3D enhancer-promoter interactions and multi-connected hubs: Organizational principles and functional roles

CM Uyehara, E Apostolou - Cell reports, 2023 - cell.com
The spatiotemporal control of gene expression is dependent on the activity of cis-acting
regulatory sequences, called enhancers, which regulate target genes over variable genomic …

Transcription regulation by long non-coding RNAs: mechanisms and disease relevance

J Ferrer, N Dimitrova - Nature Reviews Molecular Cell Biology, 2024 - nature.com
Long non-coding RNAs (lncRNAs) outnumber protein-coding transcripts, but their functions
remain largely unknown. In this Review, we discuss the emerging roles of lncRNAs in the …

Enhancer–promoter contact formation requires RNAPII and antagonizes loop extrusion

S Zhang, N Übelmesser, M Barbieri, A Papantonis - Nature genetics, 2023 - nature.com
Homotypic chromatin interactions and loop extrusion are thought to be the two main drivers
of mammalian chromosome folding. Here we tested the role of RNA polymerase II (RNAPII) …

Looping the genome with SMC complexes

E Kim, R Barth, C Dekker - Annual review of biochemistry, 2023 - annualreviews.org
SMC (structural maintenance of chromosomes) protein complexes are an evolutionarily
conserved family of motor proteins that hold sister chromatids together and fold genomes …

New insights into genome folding by loop extrusion from inducible degron technologies

E de Wit, EP Nora - Nature Reviews Genetics, 2023 - nature.com
Chromatin folds into dynamic loops that often span hundreds of kilobases and physically
wire distant loci together for gene regulation. These loops are continuously created …

YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle

JC Lam, NG Aboreden, SC Midla, S Wang, A Huang… - Nature Genetics, 2024 - nature.com
Few transcription factors have been examined for their direct roles in physically connecting
enhancers and promoters. Here acute degradation of Yin Yang 1 (YY1) in erythroid cells …

Transcription-induced domains form the elementary constraining building blocks of bacterial chromosomes

A Bignaud, C Cockram, C Borde, J Groseille… - Nature Structural & …, 2024 - nature.com
Transcription generates local topological and mechanical constraints on the DNA fiber,
leading to the generation of supercoiled chromosome domains in bacteria. However, the …

CTCF and R-loops are boundaries of cohesin-mediated DNA looping

H Zhang, Z Shi, EJ Banigan, Y Kim, H Yu, X Bai… - Molecular cell, 2023 - cell.com
Cohesin and CCCTC-binding factor (CTCF) are key regulatory proteins of three-dimensional
(3D) genome organization. Cohesin extrudes DNA loops that are anchored by CTCF in a …

[HTML][HTML] The role of loop extrusion in enhancer-mediated gene activation

MA Karpinska, AM Oudelaar - Current Opinion in Genetics & Development, 2023 - Elsevier
Gene expression patterns in complex multicellular organisms are regulated by enhancers,
which communicate with their target gene promoters in three-dimensional (3D) chromatin …

[HTML][HTML] Chromatin jets define the properties of cohesin-driven in vivo loop extrusion

Y Guo, E Al-Jibury, R Garcia-Millan, K Ntagiantas… - Molecular Cell, 2022 - cell.com
Complex genomes show intricate organization in three-dimensional (3D) nuclear space.
Current models posit that cohesin extrudes loops to form self-interacting domains delimited …