ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs

Autor: Haoxi Chai, Harianto Tjong, Peng Li, Wei Liao, Ping Wang, Chee Hong Wong, Chew Yee Ngan, Warren J. Leonard, Chia-Lin Wei, Yijun Ruan

Publikováno v: Nature Communications, Vol 14, Iss 1, Pp 1-17 (2023)

Methods connecting genes to their cis-regulatory elements usually requires millions of input cells. Here the authors combine proximity ligation in ChIA-PET and transposase accessibility in ATAC-seq, reporting ChIATAC, to map interactions between open

Externí odkaz: https://doaj.org/article/033e820988274ab0a1c82354bd20c47f

FOS Rescues Neuronal Differentiation of Sox2-Deleted Neural Stem Cells by Genome-Wide Regulation of Common SOX2 and AP1(FOS-JUN) Target Genes

Autor: Miriam Pagin, Mattias Pernebrink, Mattia Pitasi, Federica Malighetti, Chew-Yee Ngan, Sergio Ottolenghi, Giulio Pavesi, Claudio Cantù, Silvia K. Nicolis

Publikováno v: Cells, Vol 10, Iss 7, p 1757 (2021)

The transcription factor SOX2 is important for brain development and for neural stem cells (NSC) maintenance. Sox2-deleted (Sox2-del) NSC from neonatal mouse brain are lost after few passages in culture. Two highly expressed genes, Fos and Socs3, are

Externí odkaz: https://doaj.org/article/08e12bf705b34efaaa37f769ea1913bd

Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response

Autor: Rahul Maurya, Hoon Kim, Sunit Das, Amit D. Gujar, Philip C. De Witt Hamer, Elise T. Courtois, Chew Yee Ngan, Kevin J. Anderson, Floris P. Barthel, Niels Verburg, Kevin C. Johnson, Dacheng Zhao, Ketan R. Bulsara, Martine Seignon, Paul Robson, Frederick S. Varn, Eun Hee Yi, Nicholas Navin, Marcos R. Estecio, Diane Luo, Roel G.W. Verhaak, Michael Samuels, Ming Tang

Publikováno v: Johnson, K C, Anderson, K J, Courtois, E T, Gujar, A D, Barthel, F P, Varn, F S, Luo, D, Seignon, M, Yi, E, Kim, H, Estecio, M R H, Zhao, D, Tang, M, Navin, N E, Maurya, R, Ngan, C Y, Verburg, N, de Witt Hamer, P C, Bulsara, K, Samuels, M L, Das, S, Robson, P & Verhaak, R G W 2021, ' Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response ', Nature Genetics, vol. 53, no. 10, pp. 1456-1468 . https://doi.org/10.1038/s41588-021-00926-8
Nature Genetics, 53(10), 1456-1468. Nature Publishing Group

Glioma intratumoral heterogeneity enables adaptation to challenging microenvironments and contributes to therapeutic resistance. We integrated 914 single-cell DNA methylomes, 55,284 single-cell transcriptomes and bulk multi-omic profiles across 11 ad

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::aad1ae7e79d3ae7c7008a19eba37ea4d
https://research.vumc.nl/en/publications/3ef3cb20-34eb-4d85-9b84-b617090e15d1

Multiplex chromatin interactions with single-molecule precision

Autor: Jacqueline Jufen Zhu, Chew Yee Ngan, Byoungkoo Lee, Emaly Piecuch, Rahul Maurya, Minji Kim, Meizhen Zheng, Liang Gong, Ping Wang, Yijun Ruan, Simon Zhongyuan Tian, Zhihui Li, Xiaoan Ruan, Daniel Capurso, Chee Hong Wong, Chia-Lin Wei

Publikováno v: Nature. 566:558-562

The genomes of multicellular organisms are extensively folded into 3D chromosome territories within the nucleus1. Advanced 3D genome-mapping methods that combine proximity ligation and high-throughput sequencing (such as chromosome conformation captu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d86c4b2bfcc43adbdfe7f604bd2f8b94
https://doi.org/10.1038/s41586-019-0949-1

