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 …

ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data

Z Zou, T Ohta, F Miura, S Oki - Nucleic acids research, 2022 - academic.oup.com
Abstract ChIP-Atlas (https://chip-atlas. org) is a web service providing both GUI-and API-
based data-mining tools to reveal the architecture of the transcription regulatory landscape …

Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer

L Xiao, A Parolia, Y Qiao, P Bawa, S Eyunni, R Mannan… - Nature, 2022 - nature.com
The switch/sucrose non-fermentable (SWI/SNF) complex has a crucial role in chromatin
remodelling and is altered in over 20% of cancers,. Here we developed a proteolysis …

BAP1 links metabolic regulation of ferroptosis to tumour suppression

Y Zhang, J Shi, X Liu, L Feng, Z Gong, P Koppula… - Nature cell …, 2018 - nature.com
The roles and regulatory mechanisms of ferroptosis (a non-apoptotic form of cell death) in
cancer remain unclear. The tumour suppressor BRCA1-associated protein 1 (BAP1) …

Targeted in situ genome-wide profiling with high efficiency for low cell numbers

PJ Skene, JG Henikoff, S Henikoff - Nature protocols, 2018 - nature.com
Cleavage under targets and release using nuclease (CUT&RUN) is an epigenomic profiling
strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases …

Transcriptional architecture of the mammalian circadian clock

JS Takahashi - Nature Reviews Genetics, 2017 - nature.com
Circadian clocks are endogenous oscillators that control 24-hour physiological and
behavioural processes in organisms. These cell-autonomous clocks are composed of a …

Plant transcription factors—being in the right place with the right company

L Strader, D Weijers, D Wagner - Current opinion in plant biology, 2022 - Elsevier
Transcriptional regulation underlies many of the growth and developmental processes that
shape plants as well as their adaptation to their environment. Key to transcriptional control …

Intrinsically disordered regions direct transcription factor in vivo binding specificity

S Brodsky, T Jana, K Mittelman, M Chapal, DK Kumar… - Molecular cell, 2020 - cell.com
Transcription factors (TFs) that bind common DNA motifs in vitro occupy distinct sets of
promoters in vivo, raising the question of how binding specificity is achieved. TFs are …

Recent advances in understanding the pathogenesis of rheumatoid arthritis: new treatment strategies

AL Mueller, Z Payandeh, N Mohammadkhani… - Cells, 2021 - mdpi.com
Rheumatoid arthritis (RA) is considered a chronic systemic, multi-factorial, inflammatory, and
progressive autoimmune disease affecting many people worldwide. While patients show …