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31 results on '"Reinberg, Danny"'

2. RNA Interactions Are Essential for CTCF-Mediated Genome Organization

Author

Saldaña-Meyer, Ricardo, Rodriguez-Hernaez, Javier, Escobar, Thelma, Nishana, Mayilaadumveettil, Jácome-López, Karina, Nora, Elphege P, Bruneau, Benoit G, Tsirigos, Aristotelis, Furlan-Magaril, Mayra, Skok, Jane, and Reinberg, Danny

Subjects
Genetics, Human Genome, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Animals, Binding Sites, CCCTC-Binding Factor, Cell Line, Chromatin, Mice, Mouse Embryonic Stem Cells, Mutation, Nucleic Acid Conformation, Protein Binding, Protein Interaction Domains and Motifs, RNA, Structure-Activity Relationship, Transcription, Genetic, Zinc Fingers, CTCF, RNA binding, RNA deficient-mutants, TADs, chromatin domains, chromatin loops, chromatin organization, gene expression, transcriptional inhibition, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

The function of the CCCTC-binding factor (CTCF) in the organization of the genome has become an important area of investigation, but the mechanisms by which CTCF dynamically contributes to genome organization are not clear. We previously discovered that CTCF binds to large numbers of endogenous RNAs, promoting its self-association. In this regard, we now report two independent features that disrupt CTCF association with chromatin: inhibition of transcription and disruption of CTCF-RNA interactions through mutations of 2 of its 11 zinc fingers that are not required for CTCF binding to its cognate DNA site: zinc finger 1 (ZF1) or zinc finger 10 (ZF10). These mutations alter gene expression profiles as CTCF mutants lose their ability to form chromatin loops and thus the ability to insulate chromatin domains and to mediate CTCF long-range genomic interactions. Our results point to the importance of CTCF-mediated RNA interactions as a structural component of genome organization.

Published
2019

3. Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF

Author

Hansen, Anders S, Hsieh, Tsung-Han S, Cattoglio, Claudia, Pustova, Iryna, Saldaña-Meyer, Ricardo, Reinberg, Danny, Darzacq, Xavier, and Tjian, Robert

Subjects
Genetics, 1.1 Normal biological development and functioning, Underpinning research, Animals, CCCTC-Binding Factor, Cell Line, Chromatin, Gene Expression Regulation, Developmental, Male, Mice, Mice, Transgenic, Mouse Embryonic Stem Cells, Mutation, Nucleic Acid Conformation, Protein Binding, Protein Interaction Domains and Motifs, Structure-Activity Relationship, CTCF, Micro-C, RNA, TAD, cohesin, genome organization, loop, loop extrusion, super-resolution imaging, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Mammalian genomes are folded into topologically associating domains (TADs), consisting of chromatin loops anchored by CTCF and cohesin. Some loops are cell-type specific. Here we asked whether CTCF loops are established by a universal or locus-specific mechanism. Investigating the molecular determinants of CTCF clustering, we found that CTCF self-association in vitro is RNase sensitive and that an internal RNA-binding region (RBRi) mediates CTCF clustering and RNA interaction in vivo. Strikingly, deleting the RBRi impairs about half of all chromatin loops in mESCs and causes deregulation of gene expression. Disrupted loop formation correlates with diminished clustering and chromatin binding of RBRi mutant CTCF, which in turn results in a failure to halt cohesin-mediated extrusion. Thus, CTCF loops fall into at least two classes: RBRi-independent and RBRi-dependent loops. We speculate that evidence for RBRi-dependent loops may provide a molecular mechanism for establishing cell-specific CTCF loops, potentially regulated by RNA(s) or other RBRi-interacting partners.

Published
2019

4. NRF1 association with AUTS2-Polycomb mediates specific gene activation in the brain

Author

Liu, Sanxiong, Aldinger, Kimberly A., Cheng, Chi Vicky, Kiyama, Takae, Dave, Mitali, McNamara, Hanna K., Zhao, Wukui, Stafford, James M., Descostes, Nicolas, Lee, Pedro, Caraffi, Stefano G., Ivanovski, Ivan, Errichiello, Edoardo, Zweier, Christiane, Zuffardi, Orsetta, Schneider, Michael, Papavasiliou, Antigone S., Perry, M. Scott, Humberson, Jennifer, Cho, Megan T., Weber, Astrid, Swale, Andrew, Badea, Tudor C., Mao, Chai-An, Garavelli, Livia, Dobyns, William B., and Reinberg, Danny

Published
2021
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29. A Unified Nomenclature for Protein Subunits of Mediator Complexes Linking Transcriptional Regulators to RNA Polymerase II

Author

Bourbon, Henri-Marc, primary, Aguilera, Andres, additional, Ansari, Aseem Z., additional, Asturias, Francisco J., additional, Berk, Arnold J., additional, Bjorklund, Stefan, additional, Blackwell, T.Keith, additional, Borggrefe, Tilman, additional, Carey, Michael, additional, Carlson, Marian, additional, Conaway, Joan W., additional, Conaway, Ronald C., additional, Emmons, Scott W., additional, Fondell, Joseph D., additional, Freedman, Leonard P., additional, Fukasawa, Toshio, additional, Gustafsson, Claes M., additional, Han, Min, additional, He, Xi, additional, Herman, Paul K., additional, Hinnebusch, Alan G., additional, Holmberg, Steen, additional, Holstege, Frank C., additional, Jaehning, Judith A., additional, Kim, Young-Joon, additional, Kuras, Laurent, additional, Leutz, Achim, additional, Lis, John T., additional, Meisterernest, Michael, additional, Naar, Anders M., additional, Nasmyth, Kim, additional, Parvin, Jeffrey D., additional, Ptashne, Mark, additional, Reinberg, Danny, additional, Ronne, Hans, additional, Sadowski, Ivan, additional, Sakurai, Hiroshi, additional, Sipiczki, Matthias, additional, Sternberg, Paul W., additional, Stillman, David J., additional, Strich, Randy, additional, Struhl, Kevin, additional, Svejstrup, Jasper Q., additional, Tuck, Simon, additional, Winston, Fred, additional, Roeder, Robert G., additional, and Kornberg, Roger D., additional

Published
2004
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