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 …

[HTML][HTML] Human SMARCA5 is continuously required to maintain nucleosome spacing

ML Bomber, J Wang, Q Liu, KR Barnett, HM Layden… - Molecular cell, 2023 - cell.com
Genetic models suggested that SMARCA5 was required for DNA-templated events including
transcription, DNA replication, and DNA repair. We engineered a degron tag into the …

Regulatory landscape of enhancer-mediated transcriptional activation

K Kawasaki, T Fukaya - Trends in Cell Biology, 2024 - cell.com
Enhancers are noncoding regulatory elements that instruct spatial and temporal specificity of
gene transcription in response to a variety of intrinsic and extrinsic signals during …

[HTML][HTML] A genome-wide screen identifies silencers with distinct chromatin properties and mechanisms of repression

L Hofbauer, LM Pleyer, F Reiter, A Schleiffer, A Vlasova… - Molecular Cell, 2024 - cell.com
Differential gene transcription enables development and homeostasis in all animals and is
regulated by two major classes of distal cis-regulatory DNA elements (CREs): enhancers …

Widespread regulatory specificities between transcriptional co-repressors and enhancers in Drosophila

J Jacobs, M Pagani, C Wenzl, A Stark - Science, 2023 - science.org
Gene expression is controlled by the precise activation and repression of transcription.
Repression is mediated by specialized transcription factors (TFs) that recruit co-repressors …

Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila

V Loubiere, BP de Almeida, M Pagani… - Nature Communications, 2024 - nature.com
Genomic enhancers are key transcriptional regulators which, upon the binding of sequence-
specific transcription factors, activate their cognate target promoters. Although enhancers …

Genomic context-dependent histone H3K36 methylation by three Drosophila methyltransferases and implications for dedicated chromatin readers

M Jayakrishnan, M Havlová, V Veverka… - Nucleic Acids …, 2024 - academic.oup.com
Methylation of histone H3 at lysine 36 (H3K36me3) marks active chromatin. The mark is
interpreted by epigenetic readers that assist transcription and safeguard the integrity of the …

[HTML][HTML] SWI/SNF-dependent genes are defined by their chromatin landscape

L Basurto-Cayuela, JA Guerrero-Martínez… - Cell Reports, 2024 - cell.com
SWI/SNF complexes are evolutionarily conserved, ATP-dependent chromatin remodeling
machines. Here, we characterize the features of SWI/SNF-dependent genes using BRM014 …

Chromatin enables precise and scalable gene regulation with factors of limited specificity

ML Perkins, J Crocker, G Tkačik - Proceedings of the National Academy of …, 2025 - pnas.org
Biophysical constraints limit the specificity with which transcription factors (TFs) can target
regulatory DNA. While individual nontarget binding events may be low affinity, the sheer …

A transcriptional cofactor regulatory network for the C. elegans intestine

BB Horowitz, S Nanda… - G3: Genes, Genomes …, 2023 - academic.oup.com
Chromatin modifiers and transcriptional cofactors (collectively referred to as CFs) work with
DNA-binding transcription factors (TFs) to regulate gene expression. In multicellular …