Principles of genome folding into topologically associating domains

Q Szabo, F Bantignies, G Cavalli - Science advances, 2019 - science.org
Understanding the mechanisms that underlie chromosome folding within cell nuclei is
essential to determine the relationship between genome structure and function. The recent …

Chromosome organization in bacteria: mechanistic insights into genome structure and function

RT Dame, FZM Rashid, DC Grainger - Nature Reviews Genetics, 2020 - nature.com
Bacterial chromosomes are folded to compact DNA and facilitate cellular processes.
Studying model bacteria has revealed aspects of chromosome folding that are applicable to …

Early metazoan cell type diversity and the evolution of multicellular gene regulation

A Sebé-Pedrós, E Chomsky, K Pang… - Nature ecology & …, 2018 - nature.com
A hallmark of metazoan evolution is the emergence of genomic mechanisms that implement
cell-type-specific functions. However, the evolution of metazoan cell types and their …

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 …

Decoding gene regulation in the fly brain

J Janssens, S Aibar, II Taskiran, JN Ismail, AE Gomez… - Nature, 2022 - nature.com
The Drosophila brain is a frequently used model in neuroscience. Single-cell transcriptome
analysis,,,,–, three-dimensional morphological classification and electron microscopy …

[HTML][HTML] The 3D architecture of the pepper genome and its relationship to function and evolution

Y Liao, J Wang, Z Zhu, Y Liu, J Chen, Y Zhou… - Nature …, 2022 - nature.com
The organization of chromatin into self-interacting domains is universal among eukaryotic
genomes, though how and why they form varies considerably. Here we report a …

[HTML][HTML] CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions

A Kaushal, G Mohana, J Dorier, I Özdemir… - Nature …, 2021 - nature.com
Vertebrate genomes are partitioned into contact domains defined by enhanced internal
contact frequency and formed by two principal mechanisms: compartmentalization of …

DeepYY1: a deep learning approach to identify YY1-mediated chromatin loops

FY Dao, H Lv, D Zhang, ZM Zhang… - Briefings in …, 2021 - academic.oup.com
Abstract The protein Yin Yang 1 (YY1) could form dimers that facilitate the interaction
between active enhancers and promoter-proximal elements. YY1-mediated enhancer …

CTCF: a Swiss-army knife for genome organization and transcription regulation

L Braccioli, E de Wit - Essays in biochemistry, 2019 - portlandpress.com
Orchestrating vertebrate genomes require a complex interplay between the linear
composition of the genome and its 3D organization inside the nucleus. This requires the …

[HTML][HTML] Unraveling the 3D genome architecture in plants: present and future

W Ouyang, D Xiong, G Li, X Li - Molecular Plant, 2020 - cell.com
The eukaryotic genome has a hierarchical three-dimensional (3D) organization with
functional implications for DNA replication, DNA repair, and transcriptional regulation. Over …