From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization DOI
Shuming Liu, Advait Athreya,

Zhuohan Lao

et al.

Annual Review of Biophysics, Journal Year: 2024, Volume and Issue: 53(1), P. 221 - 245

Published: Feb. 12, 2024

Chromatin organization plays a critical role in cellular function by regulating access to genetic information. However, understanding chromatin folding is challenging due its complex, multiscale nature. Significant progress has been made studying vitro systems, uncovering the structure of individual nucleosomes and their arrays, elucidating physicochemical forces stabilizing these structures. Additionally, remarkable advancements have achieved characterizing vivo, particularly at whole-chromosome level, revealing important features such as loops, topologically associating domains, nuclear compartments. bridging gap between vivo studies remains challenging. The resemblance conformations relevance internucleosomal interactions for are subjects debate. This article reviews experimental computational conducted various length scales, highlighting significance intrinsic roles vivo.

Language: Английский

Long non-coding RNAs: definitions, functions, challenges and recommendations DOI Open Access
John S. Mattick, Paulo Amaral, Piero Carninci

et al.

Nature Reviews Molecular Cell Biology, Journal Year: 2023, Volume and Issue: 24(6), P. 430 - 447

Published: Jan. 3, 2023

Language: Английский

Citations

1157

RNA promotes the formation of spatial compartments in the nucleus DOI Creative Commons
Sofia A. Quinodoz, Joanna W. Jachowicz, Prashant Bhat

et al.

Cell, Journal Year: 2021, Volume and Issue: 184(23), P. 5775 - 5790.e30

Published: Nov. 1, 2021

Language: Английский

Citations

299

Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics DOI
Takayuki Nojima, Nicholas Proudfoot

Nature Reviews Molecular Cell Biology, Journal Year: 2022, Volume and Issue: 23(6), P. 389 - 406

Published: Jan. 25, 2022

Language: Английский

Citations

295

The Mediator complex as a master regulator of transcription by RNA polymerase II DOI Open Access
William F. Richter, Shraddha Nayak, Janet Iwasa

et al.

Nature Reviews Molecular Cell Biology, Journal Year: 2022, Volume and Issue: 23(11), P. 732 - 749

Published: June 20, 2022

Language: Английский

Citations

198

The molecular basis of heterochromatin assembly and epigenetic inheritance DOI Creative Commons
Shiv I. S. Grewal

Molecular Cell, Journal Year: 2023, Volume and Issue: 83(11), P. 1767 - 1785

Published: May 18, 2023

Language: Английский

Citations

103

Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing DOI
Aditya Deshpande,

Netha Ulahannan,

Matthew Pendleton

et al.

Nature Biotechnology, Journal Year: 2022, Volume and Issue: 40(10), P. 1488 - 1499

Published: May 30, 2022

Language: Английский

Citations

95

Complementary Alu sequences mediate enhancer–promoter selectivity DOI
Liang Liang, Changchang Cao, Lei Ji

et al.

Nature, Journal Year: 2023, Volume and Issue: 619(7971), P. 868 - 875

Published: July 12, 2023

Language: Английский

Citations

86

Xist spatially amplifies SHARP/SPEN recruitment to balance chromosome-wide silencing and specificity to the X chromosome DOI
Joanna W. Jachowicz, Mackenzie Strehle, Abhik K. Banerjee

et al.

Nature Structural & Molecular Biology, Journal Year: 2022, Volume and Issue: 29(3), P. 239 - 249

Published: March 1, 2022

Language: Английский

Citations

75

Genome organization around nuclear speckles drives mRNA splicing efficiency DOI
Prashant Bhat,

Amy Chow,

Benjamin Emert

et al.

Nature, Journal Year: 2024, Volume and Issue: 629(8014), P. 1165 - 1173

Published: May 8, 2024

Language: Английский

Citations

58

Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain DOI Creative Commons
Hanqing Liu, Qiurui Zeng, Jingtian Zhou

et al.

Nature, Journal Year: 2023, Volume and Issue: 624(7991), P. 366 - 377

Published: Dec. 13, 2023

Cytosine DNA methylation is essential in brain development and implicated various neurological disorders. Understanding diversity across the entire a spatial context fundamental for complete molecular atlas of cell types their gene regulatory landscapes. Here we used single-nucleus methylome sequencing (snmC-seq3) multi-omic (snm3C-seq)

Language: Английский

Citations

55