Chromatin accessibility and the regulatory epigenome

SL Klemm, Z Shipony, WJ Greenleaf - Nature Reviews Genetics, 2019 - nature.com
Physical access to DNA is a highly dynamic property of chromatin that plays an essential
role in establishing and maintaining cellular identity. The organization of accessible …

Epigenetic modulators, modifiers and mediators in cancer aetiology and progression

AP Feinberg, MA Koldobskiy, A Göndör - Nature Reviews Genetics, 2016 - nature.com
This year is the tenth anniversary of the publication in this journal of a model suggesting the
existence of'tumour progenitor genes'. These genes are epigenetically disrupted at the …

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

AN Boettiger, B Bintu, JR Moffitt, S Wang, BJ Beliveau… - Nature, 2016 - nature.com
Metazoan genomes are spatially organized at multiple scales, from packaging of DNA
around individual nucleosomes to segregation of whole chromosomes into distinct …

[HTML][HTML] 3D chromosome regulatory landscape of human pluripotent cells

X Ji, DB Dadon, BE Powell, ZP Fan, D Borges-Rivera… - Cell stem cell, 2016 - cell.com
In this study, we describe the 3D chromosome regulatory landscape of human naive and
primed embryonic stem cells. To devise this map, we identified transcriptional enhancers …

Loop stacking organizes genome folding from TADs to chromosomes

A Hafner, M Park, SE Berger, SE Murphy, EP Nora… - Molecular cell, 2023 - cell.com
Although population-level analyses revealed significant roles for CTCF and cohesin in
mammalian genome organization, their contributions at the single-cell level remain …

KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks

DC Di Giammartino, A Kloetgen, A Polyzos, Y Liu… - Nature cell …, 2019 - nature.com
Cell fate transitions are accompanied by global transcriptional, epigenetic and topological
changes driven by transcription factors, as is exemplified by reprogramming somatic cells to …

Boundary stacking interactions enable cross-TAD enhancer–promoter communication during limb development

TC Hung, DM Kingsley, AN Boettiger - Nature Genetics, 2024 - nature.com
Although promoters and their enhancers are frequently contained within a topologically
associating domain (TAD), some developmentally important genes have their promoter and …

[HTML][HTML] Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III

Y Jiang, J Huang, K Lun, B Li, H Zheng, Y Li, R Zhou… - Genome biology, 2020 - Springer
Background The relationship between transcription and the 3D chromatin structure is
debated. Multiple studies have shown that transcription affects global Cohesin binding and …

[图书][B] Impressionable biologies: From the archaeology of plasticity to the sociology of epigenetics

M Meloni - 2019 - taylorfrancis.com
During the twentieth century, genes were considered the controlling force of life processes,
and the transfer of DNA the definitive explanation for biological heredity. Such views shaped …

[HTML][HTML] HiCPlotter integrates genomic data with interaction matrices

KC Akdemir, L Chin - Genome biology, 2015 - Springer
Metazoan genomic material is folded into stable non-randomly arranged chromosomal
structures that are tightly associated with transcriptional regulation and DNA replication …