Longitudinal molecular trajectories of diffuse glioma in adults

Autor: Lucy F. Stead, Daniel J. Brat, Michael D. Jenkinson, Michael Schuster, Michael Weller, Hiromichi Suzuki, Raul Rabadan, Kristin Alfaro, Do-Hyun Nam, D. Ryan Ormond, Gaetano Finocchiaro, Anzhela D. Moskalik, Hoon Kim, Jason K. Sa, Mustafa Khasraw, Chew Yee Ngan, Andrew E. Sloan, Peter Gould, Mark R. Gilbert, Ganesh Rao, Michael N. C. Fletcher, Brian L. Shaw, Houtan Noushmehr, Ketan R. Bulsara, Naema Nayyar, Elizabeth B. Claus, Colin Watts, Samirkumar B. Amin, Pim J. French, Rameen Beroukhim, Azzam Ismail, Erwin G. Van Meir, Matthew R. Grimmer, Andrew R Brodbelt, Joseph F. Costello, W. K. Alfred Yung, Susan C Short, Meihong Li, Guido Reifenberger, Adelheid Woehrer, Aruna Chakrabarty, Hui K Gan, Keith L. Ligon, Roel G.W. Verhaak, Chul-Kee Park, Simone P. Niclou, Georgette Tanner, Frederick S. Varn, Arnab Chakravarti, Javad Noorbakhsh, Floris P. Barthel, Jason T. Huse, Christoph Bock, Annette M. Molinaro, Georg Widhalm, Alexander F. Bruns, Olajide Abiola, Tathiane M. Malta, Pieter Wesseling, Tali Mazor, Donát Alpár, Peter Lichter, Jill S. Barnholtz-Sloan, Priscilla K. Brastianos, Antonio Iavarone, Laila M. Poisson, Jennifer Connelly, Bernhard Radlwimmer, Gelareh Zadeh, David M. Ashley, Ho Keung Ng, Ghazaleh Tabatabai, Peter A. E. Sillevis Smitt, Mathilde C.M. Kouwenhoven, Elizabeth J. Cochran, Jeffrey H. Chuang, Pratiti Bandopadhayay, Kevin C. Johnson, Marion Smits, Allison Lowman, John de Groot, Kevin J. Anderson, Johanna M. Niers, Bart A. Westerman, Peter S. LaViolette, Emre Kocakavuk, Kenneth Aldape, Kerrie L. McDonald

Publikováno v: Nature, vol 576, iss 7785
Nature, 576(7785), 112-120. Nature Publishing Group
Nature
Barthel, F P, Johnson, K C, Varn, F S, Moskalik, A D, Tanner, G, Kocakavuk, E, Anderson, K J, Abiola, O, Aldape, K, Alfaro, K D, Alpar, D, Amin, S B, Ashley, D M, Bandopadhayay, P, Barnholtz-Sloan, J S, Beroukhim, R, Bock, C, Brastianos, P K, Brat, D J, Brodbelt, A R, Bruns, A F, Bulsara, K R, Chakrabarty, A, Chakravarti, A, Chuang, J H, Claus, E B, Cochran, E J, Connelly, J, Costello, J F, Finocchiaro, G, Fletcher, M N, French, P J, Gan, H K, Gilbert, M R, Gould, P V, Grimmer, M R, Iavarone, A, Ismail, A, Jenkinson, M D, Khasraw, M, Kim, H, Kouwenhoven, M C M, LaViolette, P S, Li, M, Lichter, P, Ligon, K L, Lowman, A K, Malta, T M, Mazor, T, McDonald, K L, Molinaro, A M, Nam, D H, Nayyar, N, Ng, H K, Ngan, C Y, Niclou, S P, Niers, J M, Noushmehr, H, Noorbakhsh, J, Ormond, D R, Park, C K, Poisson, L M, Rabadan, R, Radlwimmer, B, Rao, G, Reifenberger, G, Sa, J K, Schuster, M, Shaw, B L, Short, S C, Smitt, P A S, Sloan, A E, Smits, M, Suzuki, H, Tabatabai, G, Van Meir, E G, Watts, C, Weller, M, Wesseling, P, Westerman, B A, Widhalm, G, Woehrer, A, Yung, W K A, Zadeh, G, Huse, J T, De Groot, J F, Stead, L F, Verhaak, R G W & The GLASS Consortium 2019, ' Longitudinal molecular trajectories of diffuse glioma in adults ', Nature, vol. 576, no. 7785, pp. 112-120 . https://doi.org/10.1038/s41586-019-1775-1, https://doi.org/10.1038/s41586-019-1775-1

The evolutionary processes that drive universal therapeutic resistance in adult patients with diffuse glioma remain unclear1,2. Here we analysed temporally separated DNA-sequencing data and matched clinical annotation from 222 adult patients with gli

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::42aa714cc58ed5e72980caca94e04350
https://pure.eur.nl/en/publications/b9198630-2a42-471b-be97-3c7b0986e7d4