatin.sup.16,17. However, these hypotheses have remained inconclusive, owing to the difficulty of disentangling intra-chromatin and chromatin-lamina interactions in conventional nuclei.sup.18. The marked reorganization of interphase chromosomes in the inverted nuclei of rods in nocturnal mammals.sup.19,20 provides an opportunity to elucidate the mechanisms that underlie spatial compartmentalization. Here we combine Hi-C analysis of inverted rod nuclei with microscopy and polymer simulations. We find that attractions between heterochromatic regions are crucial for establishing both compartmentalization and the concentric shells of pericentromeric heterochromatin, facultative heterochromatin and euchromatin in the inverted nucleus. When interactions between heterochromatin and the lamina are added, the same model recreates the conventional nuclear organization. In addition, our models allow us to rule out mechanisms of compartmentalization that involve strong euchromatin interactions. Together, our experiments and modelling suggest that attractions between heterochromatic regions are essential for the phase separation of the active and inactive genome in inverted and conventional nuclei, whereas interactions of the chromatin with the lamina are necessary to build the conventional architecture from these segregated phases. Attractions between heterochromatic regions are essential for phase separation of the active and inactive genome in inverted and conventional nuclei, whereas chromatin-lamina interactions are necessary to build the conventional genomic architecture from these segregated phases., Author(s): Martin Falk [sup.1] , Yana Feodorova [sup.2] [sup.3] , Natalia Naumova [sup.4] [sup.5] , Maxim Imakaev [sup.1] , Bryan R. Lajoie [sup.4] [sup.6] , Heinrich Leonhardt [sup.3] , Boris [...]

Published
2019
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10. Accurate human genome analysis with Element Avidity sequencing

Author

Carroll, Andrew, primary, Kolesnikov, Alexey, additional, Cook, Daniel E., additional, Brambrink, Lucas, additional, Wiseman, Kelly N., additional, Billings, Sophie M., additional, Kruglyak, Semyon, additional, Lajoie, Bryan R., additional, Zhao, June, additional, Levy, Shawn E, additional, McLean, Cory Y, additional, Shafin, Kishwar, additional, Nattestad, Maria, additional, and Chang, Pi-Chuan, additional

Published
2023
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11. ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data

Author

Dolzhenko, Egor, Bennett, Mark F., Richmond, Phillip A., Trost, Brett, Chen, Sai, van Vugt, Joke J. F. A., Nguyen, Charlotte, Narzisi, Giuseppe, Gainullin, Vladimir G., Gross, Andrew M., Lajoie, Bryan R., Taft, Ryan J., Wasserman, Wyeth W., Scherer, Stephen W., Veldink, Jan H., Bentley, David R., Yuen, Ryan K. C., Bahlo, Melanie, and Eberle, Michael A.

Published
2020
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12. Integrative detection and analysis of structural variation in cancer genomes

Author

Dixon, Jesse R., Xu, Jie, Dileep, Vishnu, Zhan, Ye, Song, Fan, Le, Victoria T., Yardımcı, Galip Gürkan, Chakraborty, Abhijit, Bann, Darrin V., Wang, Yanli, Clark, Royden, Zhang, Lijun, Yang, Hongbo, Liu, Tingting, Iyyanki, Sriranga, An, Lin, Pool, Christopher, Sasaki, Takayo, Rivera-Mulia, Juan Carlos, Ozadam, Hakan, Lajoie, Bryan R., Kaul, Rajinder, Buckley, Michael, Lee, Kristen, Diegel, Morgan, Pezic, Dubravka, Ernst, Christina, Hadjur, Suzana, Odom, Duncan T., Stamatoyannopoulos, John A., Broach, James R., Hardison, Ross C., Ay, Ferhat, Noble, William Stafford, Dekker, Job, Gilbert, David M., and Yue, Feng

Published
2018
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13. Sequencing by avidity enables high accuracy with low reagent consumption

