[HTML][HTML] Histone post-translational modifications—cause and consequence of genome function

G Millán-Zambrano, A Burton, AJ Bannister… - Nature Reviews …, 2022 - nature.com
Much has been learned since the early 1960s about histone post-translational modifications
(PTMs) and how they affect DNA-templated processes at the molecular level. This …

Origins of DNA replication in eukaryotes

Y Hu, B Stillman - Molecular cell, 2023 - cell.com
Errors occurring during DNA replication can result in inaccurate replication, incomplete
replication, or re-replication, resulting in genome instability that can lead to diseases such as …

[HTML][HTML] Methods for mapping 3D chromosome architecture

R Kempfer, A Pombo - Nature Reviews Genetics, 2020 - nature.com
Determining how chromosomes are positioned and folded within the nucleus is critical to
understanding the role of chromatin topology in gene regulation. Several methods are …

[HTML][HTML] The plasticity of DNA replication forks in response to clinically relevant genotoxic stress

M Berti, D Cortez, M Lopes - Nature reviews Molecular cell biology, 2020 - nature.com
Complete and accurate DNA replication requires the progression of replication forks through
DNA damage, actively transcribed regions, structured DNA and compact chromatin. Recent …

[HTML][HTML] YY1 is a structural regulator of enhancer-promoter loops

AS Weintraub, CH Li, AV Zamudio, AA Sigova… - Cell, 2017 - cell.com
There is considerable evidence that chromosome structure plays important roles in gene
control, but we have limited understanding of the proteins that contribute to structural …

[HTML][HTML] Chromatin-state discovery and genome annotation with ChromHMM

J Ernst, M Kellis - Nature protocols, 2017 - nature.com
Noncoding DNA regions have central roles in human biology, evolution, and disease.
ChromHMM helps to annotate the noncoding genome using epigenomic information across …

Lamina-associated domains: links with chromosome architecture, heterochromatin, and gene repression

B Van Steensel, AS Belmont - Cell, 2017 - cell.com
In metazoan cell nuclei, hundreds of large chromatin domains are in close contact with the
nuclear lamina. Such lamina-associated domains (LADs) are thought to help organize …

[HTML][HTML] Defining genome architecture at base-pair resolution

P Hua, M Badat, LLP Hanssen, LD Hentges, N Crump… - Nature, 2021 - nature.com
In higher eukaryotes, many genes are regulated by enhancers that are 104–106 base pairs
(bp) away from the promoter. Enhancers contain transcription-factor-binding sites (which are …

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 …

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 …