scholarly journals Comparative Epigenomics Reveals that RNA Polymerase II Pausing and Chromatin Domain Organization Control Nematode piRNA Biogenesis

2019 ◽  
Vol 48 (6) ◽  
pp. 793-810.e6 ◽  
Author(s):  
Toni Beltran ◽  
Consuelo Barroso ◽  
Timothy Y. Birkle ◽  
Lewis Stevens ◽  
Hillel T. Schwartz ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Chromatin Domain ◽  
Domain Organization ◽  
Comparative Epigenomics

scholarly journals Cooperative activities of hematopoietic regulators recruit RNA polymerase II to a tissue-specific chromatin domain

2002 ◽  
Vol 99 (18) ◽  
pp. 11760-11765 ◽  
Author(s):  
K. D. Johnson ◽  
J. A. Grass ◽  
M. E. Boyer ◽  
C. M. Kiekhaefer ◽  
G. A. Blobel ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Chromatin Domain ◽  
Tissue Specific

scholarly journals Evolutionary analysis implicates RNA polymerase II pausing and chromatin structure in nematode piRNA biogenesis

2018 ◽  
Author(s):  
T. Beltran ◽  
C. Barroso ◽  
T.Y. Birkle ◽  
L. Stevens ◽  
H. T. Schwartz ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Core Promoter ◽  
Evolutionary Analysis ◽  
C Elegans ◽  
Comparative Epigenomics ◽  
Genome Wide ◽  
Almost All ◽  
Precursor Transcript ◽  
Insight Into

AbstractPiwi-interacting RNAs (piRNAs) control transposable elements widely across metazoans but have rapidly evolving biogenesis pathways. In Caenorhabditis elegans, almost all piRNA loci are found within two 3Mb clusters on Chromosome IV. Each piRNA locus possesses an upstream motif that recruits RNA polymerase II to produce a ∼28 nt precursor transcript. Here, we use comparative epigenomics across nematodes to gain insight into piRNA biogenesis. We show that the piRNA upstream motif is derived from core promoter elements controlling snRNA biogenesis. We describe two alternative modes of piRNA organisation in nematodes: in C. elegans and closely related nematodes, piRNAs are clustered within repressive H3K27me3 chromatin, whilst in other species, typified by Pristionchus pacificus, piRNAs are distributed genome-wide within introns of actively transcribed genes. In both groups, piRNA production depends on downstream sequence signals associated with RNA polymerase II pausing, which synergise with the chromatin environment to control piRNA precursor transcription.

scholarly journals Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II

2019 ◽  
Vol 218 (5) ◽  
pp. 1511-1530 ◽  
Author(s):  
Ryosuke Nagashima ◽  
Kayo Hibino ◽  
S.S. Ashwin ◽  
Michael Babokhov ◽  
Shin Fujishiro ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Computational Modeling ◽  
Rna Polymerase Ii ◽  
Gene Transcription ◽  
Liquid Droplet ◽  
Critical Role ◽  
Chromatin Domain ◽  
Related Factors ◽  
Chromatin Dynamics ◽  
Genome Wide

Although chromatin organization and dynamics play a critical role in gene transcription, how they interplay remains unclear. To approach this issue, we investigated genome-wide chromatin behavior under various transcriptional conditions in living human cells using single-nucleosome imaging. While transcription by RNA polymerase II (RNAPII) is generally thought to need more open and dynamic chromatin, surprisingly, we found that active RNAPII globally constrains chromatin movements. RNAPII inhibition or its rapid depletion released the chromatin constraints and increased chromatin dynamics. Perturbation experiments of P-TEFb clusters, which are associated with active RNAPII, had similar results. Furthermore, chromatin mobility also increased in resting G0 cells and UV-irradiated cells, which are transcriptionally less active. Our results demonstrated that chromatin is globally stabilized by loose connections through active RNAPII, which is compatible with models of classical transcription factories or liquid droplet formation of transcription-related factors. Together with our computational modeling, we propose the existence of loose chromatin domain networks for various intra-/interchromosomal contacts via active RNAPII clusters/droplets.

scholarly journals Highly Restricted Localization of RNA Polymerase II within a Locus Control Region of a Tissue-Specific Chromatin Domain

2003 ◽  
Vol 23 (18) ◽  
pp. 6484-6493 ◽  
Author(s):  
Kirby D. Johnson ◽  
Jeffrey A. Grass ◽  
Changwon Park ◽  
Hogune Im ◽  
Kyunghee Choi ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Histone Modification ◽  
Rna Polymerase Ii ◽  
Control Region ◽  
Locus Control Region ◽  
Regulatory Elements ◽  
Chromatin Domain ◽  
Pol Ii ◽  
Reading Frame ◽  
Hypersensitive Sites

ABSTRACT RNA polymerase II (Pol II) can associate with regulatory elements far from promoters. For the murine β-globin locus, Pol II binds the β-globin locus control region (LCR) far upstream of the β-globin promoters, independent of recruitment to and activation of the βmajor promoter. We describe here an analysis of where Pol II resides within the LCR, how it is recruited to the LCR, and the functional consequences of recruitment. High-resolution analysis of the distribution of Pol II revealed that Pol II binding within the LCR is restricted to the hypersensitive sites. Blocking elongation eliminated the synthesis of genic and extragenic transcripts and eliminated Pol II from the βmajor open reading frame. However, the elongation blockade did not redistribute Pol II at the hypersensitive sites, suggesting that Pol II is recruited to these sites. The distribution of Pol II did not strictly correlate with the distributions of histone acetylation and methylation. As Pol II associates with histone-modifying enzymes, Pol II tracking might be critical for establishing and maintaining broad histone modification patterns. However, blocking elongation did not disrupt the histone modification pattern of the β-globin locus, indicating that Pol II tracking is not required to maintain the pattern.

Nutrient-regulated gene expression in eukaryotes

2006 ◽  
Vol 73 ◽  
pp. 85-96 ◽  
Author(s):  
Richard J. Reece ◽  
Laila Beynon ◽  
Stacey Holden ◽  
Amanda D. Hughes ◽  
Karine Rébora ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Control ◽  
Direct Interaction ◽  
Signalling Pathways ◽  
A Cell ◽  
One Step ◽  
Higher Eukaryotes ◽  
Regulated Gene Expression

The recognition of changes in environmental conditions, and the ability to adapt to these changes, is essential for the viability of cells. There are numerous well characterized systems by which the presence or absence of an individual metabolite may be recognized by a cell. However, the recognition of a metabolite is just one step in a process that often results in changes in the expression of whole sets of genes required to respond to that metabolite. In higher eukaryotes, the signalling pathway between metabolite recognition and transcriptional control can be complex. Recent evidence from the relatively simple eukaryote yeast suggests that complex signalling pathways may be circumvented through the direct interaction between individual metabolites and regulators of RNA polymerase II-mediated transcription. Biochemical and structural analyses are beginning to unravel these elegant genetic control elements.

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