Author

Arslan, Sinan, primary, Garcia, Francisco J., additional, Guo, Minghao, additional, Kellinger, Matthew W., additional, Kruglyak, Semyon, additional, LeVieux, Jake A., additional, Mah, Adeline H., additional, Wang, Haosen, additional, Zhao, Junhua, additional, Zhou, Chunhong, additional, Altomare, Andrew, additional, Bailey, John, additional, Byrne, Matthew B., additional, Chang, Chiting, additional, Chen, Steve X., additional, Cho, Byungrae, additional, Dennler, Claudia N., additional, Dien, Vivian T., additional, Fuller, Derek, additional, Kelley, Ryan, additional, Khandan, Omid, additional, Klein, Michael G., additional, Kim, Michael, additional, Lajoie, Bryan R., additional, Lin, Bill, additional, Liu, Yu, additional, Lopez, Tyler, additional, Mains, Peter T., additional, Price, Andrew D., additional, Robertson, Samantha R., additional, Taylor-Weiner, Hermes, additional, Tippana, Ramreddy, additional, Tomaney, Austin B., additional, Zhang, Su, additional, Abtahi, Minna, additional, Ambroso, Mark R., additional, Bajari, Rosita, additional, Bellizzi, Ava M., additional, Benitez, Chris B., additional, Berard, Daniel R., additional, Berti, Lorenzo, additional, Blease, Kelly N., additional, Blum, Angela P., additional, Boddicker, Andrew M., additional, Bondar, Leo, additional, Brown, Chris, additional, Bui, Chris A., additional, Calleja-Aguirre, Juan, additional, Cappa, Kevin, additional, Chan, Joshua, additional, Chang, Victor W., additional, Charov, Katherine, additional, Chen, Xiyi, additional, Constandse, Rodger M., additional, Damron, Weston, additional, Dawood, Mariam, additional, DeBuono, Nicole, additional, Dimalanta, John D., additional, Edoli, Laure, additional, Elango, Keerthana, additional, Faustino, Nikka, additional, Feng, Chao, additional, Ferrari, Matthew, additional, Frankie, Keith, additional, Fries, Adam, additional, Galloway, Anne, additional, Gavrila, Vlad, additional, Gemmen, Gregory J., additional, Ghadiali, James, additional, Ghorbani, Arash, additional, Goddard, Logan A., additional, Guetter, Adriana Roginski, additional, Hendricks, Garren L., additional, Hentschel, Jendrik, additional, Honigfort, Daniel J., additional, Hsieh, Yun-Ting, additional, Hwang Fu, Yu-Hsien, additional, Im, Scott K., additional, Jin, Chaoyi, additional, Kabu, Shradha, additional, Kincade, Daniel E., additional, Levy, Shawn, additional, Li, Yu, additional, Liang, Vincent K., additional, Light, William H., additional, Lipsher, Jonathan B., additional, Liu, Tsung-li, additional, Long, Grace, additional, Ma, Rui, additional, Mailloux, John M., additional, Mandla, Kyle A., additional, Martinez, Anyssa R., additional, Mass, Max, additional, McKean, Daniel T., additional, Meron, Michael, additional, Miller, Edmund A., additional, Moh, Celyne S., additional, Moore, Rachel K., additional, Moreno, Juan, additional, Neysmith, Jordan M., additional, Niman, Cassandra S., additional, Nunez, Jesus M., additional, Ojeda, Micah T., additional, Ortiz, Sara Espinosa, additional, Owens, Jenna, additional, Piland, Geoffrey, additional, Proctor, Daniel J., additional, Purba, Josua B., additional, Ray, Michael, additional, Rong, Daisong, additional, Saade, Virginia M., additional, Saha, Sanchari, additional, Tomas, Gustav Santo, additional, Scheidler, Nicholas, additional, Sirajudeen, Luqmanal H., additional, Snow, Samantha, additional, Stengel, Gudrun, additional, Stinson, Ryan, additional, Stone, Michael J., additional, Sundseth, Keoni J., additional, Thai, Eileen, additional, Thompson, Connor J., additional, Tjioe, Marco, additional, Trejo, Christy L., additional, Trieger, Greg, additional, Truong, Diane Ni, additional, Tse, Ben, additional, Voiles, Benjamin, additional, Vuong, Henry, additional, Wong, Jennifer C., additional, Wu, Chiung-Ting, additional, Yu, Hua, additional, Yu, Yingxian, additional, Yu, Ming, additional, Zhang, Xi, additional, Zhao, Da, additional, Zheng, Genhua, additional, He, Molly, additional, and Previte, Michael, additional

Published
2023
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16. Activation of proto-oncogenes by disruption of chromosome neighborhoods

Author

Hnisz, Denes, Weintraub, Abraham S., Day, Daniel S., Valton, Anne-Laure, Bak, Rasmus O., Li, Charles H., Goldmann, Johanna, Lajoie, Bryan R., Fan, Zi Peng, Sigova, Alla A., Reddy, Jessica, Borges-Rivera, Diego, Lee, Tong Ihn, Jaenisch, Rudolf, Porteus, Matthew H., Dekker, Job, and Young, Richard A.

Published
2016

19. Measuring the reproducibility and quality of Hi-C data

Author

Yardımcı, Galip Gürkan, Ozadam, Hakan, Sauria, Michael E. G., Ursu, Oana, Yan, Koon-Kiu, Yang, Tao, Chakraborty, Abhijit, Kaul, Arya, Lajoie, Bryan R., Song, Fan, Zhan, Ye, Ay, Ferhat, Gerstein, Mark, Kundaje, Anshul, Li, Qunhua, Taylor, James, Yue, Feng, Dekker, Job, and Noble, William S.

Published
2019
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23. X-linked hypomyelination with spondylometaphyseal dysplasia (H-SMD) associated with mutations in AIFM1

Author

Miyake, Noriko, Wolf, Nicole I., Cayami, Ferdy K., Crawford, Joanna, Bley, Annette, Bulas, Dorothy, Conant, Alex, Bent, Stephen J., Gripp, Karen W., Hahn, Andreas, Humphray, Sean, Kimura-Ohba, Shihoko, Kingsbury, Zoya, Lajoie, Bryan R., Lal, Dennis, Micha, Dimitra, Pizzino, Amy, Sinke, Richard J., Sival, Deborah, Stolte-Dijkstra, Irene, Superti-Furga, Andrea, Ulrick, Nicole, Taft, Ryan J., Ogata, Tsutomu, Ozono, Keiichi, Matsumoto, Naomichi, Neubauer, Bernd A., Simons, Cas, and Vanderver, Adeline

Published
2017
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25. Sequencing by avidity enables high accuracy with low reagent consumption

