Deciphering the multi-scale, quantitative cis-regulatory code

S Kim, J Wysocka - Molecular cell, 2023 - cell.com
Uncovering the cis-regulatory code that governs when and how much each gene is
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …

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 …

tRNA dysregulation and disease

EA Orellana, E Siegal, RI Gregory - Nature Reviews Genetics, 2022 - nature.com
Abstract tRNAs are key adaptor molecules that decipher the genetic code during translation
of mRNAs in protein synthesis. In contrast to the traditional view of tRNAs as ubiquitously …

[HTML][HTML] Organization of chromatin by intrinsic and regulated phase separation

BA Gibson, LK Doolittle, MWG Schneider, LE Jensen… - Cell, 2019 - cell.com
Eukaryotic chromatin is highly condensed but dynamically accessible to regulation and
organized into subdomains. We demonstrate that reconstituted chromatin undergoes …

Alternative polyadenylation of mRNA precursors

B Tian, JL Manley - Nature reviews Molecular cell biology, 2017 - nature.com
Alternative polyadenylation (APA) is an RNA-processing mechanism that generates distinct
3′ termini on mRNAs and other RNA polymerase II transcripts. It is widespread across all …

Understanding nucleosome dynamics and their links to gene expression and DNA replication

WKM Lai, BF Pugh - Nature reviews Molecular cell biology, 2017 - nature.com
Advances in genomics technology have provided the means to probe myriad chromatin
interactions at unprecedented spatial and temporal resolution. This has led to a profound …

Chromatin replication and epigenetic cell memory

KR Stewart-Morgan, N Petryk, A Groth - Nature cell biology, 2020 - nature.com
Propagation of the chromatin landscape across cell divisions is central to epigenetic cell
memory. Mechanistic analysis of the interplay between DNA replication, the cell cycle, and …

Energy-driven genome regulation by ATP-dependent chromatin remodellers

S Eustermann, AB Patel, KP Hopfner, Y He… - … Reviews Molecular Cell …, 2024 - nature.com
The packaging of DNA into chromatin in eukaryotes regulates gene transcription, DNA
replication and DNA repair. ATP-dependent chromatin remodelling enzymes (re) arrange …

Chromatin accessibility profiling methods

L Minnoye, GK Marinov, T Krausgruber, L Pan… - Nature Reviews …, 2021 - nature.com
Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied
characteristic of the eukaryotic genome. As active regulatory DNA elements are generally …

The interaction landscape between transcription factors and the nucleosome

F Zhu, L Farnung, E Kaasinen, B Sahu, Y Yin, B Wei… - Nature, 2018 - nature.com
Nucleosomes cover most of the genome and are thought to be displaced by transcription
factors in regions that direct gene expression. However, the modes of interaction between …