• Publications
  • Influence
Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters
TLDR
Global run-on sequencing, GRO-seq, shows that peaks of promoter-proximal polymerase reside on ∼30% of human genes, transcription extends beyond pre-messenger RNA 3′ cleavage, and antisense transcription is prevalent. Expand
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers
TLDR
Analysis of comprehensive mapping of transcription start sites in human lymphoblastoid B cell and chronic myelogenous leukemic ENCODE Tier 1 cell lines identifies a common architecture of initiation, including tightly spaced (110 bp apart) divergent initiation, similar frequencies of core promoter sequence elements, highly positioned flanking nucleosomes and two modes of transcription factor binding. Expand
Breaking barriers to transcription elongation
TLDR
Hundreds of protein factors participate in transcription and its regulation in eukaryotes by targeting upstream promoter regions, whereas a smaller but mechanistically diverse set of factors functions at most genes during RNA polymerase II (Pol II) elongation. Expand
Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans
TLDR
The evidence for pausing of Pol II from recent high-throughput studies will be discussed, as well as the potential interconnected functions of promoter-proximally paused Pol II. Expand
Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing
TLDR
A precision nuclear run-on and sequencing assay to map the genome-wide distribution of transcriptionally engaged Pol II at base pair resolution and shows how the promoter dictates transcriptional pausing and detects the preferential localization of active transcription complexes within the genome. Expand
Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons
TLDR
Notably, Pol II accelerates dramatically while transcribing through genes, but slows at exons, and intergenic variance in elongation rates is substantial, and is influenced by a positive effect of H3K79me2 and negative effects of exon density and CG content within genes. Expand
CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1.
TLDR
It is demonstrated that metazoan CDK12 and CDK13 are CTD kinases, and that dCDK12 is orthologous to yeast Ctk1, and the following orthology relationships are suggested. Expand
PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin.
TLDR
The hypothesis that methylation of H4 lysine 20 maintains silent chromatin, in part, by precluding neighboring acetylation on the H4 tail is supported. Expand
Getting up to speed with transcription elongation by RNA polymerase II
  • I. Jonkers, J. Lis
  • Biology, Medicine
  • Nature Reviews Molecular Cell Biology
  • 1 March 2015
TLDR
Elongation is recognized as a key phase in the regulation of transcription by Pol II, revealing that elongation is a highly complex process. Expand
Rapid, Transcription-Independent Loss of Nucleosomes over a Large Chromatin Domain at Hsp70 Loci
TLDR
An RNAi screen of 28 transcription and chromatin-related factors reveals that depletion of heat shock factor, GAGA Factor, or Poly(ADP)-Ribose Polymerase or its activity abolishes the loss of nucleosomes upon Hsp70 activation. Expand
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