Author

Arslan, Sinan, primary, Garcia, Francisco Jose, additional, Guo, Minghao, additional, Kellinger, Matthew William, additional, Kruglyak, Semyon, additional, LeVieux, Jake Allen, additional, Mah, Adeline Huizhen, additional, Wang, Haosen, additional, Zhao, Junhua, additional, Zhou, Chunhong, additional, Altomare, Andrew, additional, Bailey, John, additional, Byrne, Matthew B, additional, Chang, Chiting, additional, Chen, Steve Xiangling, additional, Dennler, Claudia N, additional, Dien, Vivian Tran, additional, Fuller, Derek, additional, Kelley, Ryan, additional, Khandan, Omid, additional, Klein, Michael Geoffrey, additional, Kim, Michael, additional, Lajoie, Bryan R, additional, Lin, Bill, additional, Liu, Yu, additional, Lopez, Tyler, additional, Mains, Peter Thomas, additional, Price, Andrew David, additional, Robertson, Samantha R, additional, Taylor-Weiner, Hermes, additional, Tippana, Ramreddy, additional, Tomaney, Austin B, additional, Zhang, Su, additional, Ambroso, Mark Robert, additional, Bajari, Rosita, additional, Bellizzi, Ava M, additional, Benitez, Chris Bryan, additional, Berard, Daniel R, additional, Berti, Lorenzo, additional, Blease, Kelly Nicole, additional, Blum, Angela Patricia, additional, Boddicker, Andrew M, additional, Bondar, Leo, additional, Brown, Chris, additional, Bui, Chris A, additional, Calleja-Aguirre, Juan, additional, Cappa, Kevin, additional, Chan, Joshua, additional, Chang, Victor W, additional, Charov, Katherine, additional, Chen, Xiyi, additional, Constandse, Rodger M, additional, Damron, Weston, additional, Dawood, Mariam, additional, DeBuono, Nicole, additional, Dimalanta, John De Vera, additional, Edoli, Laure, additional, Elango, Keerthana, additional, Faustino, Nikka, additional, Feng, Chao, additional, Ferrari, Mathhew, additional, Frankie, Keith, additional, Fries, Adam, additional, Galloway, Anne, additional, Gavrila, Vlad, additional, Gemmen, Gregory J, additional, Ghadiali, James, additional, Ghorbani, Arash, additional, Goddard, Logan A, additional, Guetter, Adriana Roginski, additional, Hendricks, Garren Lee Lewis, additional, Hentschel, Jendrik, additional, Honigfort, Daniel J, additional, Hsieh, Yun-Ting, additional, Hwang Fu, Yu-Hsien, additional, Im, Scott Kang, additional, Jin, Chaoyi, additional, Kabu, Shradha, additional, Kincade, Daniel Eugene, additional, Levy, Shawn, additional, Li, Yu, additional, Liang, Vincent K, additional, Light, William H, additional, Lipsher, Jonathan Brian, additional, Liu, Tsung-li, additional, Long, Grace, additional, Ma, Rui, additional, Mailloux, John Michael, additional, Mandla, Kyle A, additional, Martinez, Anyssa Rae, additional, Mass, Max, additional, McKean, Daniel T, additional, Meron, Michael, additional, Moh, Celyne Shaoyun, additional, Moore, Rachel Kaye, additional, Moreno, Juan, additional, Neysmith, Jordan M, additional, Niman, Cassandra Sekol, additional, Nunez, Jesus M, additional, Ojeda, Micah Tate, additional, Espinosa Ortiz, Sara, additional, Owens, Jenna, additional, Piland, Geoffrey, additional, Proctor, Daniel J, additional, Purba, Josua B, additional, Ray, Michael, additional, Rong, Daisong, additional, Saade, Virginia Myanh, additional, Saha, Sanchari, additional, Santo Tomas, Gustav, additional, Scheidler, Nicholas, additional, Sirajudeen, Luqmanal Hakim, additional, Snow, Samantha, additional, Stengel, Gudrun, additional, Stinson, Ryan, additional, Stone, Michael Joseph, additional, Sundseth, Keoni John, additional, Thai, Eileen, additional, Thompson, Connor J, additional, Tjioe, Marco, additional, Trejo, Christy L, additional, Trieger, Greg, additional, Truong, Diane Ni, additional, Tse, Ben, additional, Voiles, Benjamin, additional, Vuong, Henry, additional, Wong, Jennifer Christine, additional, Wu, Chiung-Ting, additional, Yu, Hua, additional, Yu, Yingxian, additional, Yu, Ming, additional, Zhang, Xi, additional, Zhao, Da, additional, Zheng, Genhua, additional, He, Molly, additional, and Previte, Michael, additional

Published
2022
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26. Structural organization of the inactive X chromosome in the mouse

Author

Giorgetti, Luca, Lajoie, Bryan R., Carter, Ava C., Attia, Mikael, Zhan, Ye, Xu, Jin, Chen, Chong Jian, Kaplan, Noam, Chang, Howard Y., Heard, Edith, and Dekker, Job

Subjects
Gene expression -- Observations, RNA sequencing -- Methods, Chromosomes -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

X-chromosome inactivation (XCI) involves major reorganization of the X chromosome as it becomes silent and heterochromatic. During female mammalian development, XCI is triggered by upregulation of the non-coding Xist RNA from one of the two X chromosomes. Xist coats the chromosome in cis and induces silencing of almost all genes via its A-repeat region (1,2), although some genes (constitutive escapees) avoid silencing in most cell types, and others (facultative escapees) escape XCI only in specific contexts (3). A role for Xist in organizing the inactive X (Xi) chromosome has been proposed (4-6). Recent chromosome conformation capture approaches have revealed global loss of local structure on the Xi chromosome and formation of large mega-domains, separated by a region containing the DXZ4 macrosatellite (7-10). However, the molecular architecture of the Xi chromosome, in both the silent and expressed regions, remains unclear. Here we investigate the structure, chromatin accessibility and expression status of the mouse Xi chromosome in highly polymorphic clonal neural progenitors (NPCs) and embryonic stem cells. We demonstrate a crucial role for Xist and the DXZ4-containing boundary in shaping Xi chromosome structure using allele-specific genome-wide chromosome conformation capture (Hi-C) analysis, an assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) and RNA sequencing. Deletion of the boundary disrupts mega-domain formation, and induction of Xist RNA initiates formation of the boundary and the loss of DNA accessibility. We also show that in NPCs, the Xi chromosome lacks active/inactive compartments and topologically associating domains (TADs), except around genes that escape XCI. Escapee gene clusters display TAD-like structures and retain DNA accessibility at promoter-proximal and CTCF-binding sites. Furthermore, altered patterns of facultative escape genes in different neural progenitor clones are associated with the presence of different TAD-like structures after XCI. These findings suggest a key role for transcription and CTCF in the formation of TADs in the context of the Xi chromosome in neural progenitors., To investigate the structure of the Xi chromosome, we performed allele-specific Hi-C in a clonal neural progenitor cell (NPC) line that was derived from highly polymorphic F1 mouse embryonic stem [...]

