Lifting the curtain on loop extrusion barriers: Single-molecule insights into cohesin stalling.

Mol Cell

Division of Gene Regulation, Netherlands Cancer Institute, the Netherlands. Electronic address:

Published: August 2023

In this issue, Zhang et al. show that CTCF blocks cohesin-mediated loop extrusion in an orientation-dependent manner. Using single-molecule imaging assays, the authors find that dCas9 and R-loops can also stall extrusion.

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molcel.2023.07.025DOI Listing

Publication Analysis

Top Keywords

loop extrusion
8
lifting curtain
4
curtain loop
4
extrusion barriers
4
barriers single-molecule
4
single-molecule insights
4
insights cohesin
4
cohesin stalling
4
stalling issue
4
issue zhang
4

Similar Publications

Two unrelated distal genes activated by a shared enhancer benefit from localizing inside the same small topological domain.

Genes Dev

January 2025

Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, Utrecht 3584 CT, the Netherlands;

Enhancers are tissue-specific regulatory DNA elements that can activate transcription of genes over distance. Their target genes most often are located in the same contact domain-chromosomal entities formed by cohesin DNA loop extrusion and typically flanked by CTCF-bound boundaries. Enhancers shared by multiple unrelated genes are underexplored but may be more common than anticipated.

View Article and Find Full Text PDF

Understanding chromatin organization requires integrating measurements of genome connectivity and physical structure. It is well established that cohesin is essential for TAD and loop connectivity features in Hi-C, but the corresponding change in physical structure has not been studied using electron microscopy. Pairing chromatin scanning transmission electron tomography with multiomic analysis and single-molecule localization microscopy, we study the role of cohesin in regulating the conformationally defined chromatin nanoscopic packing domains.

View Article and Find Full Text PDF

Convergent pairs of highly transcribed genes restrict chromatin looping in Dictyostelium discoideum.

Nucleic Acids Res

January 2025

Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia.

Dictyostelium discoideum is a unicellular slime mold, developing into a multicellular fruiting body upon starvation. Development is accompanied by large-scale shifts in gene expression program, but underlying features of chromatin spatial organization remain unknown. Here, we report that the Dictyostelium 3D genome is organized into positionally conserved, largely consecutive, non-hierarchical and weakly insulated loops at the onset of multicellular development.

View Article and Find Full Text PDF

SMC translocation is unaffected by an excess of nucleoid associated proteins in vivo.

Sci Rep

January 2025

Department of Biology, Indiana University, 1001 E 3rd Street, Bloomington, IN 47405, USA.

Genome organization is important for DNA replication, gene expression, and chromosome segregation. In bacteria, two large families of proteins, nucleoid-associated proteins (NAPs) and SMC complexes, play important roles in organizing the genome. NAPs are highly abundant DNA-binding proteins that can bend, wrap, bridge, and compact DNA, while SMC complexes load onto the chromosome, translocate on the DNA, and extrude DNA loops.

View Article and Find Full Text PDF

Genome folding by cohesion.

Curr Opin Genet Dev

January 2025

School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; New Cornerstone Science Laboratory, Westlake University, Hangzhou, Zhejiang, China. Electronic address:

Chromosomes in eukaryotic cells undergo compaction at multiple levels and are folded into hierarchical structures to fit into the nucleus with limited dimensions. Three-dimensional genome organization needs to be coordinated with chromosome-templated processes, including DNA replication and gene transcription. As an ATPase molecular machine, the cohesin complex is a major driver of genome folding, which regulates transcription by modulating promoter-enhancer contacts.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!