scholarly journals RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis

2020 ◽  
Author(s):  
Shu Zhang ◽  
Nadine Übelmesser ◽  
Natasa Josipovic ◽  
Giada Forte ◽  
Johan A. Slotman ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Three Dimensional ◽  
Super Resolution ◽  
Mitotic Cell ◽  
Cycle Phase ◽  
Loop Formation ◽  
A Cell ◽  
Resolution Imaging ◽  
Chromatin Fractionation

SUMMARYMammalian chromosomes are three-dimensional entities shaped by converging and opposing forces. Mitotic cell division induces drastic chromosome condensation, but following reentry into the G1 cell cycle phase, condensed chromosomes unwind to reestablish interphase organization. Here, we use a cell line allowing auxin-mediated degradation of RNA polymerase II to test its role in this transition. In situ Hi-C showed that RNAPII is required for compartment and loop formation following mitosis. RNAPs often counteract loop extrusion and, in their absence, longer and more prominent loops arise. Evidence from chromatin fractionation, super-resolution imaging and in silico modeling attribute these effects to RNAPII-mediated cohesin loading at active promoters upon reentry into G1. Our findings reconcile the role of RNAPII in gene expression with that in chromatin architecture.

scholarly journals Spatial Organization of RNA Polymerase II Revealed by Super-Resolution Imaging of Mammalian Cell Nucleus

2013 ◽  
Vol 104 (2) ◽  
pp. 339a
Author(s):  
Ziqing Zhao ◽  
Rahul Roy ◽  
J. Christof M. Gebhardt ◽  
David M. Suter ◽  
Alec R. Chapman ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Mammalian Cell ◽  
Cell Nucleus ◽  
Spatial Organization ◽  
Super Resolution ◽  
Resolution Imaging

scholarly journals Super-resolution imaging of fluorescently labeled, endogenous RNA Polymerase II in living cells with CRISPR/Cas9-mediated gene editing

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Won-Ki Cho ◽  
Namrata Jayanth ◽  
Susan Mullen ◽  
Tzer Han Tan ◽  
Yoon J. Jung ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Gene Editing ◽  
Super Resolution ◽  
Living Cells ◽  
Resolution Imaging

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.

scholarly journals Three-dimensional super-resolution imaging for fluorescence emission difference microscopy

AIP Advances ◽  
2015 ◽  
Vol 5 (8) ◽  
pp. 084901 ◽  
Author(s):  
Shangting You ◽  
Cuifang Kuang ◽  
Shuai Li ◽  
Xu Liu ◽  
Zhihua Ding
Keyword(s):  
Three Dimensional ◽  
Fluorescence Emission ◽  
Super Resolution ◽  
Resolution Imaging

Super-resolution imaging using a three-dimensional metamaterials nanolens

2010 ◽  
Vol 96 (2) ◽  
pp. 023114 ◽  
Author(s):  
B. D. F. Casse ◽  
W. T. Lu ◽  
Y. J. Huang ◽  
E. Gultepe ◽  
L. Menon ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Super Resolution ◽  
Resolution Imaging

Pausing and termination of human RNA polymerase II transcription at a procaryotic terminator

1983 ◽  
Vol 3 (10) ◽  
pp. 1687-1693
Author(s):  
G W Hatfield ◽  
J A Sharp ◽  
M Rosenberg
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Sequence Specificity ◽  
Late Promoter ◽  
Transcription System ◽  
A Cell ◽  
Major Late Promoter ◽  
Dyad Symmetry ◽  
Rna Polymerase Ii Transcription ◽  
Terminator Sequence

Kinetic analyses of runoff transcription in a cell-free eucaryotic transcription system revealed that the bacteriophage lambda 4S RNA terminator caused human RNA polymerase II to pause on the template and partially terminate transcription of transcripts initiated by the adenovirus 2 major late promoter. Analogous to the procaryotic RNA polymerase, the eucaryotic enzyme terminated just beyond the guanine-plus-cytosine-rich region of dyad symmetry in the terminator sequence. These results suggest that the eucaryotic RNA polymerase II may respond to transcription termination sequences similar to those used by the procaryotic enzyme. However, similar templates containing lambda tint or lambda tR1 terminators did not elicit pausing or termination, suggesting that other features, such as sequence specificity, may also be involved.