Published
2016

34. Patterns of Growth and Decline in Lung Function in Persistent Childhood Asthma

Author

McGeachie, Michael J., Yates, Katherine P., Zhou, Xiaobo, Guo, Feng, Sternberg, Alice L., Van Natta, Mark L., Wise, Robert A., Szefler, Stanley J., Sharma, Sunita, Kho, Alvin T., Cho, Michael H., Croteau-Chonka, Damien C., Castaldi, Peter J., Jain, Gaurav, Sanyal, Amartya, Zhan, Ye, Lajoie, Bryan R., Dekker, Job, Stamatoyannopoulos, John, Covar, Ronina A., Zeiger, Robert S., Adkinson, N. Franklin, Williams, Paul V., Kelly, H. William, Grasemann, Hartmut, Vonk, Judith M., Koppelman, Gerard H., Postma, Dirkje S., Raby, Benjamin A., Houston, Isaac, Lu, Quan, Fuhlbrigge, Anne L., Tantisira, Kelan G., Silverman, Edwin K., Tonascia, James, Weiss, Scott T., and Strunk, Robert C.

Published
2016
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36. An integrated encyclopedia of DNA elements in the human genome

Author

Dunham, Ian, Kundaje, Anshul, Aldred, Shelley F., Collins, Patrick J., Davis, Carrie A., Doyle, Francis, Epstein, Charles B., Frietze, Seth, Harrow, Jennifer, Kaul, Rajinder, Khatun, Jainab, Lajoie, Bryan R., Landt, Stephen G., Lee, Bum-Kyu, Pauli, Florencia, Rosenbloom, Kate R., Sabo, Peter, Safi, Alexias, Sanyal, Amartya, Shoresh, Noam, Simon, Jeremy M., Song, Lingyun, Trinklein, Nathan D., Altshuler, Robert C., Birney, Ewan, Brown, James B., Cheng, Chao, Djebali, Sarah, Dong, Xianjun, Ernst, Jason, Furey, Terrence S., Gerstein, Mark, Giardine, Belinda, Greven, Melissa, Hardison, Ross C., Harris, Robert S., Herrero, Javier, Hoffman, Michael M., Iyer, Sowmya, Kellis, Manolis, Kheradpour, Pouya, Lassmann, Timo, Li, Qunhua, Lin, Xinying, Marinov, Georgi K., Merkel, Angelika, Mortazavi, Ali, Parker, Stephen C. J., Reddy, Timothy E., Rozowsky, Joel, Schlesinger, Felix, Thurman, Robert E., Wang, Jie, Ward, Lucas D., Whitfield, Troy W., Wilder, Steven P., Wu, Weisheng, Xi, Hualin S., Yip, Kevin Y., Zhuang, Jiali, Bernstein, Bradley E., Green, Eric D., Gunter, Chris, Snyder, Michael, Pazin, Michael J., Lowdon, Rebecca F., Dillon, Laura A. L., Adams, Leslie B., Kelly, Caroline J., Zhang, Julia, Wexler, Judith R., Good, Peter J., Feingold, Elise A., Crawford, Gregory E., Dekker, Job, Elnitski, Laura, Farnham, Peggy J., Giddings, Morgan C., Gingeras, Thomas R., Guigo, Roderic, Hubbard, Timothy J., Kent, W. James, Lieb, Jason D., Margulies, Elliott H., Myers, Richard M., Stamatoyannopoulos, John A., Tenenbaum, Scott A., Weng, Zhiping, White, Kevin P., Wold, Barbara, Yu, Yanbao, Wrobel, John, Risk, Brian A., Gunawardena, Harsha P., Kuiper, Heather C., Maier, Christopher W., Xie, Ling, Chen, Xian, Mikkelsen, Tarjei S., Gillespie, Shawn, Goren, Alon, Ram, Oren, Zhang, Xiaolan, Wang, Li, Issner, Robbyn, Coyne, Michael J., Durham, Timothy, Ku, Manching, Truong, Thanh, Eaton, Matthew L., Dobin, Alex, Tanzer, Andrea, Lagarde, Julien, Lin, Wei, Xue, Chenghai, Williams, Brian A., Zaleski, Chris, Roder, Maik, Kokocinski, Felix, Abdelhamid, Rehab F., Alioto, Tyler, Antoshechkin, Igor, Baer, Michael T., Batut, Philippe, Bell, Ian, Bell, Kimberly, Chakrabortty, Sudipto, Chrast, Jacqueline, Curado, Joao, Derrien, Thomas, Drenkow, Jorg, Dumais, Erica, Dumais, Jackie, Duttagupta, Radha, Fastuca, Megan, Fejes-Toth, Kata, Ferreira, Pedro, Foissac, Sylvain, Fullwood, Melissa J., Gao, Hui, Gonzalez, David, Gordon, Assaf, Howald, Cedric, Jha, Sonali, Johnson, Rory, Kapranov, Philipp, King, Brandon, Kingswood, Colin, Li, Guoliang, Luo, Oscar J., Park, Eddie, Preall, Jonathan B., Presaud, Kimberly, Ribeca, Paolo, Robyr, Daniel, Ruan, Xiaoan, Sammeth, Michael, Sandhu, Kuljeet Singh, Schaeffer, Lorain, See, Lei-Hoon, Shahab, Atif, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Trout, Diane, Walters, Nathalie, Wang, Huaien, Hayashizaki, Yoshihide, Reymond, Alexandre, Antonarakis, Stylianos E., Hannon, Gregory J., Ruan, Yijun, Carninci, Piero, Sloan, Cricket A., Learned, Katrina, Malladi, Venkat S., Wong, Matthew C., Barber, Galt P., Cline, Melissa S., Dreszer, Timothy R., Heitner, Steven G., Karolchik, Donna, Kirkup, Vanessa M., Meyer, Laurence R., Long, Jeffrey C., Maddren, Morgan, Raney, Brian J., Grasfeder, Linda L., Giresi, Paul G., Battenhouse, Anna, Sheffield, Nathan C., Showers, Kimberly A., London, Darin, Bhinge, Akshay A., Shestak, Christopher, Schaner, Matthew