[HTML][HTML] RNA polymerases reshape chromatin and coordinate transcription on individual fibers

TW Tullius, RS Isaac, J Ranchalis, D Dubocanin… - bioRxiv, 2023 - ncbi.nlm.nih.gov
During eukaryotic transcription, RNA polymerases must initiate and pause within a crowded,
complex environment, surrounded by nucleosomes and other transcriptional activity. This …

[HTML][HTML] Regulation of Pol II Pausing during Daily Gene Transcription in Mouse Liver

W Xu, X Li - Biology, 2023 - mdpi.com
Simple Summary Clock proteins and their collaborating transcription factors often act as
distal enhancers to regulate the rhythmic transcription of gene promoters. Those …

TFII-I-mediated polymerase pausing antagonizes GLI2 induction by TGFβ

AL McCleary-Wheeler, BD Paradise… - Nucleic acids …, 2020 - academic.oup.com
The modulation of GLI2, an oncogenic transcription factor commonly upregulated in cancer,
is in many cases not due to genetic defects, suggesting dysregulation through alternative …

Predictive model of transcriptional elongation control identifies trans regulatory factors from chromatin signatures

TS Akcan, S Vilov, M Heinig - Nucleic Acids Research, 2023 - academic.oup.com
Abstract Promoter-proximal Polymerase II (Pol II) pausing is a key rate-limiting step for gene
expression. DNA and RNA-binding trans-acting factors regulating the extent of pausing have …

[HTML][HTML] A role for the Cockayne Syndrome B (CSB)-Elongin ubiquitin ligase complex in signal-dependent RNA polymerase II transcription

JC Weems, BD Slaughter, JR Unruh, KJ Weaver… - Journal of Biological …, 2021 - ASBMB
The Elongin complex was originally identified as an RNA polymerase II (RNAPII) elongation
factor and subsequently as the substrate recognition component of a Cullin-RING E3 …

[HTML][HTML] DNA-sequence and epigenomic determinants of local rates of transcription elongation

L Liu, Y Zhao, A Siepel - bioRxiv, 2023 - ncbi.nlm.nih.gov
Across all branches of life, transcription elongation is a crucial, regulated phase in gene
expression. Many recent studies in eukaryotes have focused on the regulation of promoter …

[HTML][HTML] KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription

U Hyder, A Challa, M Thornton, T Nandu, WL Kraus… - bioRxiv, 2024 - ncbi.nlm.nih.gov
Signal-induced transcriptional programs regulate critical biological processes through the
precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the …

FACT maintains pluripotency factor expression through gene-distal regulation in embryonic stem cells

DC Klein, SM Lardo, KN McCannell, SJ Hainer - BioRxiv, 2021 - biorxiv.org
The mammalian FACT complex is a highly conserved histone chaperone with essential
roles in transcription elongation, histone deposition, and maintenance of stem cell state …

Interdependence between histone marks and steps in Pol II transcription

Z Wang, AG Chivu, LA Choate, EJ Rice, DC Miller… - bioRxiv, 2020 - biorxiv.org
The role of histone modifications in transcription remains incompletely understood. Here we
used experimental perturbations combined with sensitive machine learning tools that infer …

Dissecting the cis-regulatory syntax of transcription initiation with deep learning

K Cochran, M Yin, A Mantripragada, J Schreiber… - bioRxiv, 2024 - biorxiv.org
Despite extensive characterization of mammalian Pol II transcription, the DNA sequence
determinants of transcription initiation at a third of human promoters and most enhancers …