The Self-Organizing Genome: Principles of Genome Architecture and Function

Cell, Год журнала: 2020, Номер 183(1), С. 28 - 45

Опубликована: Сен. 24, 2020

Язык: Английский

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Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging

Science, Год журнала: 2022, Номер 376(6592), С. 496 - 501

Опубликована: Апрель 14, 2022

Animal genomes are folded into loops and topologically associating domains (TADs) by CTCF loop-extruding cohesins, but the live dynamics of loop formation stability remain unknown. Here, we directly visualized chromatin looping at

Язык: Английский

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On the existence and functionality of topologically associating domains

Nature Genetics, Год журнала: 2020, Номер 52(1), С. 8 - 16

Опубликована: Янв. 1, 2020

Язык: Английский

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Understanding 3D genome organization by multidisciplinary methods

Nature Reviews Molecular Cell Biology, Год журнала: 2021, Номер 22(8), С. 511 - 528

Опубликована: Май 5, 2021

Язык: Английский

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Mechanisms of enhancer action: the known and the unknown

Genome biology, Год журнала: 2021, Номер 22(1)

Опубликована: Апрель 15, 2021

Abstract Differential gene expression mechanisms ensure cellular differentiation and plasticity to shape ontogenetic phylogenetic diversity of cell types. A key regulator differential programs are the enhancers, gene-distal cis -regulatory sequences that govern spatiotemporal quantitative dynamics target genes. Enhancers widely believed physically contact promoters effect transcriptional activation. However, our understanding full complement regulatory proteins definitive mechanics enhancer action is incomplete. Here, we review recent findings present some emerging concepts on also outline a set outstanding questions.

Язык: Английский

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The relationship between genome structure and function

Nature Reviews Genetics, Год журнала: 2020, Номер 22(3), С. 154 - 168

Опубликована: Ноя. 24, 2020

Язык: Английский

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Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1

Nature Genetics, Год журнала: 2022, Номер 54(12), С. 1919 - 1932

Опубликована: Дек. 1, 2022

It remains unclear why acute depletion of CTCF (CCCTC-binding factor) and cohesin only marginally affects expression most genes despite substantially perturbing three-dimensional (3D) genome folding at the level domains structural loops. To address this conundrum, we used high-resolution Micro-C nascent transcript profiling in mouse embryonic stem cells. We find that enhancer-promoter (E-P) interactions are largely insensitive to (3-h) CTCF, or WAPL. YY1 has been proposed as a regulator E-P loops, but also had minimal effects on transcription 3D folding. Strikingly, live-cell, single-molecule imaging revealed reduced factor (TF) binding chromatin. Thus, although cohesin, WAPL is not required for short-term maintenance gene expression, our results suggest may facilitate TFs search bind their targets more efficiently.

Язык: Английский

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Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

Nature Structural & Molecular Biology, Год журнала: 2021, Номер 28(2), С. 152 - 161

Опубликована: Янв. 4, 2021

Язык: Английский

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Predicting 3D genome folding from DNA sequence with Akita

Nature Methods, Год журнала: 2020, Номер 17(11), С. 1111 - 1117

Опубликована: Окт. 12, 2020

Язык: Английский

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Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function

Molecular Cell, Год журнала: 2020, Номер 77(4), С. 688 - 708

Опубликована: Янв. 27, 2020

Язык: Английский

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