R., Ki Kim, Seul, Zhang, Zhuzhu Z., Mieczkowski, Piotr A., Mieczkowska, Joanna O., Liu, Zheng, McDaniell, Ryan M., Ni, Yunyun, Rashid, Naim U., Kim, Min Jae, Adar, Sheera, Zhang, Zhancheng, Wang, Tianyuan, Winter, Deborah, Keefe, Damian, Iyer, Vishwanath R., Zheng, Meizhen, Wang, Ping, Gertz, Jason, Vielmetter, Jost, Partridge, E., Varley, Katherine E., Gasper, Clarke, Bansal, Anita, Pepke, Shirley, Jain, Preti, Amrhein, Henry, Bowling, Kevin M., Anaya, Michael, Cross, Marie K., Muratet, Michael A., Newberry, Kimberly M., McCue, Kenneth, Nesmith, Amy S., Fisher-Aylor, Katherine I., Pusey, Barbara, DeSalvo, Gilberto, Parker, Stephanie L., Balasubramanian, Sreeram, Davis, Nicholas S., Meadows, Sarah K., Eggleston, Tracy, Newberry, J. Scott, Levy, Shawn E., Absher, Devin M., Wong, Wing H., Blow, Matthew J., Visel, Axel, Pennachio, Len A., Petrykowska, Hanna M., Abyzov, Alexej, Aken, Bronwen, Barrell, Daniel, Barson, Gemma, Berry, Andrew, Bignell, Alexandra, Boychenko, Veronika, Bussotti, Giovanni, Davidson, Claire, Despacio-Reyes, Gloria, Diekhans, Mark, Ezkurdia, Iakes, Frankish, Adam, Gilbert, James, Gonzalez, Jose Manuel, Griffiths, Ed, Harte, Rachel, Hendrix, David A., Hunt, Toby, Jungreis, Irwin, Kay, Mike, Khurana, Ekta, Leng, Jing, Lin, Michael F., Loveland, Jane, Lu, Zhi, Manthravadi, Deepa, Mariotti, Marco, Mudge, Jonathan, Mukherjee, Gaurab, Notredame, Cedric, Pei, Baikang, Rodriguez, Jose Manuel, Saunders, Gary, Sboner, Andrea, Searle, Stephen, Sisu, Cristina, Snow, Catherine, Steward, Charlie, Tapanari, Electra, Tress, Michael L., van Baren, Marijke J., Washietl, Stefan, Wilming, Laurens, Zadissa, Amonida, Zhang, Zhengdong, Brent, Michael, Haussler, David, Valencia, Alfonso, Addleman, Nick, Alexander, Roger P., Auerbach, Raymond K., Balasubramanian, Suganthi, Bettinger, Keith, Bhardwaj, Nitin, Boyle, Alan P., Cao, Alina R., Cayting, Philip, Charos, Alexandra, Cheng, Yong, Eastman, Catharine, Euskirchen, Ghia, Fleming, Joseph D., Grubert, Fabian, Habegger, Lukas, Hariharan, Manoj, Harmanci, Arif, Iyengar, Sushma, Jin, Victor X., Karczewski, Konrad J., Kasowski, Maya, Lacroute, Phil, Lam, Hugo, Lamarre-Vincent, Nathan, Lian, Jin, Lindahl-Allen, Marianne, Min, Renqiang, Miotto, Benoit, Monahan, Hannah, Moqtaderi, Zarmik, Mu, Xinmeng J., Ouyang, Zhengqing, Patacsil, Dorrelyn, Raha, Debasish, Ramirez, Lucia, Reed, Brian, Shi, Minyi, Slifer, Teri, Witt, Heather, Wu, Linfeng, Xu, Xiaoqin, Yan, Koon-Kiu, Yang, Xinqiong, Struhl, Kevin, Weissman, Sherman M., Penalva, Luiz O., Karmakar, Subhradip, Bhanvadia, Raj R., Choudhury, Alina, Domanus, Marc, Ma, Lijia, Moran, Jennifer, Victorsen, Alec, Auer, Thomas, Centanin, Lazaro, Eichenlaub, Michael, Gruhl, Franziska, Heermann, Stephan, Hoeckendorf, Burkhard, Inoue, Daigo, Kellner, Tanja, Kirchmaier, Stephan, Mueller, Claudia, Reinhardt, Robert, Schertel, Lea, Schneider, Stephanie, Sinn, Rebecca, Wittbrodt, Beate, Wittbrodt, Jochen, Partridge, E. Christopher, Jain, Gaurav, Balasundaram, Gayathri, Bates, Daniel L., Byron, Rachel, Canfield, Theresa K., Diegel, Morgan J., Dunn, Douglas, Ebersol, Abigail K., Frum, Tristan, Garg, Kavita, Gist, Erica, Hansen, R. Scott, Boatman, Lisa, Haugen, Eric, Humbert, Richard, Johnson, Audra K., Johnson, Ericka M., Kutyavin, Tattyana V., Lee, Kristen, Lotakis, Dimitra, Maurano, Matthew T., Neph, Shane J., Neri, Fiedencio V., Nguyen, Eric D., Qu, Hongzhu, Reynolds, Alex P., Roach, Vaughn, Rynes, Eric, Sanchez, Minerva E., Sandstrom, Richard S., Shafer, Anthony O., Stergachis, Andrew B., Thomas, Sean, Vernot, Benjamin, Vierstra, Jeff, Vong, Shinny, Weaver, Molly A., Yan, Yongqi, Zhang, Miaohua, Akey, Joshua M., Bender, Michael, Dorschner, Michael O., Groudine, Mark, MacCoss, Michael J., Navas, Patrick, Stamatoyannopoulos, George, Beal, Kathryn, Brazma, Alvis, Flicek, Paul, Johnson, Nathan, Lukk, Margus, Luscombe, Nicholas M., Sobral, Daniel, Vaquerizas, Juan M., Batzoglou, Serafim, Sidow, Arend, Hussami, Nadine, Kyriazopoulou-Panagiotopoulou, Sofia, Libbrecht, Max W., Schaub, Marc A., Miller, Webb, Bickel, Peter J., Banfai, Balazs, Boley, Nathan P., Huang, Haiyan, Li, Jingyi Jessica, Noble, William Stafford, Bilmes, Jeffrey A., Buske, Orion J., Sahu, Avinash D., Kharchenko, Peter V., Park, Peter J., Baker, Dannon, Taylor, James, and Lochovsky, Lucas

