Transcription factories: genome organization and gene regulation

A Papantonis, PR Cook - Chemical reviews, 2013 - ACS Publications
All eukaryotic cells contain four RNA polymerases originally defined by their sensitivity to
different drugs, and now by the sets of genes they transcribe. 1− 4 Polymerase I produces …

Functional consequences of bidirectional promoters

W Wei, V Pelechano, AI Järvelin, LM Steinmetz - Trends in Genetics, 2011 - cell.com
Several studies have shown that promoters of protein-coding genes are origins of pervasive
non-coding RNA transcription and can initiate transcription in both directions. However, only …

Precise estimates of mutation rate and spectrum in yeast

YO Zhu, ML Siegal, DW Hall… - Proceedings of the …, 2014 - National Acad Sciences
Mutation is the ultimate source of genetic variation. The most direct and unbiased method of
studying spontaneous mutations is via mutation accumulation (MA) lines. Until recently, MA …

S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation

L Wahba, L Costantino, FJ Tan, A Zimmer… - Genes & …, 2016 - genesdev.cshlp.org
R loops form when transcripts hybridize to homologous DNA on chromosomes, yielding a
DNA: RNA hybrid and a displaced DNA single strand. R loops impact the genome of many …

Determinants of histone H3K4 methylation patterns

LM Soares, PC He, Y Chun, H Suh, TS Kim… - Molecular cell, 2017 - cell.com
Various factors differentially recognize trimethylated histone H3 lysine 4 (H3K4me3) near
promoters, H3K4me2 just downstream, and promoter-distal H3K4me1 to modulate gene …

Spatiotemporal coordination of transcription preinitiation complex assembly in live cells

VQ Nguyen, A Ranjan, S Liu, X Tang, YH Ling… - Molecular cell, 2021 - cell.com
Transcription initiation by RNA polymerase II (RNA Pol II) requires preinitiation complex
(PIC) assembly at gene promoters. In the dynamic nucleus, where thousands of promoters …

H3K36 methylation promotes longevity by enhancing transcriptional fidelity

P Sen, W Dang, G Donahue, J Dai… - Genes & …, 2015 - genesdev.cshlp.org
Epigenetic mechanisms, including histone post-translational modifications, control longevity
in diverse organisms. Relatedly, loss of proper transcriptional regulation on a global scale is …

Global view on the metabolism of RNA poly(A) tails in yeast Saccharomyces cerevisiae

A Tudek, PS Krawczyk, S Mroczek, R Tomecki… - Nature …, 2021 - nature.com
The polyadenosine tail (poly [A]-tail) is a universal modification of eukaryotic messenger
RNAs (mRNAs) and non-coding RNAs (ncRNAs). In budding yeast, Pap1-synthesized …

Redefining the translational status of 80S monosomes

EE Heyer, MJ Moore - Cell, 2016 - cell.com
Fully assembled ribosomes exist in two populations: polysomes and monosomes. While the
former has been studied extensively, to what extent translation occurs on monosomes and …

Size-dependent increase in RNA polymerase II initiation rates mediates gene expression scaling with cell size

XM Sun, A Bowman, M Priestman, F Bertaux… - Current Biology, 2020 - cell.com
Cell size varies during the cell cycle and in response to external stimuli. This requires the
tight coordination, or" scaling," of mRNA and protein quantities with the cell volume in order …