Subjects
Genetic research, Human genome -- Research, Genetic transcription -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research., Author(s): The ENCODE Project Consortium; Overall coordination (data analysis coordination); Ian Dunham [2]; Anshul Kundaje [3, 82]; Data production leads (data production); Shelley F. Aldred [4]; Patrick J. Collins [4]; [...]

Published
2012
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37. The long-range interaction landscape of gene promoters

Author

Sanyal, Amartya, Lajoie, Bryan R., Jain, Gaurav, and Dekker, Job

Subjects
Primers (Molecular genetics) -- Properties, Chromatin -- Properties, Promoters (Genetics) -- Properties, Protein-protein interactions -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The vast non-coding portion of the human genome is full of functional elements and disease-causing regulatory variants. The principles defining the relationships between these elements and distal target genes remain [...]

Published
2012
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38. Spatial partitioning of the regulatory landscape of the X-inactivation centre

Author

Nora, Elphege P., Lajoie, Bryan R., Schulz, Edda G., Giorgetti, Luca, Okamoto, Ikuhiro, Servant, Nicolas, Piolot, Tristan, van Berkum, Nynke L., Meisig, Johannes, Sedat, John, Gribnau, Joost, Barillot, Emmanuel, Bluthgen, Nils, Dekker, Job, and Heard, Edith

Subjects
DNA -- Physiological aspects -- Research, Stem cells -- Physiological aspects -- Genetic aspects -- Research, Genetic transcription -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

In eukaryotes transcriptional regulation often involves multiple long-range elements and is influenced by the genomic environment (1). A prime example of this concerns the mouse X-inactivation centre (Xic), which orchestrates the initiation of X-chromosome inactivation (XCI) by controlling the expression of the nonprotein-coding Xist transcript. The extent of Xic sequences required for the proper regulation of Xist remains unknown. Here we use chromosome conformation capture carbon-copy (5C) (2) and super-resolution microscopy to analyse the spatial organization of a 4.5-megabases (Mb) region including Xist.We discover a series of discrete 200-kilobase to 1 Mb topologically associating domains (TADs), present both before and after cell differentiation and on the active and inactive X. TADs align with, but do not rely on, several domain-wide features of the epigenome, such as H3K27me3 or H3K9me2 blocks and lamina-associated domains. TADs also align with coordinately regulated gene clusters. Disruption of a TAD boundary causes ectopic chromosomal contacts and long-range transcriptional misregulation. The Xist/Tsix sense/antisense unit illustrates how TADs enable the spatial segregation of oppositely regulated chromosomal neighbourhoods, with the respective promoters of Xist and Tsix lying in adjacent TADs, each containing their known positive regulators. We identify a novel distal regulatory region of Tsix within its TAD, which produces a long intervening RNA, Linx. In addition to uncovering a new principle of cis-regulatory architecture of mammalian chromosomes, our study sets the stage for the full genetic dissection of the X-inactivation centre., The X-inactivation centre was originally defined by deletions and translocations as a region spanning several megabases (3,4), and contains several elements known to affect Xist activity, including its repressive antisense [...]

Published
2012
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39. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

Author

Wang, Kevin C., Yang, Yul W., Liu, Bo, Sanyal, Amartya, Corces-Zimmerman, Ryan, Chen, Yong, Lajoie, Bryan R., Protacio, Angeline, Flynn, Ryan A., Gupta, Rajnish A., Wysocka, Joanna, Lei, Ming, Dekker, Job, Helms, Jill A., and Chang, Howard Y.

Subjects
Gene expression -- Research -- Physiological aspects, Chromatin -- Physiological aspects -- Research, RNA -- Physiological aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The genome is extensively transcribed into long intergenic non-coding RNAs (lincRNAs), many of which are implicated in gene silencing (1,2). Potential roles of lincRNAs in gene activation are much less understood (3-5). Development and homeostasis require coordinate regulation of neighbouring genes through a process termed locus control (6). Some locus control elements and enhancers transcribe lincRNAs (7-10), hinting at possible roles in long-range control. In vertebrates, 39 Hox genes, encoding homeodomain transcription factors critical for positional identity, are clustered in four chromosomal loci; the Hox genes are expressed in nested anterior-posterior and proximal-distal patterns colinear with their genomic position from 3' to 5'of the cluster (11). Here we identify HOTTIP, alincRNA transcribed from the 5' tip of the HOXA locus that coordinates the activation of several 5' HOXA genes in vivo. Chromosomal looping brings HOTTIP into close proximity to its target genes. HOTTIP RNA binds the adaptor protein WDR5 directly and targets WDR5/MLL complexes across HOXA, driving histone H3 lysine 4 trimethylation and gene transcription. Induced proximity is necessary and sufficient for HOTTIP RNA activation of its target genes. Thus, by serving as key intermediates that transmit information from higher order chromosomal looping into chromatin modifications, lincRNAs may organize chromatin domains to coordinate long-range gene activation., We examined chromosome structure and histone modifications in human primary fibroblasts derived from several anatomic sites (12), and found distinctive differences in the HOXA locus. High throughput chromosome conformation capture [...]

Published
2011
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40. Rapid Sequencing-Based Diagnosis of Thiamine Metabolism Dysfunction Syndrome

Author

Owen, Mallory J., primary, Niemi, Anna-Kaisa, additional, Dimmock, David P., additional, Speziale, Mark, additional, Nespeca, Mark, additional, Chau, Kevin K., additional, Van Der Kraan, Luca, additional, Wright, Meredith S., additional, Hansen, Christian, additional, Veeraraghavan, Narayanan, additional, Ding, Yan, additional, Lenberg, Jerica, additional, Chowdhury, Shimul, additional, Hobbs, Charlotte A., additional, Batalov, Sergey, additional, Zhu, Zhanyang, additional, Nahas, Shareef A., additional, Gilmer, Sheldon, additional, Knight, Gail, additional, Lefebvre, Sebastien, additional, Reynders, John, additional, Defay, Thomas, additional, Weir, Jacqueline, additional, Thomson, Vicki S., additional, Fraser, Louise, additional, Lajoie, Bryan R., additional, McPhail, Tim K., additional, Mehtalia, Shyamal S., additional, Kunard, Chris M., additional, Hall, Kevin P., additional, and Kingsmore, Stephen F., additional

Published
2021
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41. Additional file 1 of ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data

Author

Dolzhenko, Egor, Bennett, Mark F., Richmond, Phillip A., Trost, Brett, Chen, Sai, Vugt, Joke J. F. A. Van, Nguyen, Charlotte, Narzisi, Giuseppe, Gainullin, Vladimir G., Gross, Andrew M., Lajoie, Bryan R., Taft, Ryan J., Wyeth W. Wasserman, Scherer, Stephen W., Veldink, Jan H., Bentley, David R., Yuen, Ryan K. C., Bahlo, Melanie, and Eberle, Michael A.

Abstract

Additional file 1. Supplementary methods, supplementary results, Figure S1-S6, and captions of Tables S1-S8.

Published
2020
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42. The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos

Author

Massachusetts Institute of Technology. Department of Physics, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Erceg, Jelena, AlHaj Abed, Jumana, Goloborodko, Anton, Lajoie, Bryan R., Fudenberg, Geoffrey, Abdennur, Nezar Alexander, Imakaev, Maksim Viktorovich, McCole, Ruth B., Nguyen, Son C., Saylor, Wren, Joyce, Eric F., Senaratne, T. Niroshini, Hannan, Mohammed A., Nir, Guy, Dekker, Job, Mirny, Leonid A, Wu, C.-ting, Massachusetts Institute of Technology. Department of Physics, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Erceg, Jelena, AlHaj Abed, Jumana, Goloborodko, Anton, Lajoie, Bryan R., Fudenberg, Geoffrey, Abdennur, Nezar Alexander, Imakaev, Maksim Viktorovich, McCole, Ruth B., Nguyen, Son C., Saylor, Wren, Joyce, Eric F., Senaratne, T. Niroshini, Hannan, Mohammed A., Nir, Guy, Dekker, Job, Mirny, Leonid A, and Wu, C.-ting

Abstract

Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first address long-standing questions regarding the structure of embryonic homolog pairing and, to this end, develop a haplotype-resolved Hi-C approach to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This computational approach, which we call Ohm, reveals pairing to be surprisingly structured genome-wide, with trans-homolog domains, compartments, and interaction peaks, many coinciding with analogous cis features. We also find a significant genome-wide correlation between pairing, transcription during zygotic genome activation, and binding of the pioneer factor Zelda. Our findings reveal a complex, highly structured organization underlying homolog pairing, first discovered a century ago in Drosophila. Finally, we demonstrate the versatility of our haplotype-resolved approach by applying it to mammalian embryos.

Published
2020

43. Highly structured homolog pairing reflects functional organization of the Drosophila genome

Author

Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Physics, AlHaj Abed, Jumana, Erceg, Jelena, Goloborodko, Anton, Nguyen, Son C., McCole, Ruth B., Saylor, Wren, Fudenberg, Geoffrey, Lajoie, Bryan R., Dekker, Job, Mirny, Leonid A., Wu, C.-ting, Goloborodko, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Massachusetts Institute of Technology. Department of Physics, AlHaj Abed, Jumana, Erceg, Jelena, Goloborodko, Anton, Nguyen, Son C., McCole, Ruth B., Saylor, Wren, Fudenberg, Geoffrey, Lajoie, Bryan R., Dekker, Job, Mirny, Leonid A., Wu, C.-ting, and Goloborodko

Abstract

Trans-homolog interactions have been studied extensively in Drosophila, where homologs are paired in somatic cells and transvection is prevalent. Nevertheless, the detailed structure of pairing and its functional impact have not been thoroughly investigated. Accordingly, we generated a diploid cell line from divergent parents and applied haplotype-resolved Hi-C, showing that homologs pair with varying precision genome-wide, in addition to establishing trans-homolog domains and compartments. We also elucidate the structure of pairing with unprecedented detail, observing significant variation across the genome and revealing at least two forms of pairing: tight pairing, spanning contiguous small domains, and loose pairing, consisting of single larger domains. Strikingly, active genomic regions (A-type compartments, active chromatin, expressed genes) correlated with tight pairing, suggesting that pairing has a functional implication genome-wide. Finally, using RNAi and haplotype-resolved Hi-C, we show that disruption of pairing-promoting factors results in global changes in pairing, including the disruption of some interaction peaks. Keywords: Computational biology and bioinformatics; Epigenetics; Functional genomics; Molecular biology, National Institute of General Medical Sciences (U.S.) (Grant R01HD091797), National Institute of General Medical Sciences (U.S.) (Grant R01GM123289), National Institute of General Medical Sciences (U.S.) (Grant DP1GM106412), National Institute of General Medical Sciences (U.S.) (Grant R01 GM114190)

Published
2020

44. ExpansionHunter Denovo: A computational method for locating known and novel repeat expansions in short-read sequencing data

Author

Neurogenetica, ZL Neuromusculaire Ziekten Medisch, Brain, Dolzhenko, Egor, Bennett, Mark F., Richmond, Phillip A., Trost, Brett, Chen, Sai, Van Vugt, Joke J.F.A., Nguyen, Charlotte, Narzisi, Giuseppe, Gainullin, Vladimir G., Gross, Andrew M., Lajoie, Bryan R., Taft, Ryan J., Wasserman, Wyeth W., Scherer, Stephen W., Veldink, Jan H., Bentley, David R., Yuen, Ryan K.C., Bahlo, Melanie, Eberle, Michael A., Neurogenetica, ZL Neuromusculaire Ziekten Medisch, Brain, Dolzhenko, Egor, Bennett, Mark F., Richmond, Phillip A., Trost, Brett, Chen, Sai, Van Vugt, Joke J.F.A., Nguyen, Charlotte, Narzisi, Giuseppe, Gainullin, Vladimir G., Gross, Andrew M., Lajoie, Bryan R., Taft, Ryan J., Wasserman, Wyeth W., Scherer, Stephen W., Veldink, Jan H., Bentley, David R., Yuen, Ryan K.C., Bahlo, Melanie, and Eberle, Michael A.

Published
2020

46. Genome sequencing in persistently unsolved white matter disorders

Author

Helman, Guy, primary, Lajoie, Bryan R., additional, Crawford, Joanna, additional, Takanohashi, Asako, additional, Walkiewicz, Marzena, additional, Dolzhenko, Egor, additional, Gross, Andrew M., additional, Gainullin, Vladimir G., additional, Bent, Stephen J., additional, Jenkinson, Emma M., additional, Ferdinandusse, Sacha, additional, Waterham, Hans R., additional, Dorboz, Imen, additional, Bertini, Enrico, additional, Miyake, Noriko, additional, Wolf, Nicole I., additional, Abbink, Truus E. M., additional, Kirwin, Susan M., additional, Tan, Christina M., additional, Hobson, Grace M., additional, Guo, Long, additional, Ikegawa, Shiro, additional, Pizzino, Amy, additional, Schmidt, Johanna L., additional, Bernard, Genevieve, additional, Schiffmann, Raphael, additional, Knaap, Marjo S., additional, Simons, Cas, additional, Taft, Ryan J., additional, and Vanderver, Adeline, additional

Published
2020
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47. An encyclopedia of mouse DNA elements (Mouse ENCODE)

Author

Stamatoyannopoulos, John A, Snyder, Michael, Hardison, Ross, Ren, Bing, Gingeras, Thomas, Gilbert, David M, Groudine, Mark, Bender, Michael, Kaul, Rajinder, Canfield, Theresa, Giste, Erica, Johnson, Audra, Zhang, Mia, Balasundaram, Gayathri, Byron, Rachel, Roach, Vaughan, Sabo, Peter J, Sandstrom, Richard, Stehling, A Sandra, Thurman, Robert E, Weissman, Sherman M, Cayting, Philip, Hariharan, Manoj, Lian, Jin, Cheng, Yong, Landt, Stephen G, Ma, Zhihai, Wold, Barbara J, Dekker, Job, Crawford, Gregory E, Keller, Cheryl A, Wu, Weisheng, Morrissey, Christopher, Kumar, Swathi A, Mishra, Tejaswini, Jain, Deepti, Byrska-Bishop, Marta, Blankenberg, Daniel, Lajoie, Bryan R, Jain, Gaurav, Sanyal, Amartya, Chen, Kaun-Bei, Denas, Olgert, Taylor, James, Blobel, Gerd A, Weiss, Mitchell J, Pimkin, Max, Deng, Wulan, Marinov, Georgi K, Williams, Brian A, Fisher-Aylor, Katherine I, Desalvo, Gilberto, Kiralusha, Anthony, Trout, Diane, Amrhein, Henry, Mortazavi, Ali, Edsall, Lee, McCleary, David, Kuan, Samantha, Shen, Yin, Yue, Feng, Ye, Zhen, Davis, Carrie A, Zaleski, Chris, Jha, Sonali, Xue, Chenghai, Dobin, Alex, Lin, Wei, Fastuca, Meagan, Wang, Huaien, Guigo, Roderic, Djebali, Sarah, Lagarde, Julien, Ryba, Tyrone, Sasaki, Takayo, Malladi, Venkat S, Cline, Melissa S, Kirkup, Vanessa M, Learned, Katrina, Rosenbloom, Kate R, Kent, W James, Feingold, Elise A, Good, Peter J, Pazin, Michael, Lowdon, Rebecca F, and Adams, Leslie B

Published
2012
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48. ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions

Author

Dolzhenko, Egor, primary, Deshpande, Viraj, additional, Schlesinger, Felix, additional, Krusche, Peter, additional, Petrovski, Roman, additional, Chen, Sai, additional, Emig-Agius, Dorothea, additional, Gross, Andrew, additional, Narzisi, Giuseppe, additional, Bowman, Brett, additional, Scheffler, Konrad, additional, van Vugt, Joke J F A, additional, French, Courtney, additional, Sanchis-Juan, Alba, additional, Ibáñez, Kristina, additional, Tucci, Arianna, additional, Lajoie, Bryan R, additional, Veldink, Jan H, additional, Raymond, F Lucy, additional, Taft, Ryan J, additional, Bentley, David R, additional, and Eberle, Michael A, additional

Published
2019
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49. The genome-wide, multi-layered architecture of chromosome pairing in earlyDrosophilaembryos

Author

Erceg, Jelena, primary, Abed, Jumana AlHaj, additional, Goloborodko, Anton, additional, Lajoie, Bryan R., additional, Fudenberg, Geoffrey, additional, Abdennur, Nezar, additional, Imakaev, Maxim, additional, McCole, Ruth B., additional, Nguyen, Son C., additional, Saylor, Wren, additional, Joyce, Eric F., additional, Senaratne, T. Niroshini, additional, Hannan, Mohammed A., additional, Nir, Guy, additional, Dekker, Job, additional, Mirny, Leonid A., additional, and Wu, Chao-ting, additional

Published
2018
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