A heat-labile factor promotes premature 3' end formation in exon 1 of the murine adenosine deaminase gene in a cell-free transcription system

1991 ◽  
Vol 11 (11) ◽  
pp. 5398-5409
Author(s):  
J W Innis ◽  
R E Kellems
Keyword(s):  
Steady State ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Adenosine Deaminase ◽  
Free System ◽  
Cell Free System ◽  
Transcription System ◽  
Exon 1 ◽  
A Cell ◽  
Processed Products

An elongation block to RNA polymerase II transcription in exon 1 is a major regulatory step in expression of the murine adenosine deaminase (ADA) gene. Previous work in the laboratory identified abundant short transcripts with 3' termini in exon 1 in steady-state RNA from injected oocytes. Using a cell-free system to investigate the mechanism of premature 3' end formation, we found that polymerase II generates prominent ADA transcripts approximately 96 to 100 nucleotides in length which are similar to the major short transcripts found in steady-state RNA from oocytes injected with ADA templates. We have determined that these transcripts are the processed products of 108- to 112-nucleotide precursors. Precursor formation is (i) favored in reactions using circular templates, (ii) not the result of a posttranscriptional processing event, (iii) sensitive to low concentrations of Sarkosyl, and (iv) dependent on a factor(s) which is inactivated in crude extracts at 47 degrees C for 15 min. The cell-free system will allow further characterization of the template and factor requirements involved in the control of premature 3' end formation by RNA polymerase II.

scholarly journals Joint changes in RNA, RNA polymerase II, and promoter activity through the cell cycle identify non-coding RNAs involved in proliferation

2021 ◽  
Author(s):  
Siv Anita Hegre ◽  
Helle Samdal ◽  
Antonin Klima ◽  
Endre B. Stovner ◽  
Kristin G. Nørsett ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Promoter Activity ◽  
Cycle Phase ◽  
Specific Expression ◽  
Chip Sequencing ◽  
Non Coding Rnas ◽  
Cycle Dependent ◽  
Rna Levels

AbstractProper regulation of the cell cycle is necessary for normal growth and development of all organisms. Conversely, altered cell cycle regulation often underlies proliferative diseases such as cancer. Long non-coding RNAs (lncRNAs) are recognized as important regulators of gene expression and are often found dysregulated in diseases, including cancers. However, identifying lncRNAs with cell cycle functions is challenging due to their often low and cell-type specific expression. We present a highly effective method that analyses changes in promoter activity, transcription, and RNA levels for identifying genes enriched for cell cycle functions. Specifically, by combining RNA sequencing with ChIP sequencing through the cell cycle of synchronized human keratinocytes, we identified 1009 genes with cell cycle-dependent expression and correlated changes in RNA polymerase II occupancy or promoter activity as measured by histone 3 lysine 4 trimethylation (H3K4me3). These genes were highly enriched for genes with known cell cycle functions and included 59 lncRNAs. We selected four of these lncRNAs – AC005682.5, RP11-132A1.4, ZFAS1, and EPB41L4A-AS1 – for further experimental validation and found that knockdown of each of the four lncRNAs affected cell cycle phase distributions and reduced proliferation in multiple cell lines. These results show that many genes with cell cycle functions have concomitant cell-cycle dependent changes in promoter activity, transcription, and RNA levels and support that our multi-omics method is well suited for identifying lncRNAs involved in the cell cycle.

scholarly journals Super-Resolution Imaging by Dual Iterative Structured Illumination Microscopy

2021 ◽  
Author(s):  
Anna Loeschberger ◽  
Yauheni Novikau ◽  
Ralf Netz ◽  
Marie-Christin Spindler ◽  
Ricardo Benavente ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Brain Slices ◽  
Super Resolution ◽  
Reconstruction Algorithm ◽  
Living Cells ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Spatiotemporal Resolution ◽  
Coated Pits ◽  
Resolution Imaging

Three-dimensional (3D) multicolor super-resolution imaging in the 50-100 nm range in fixed and living cells remains challenging. We extend the resolution of structured illumination microscopy (SIM) by an improved nonlinear iterative reconstruction algorithm that enables 3D multicolor imaging with improved spatiotemporal resolution at low illumination intensities. We demonstrate the performance of dual iterative SIM (diSIM) imaging cellular structures in fixed cells including synaptonemal complexes, clathrin coated pits and the actin cytoskeleton with lateral resolutions of 60-100 nm with standard fluorophores. Furthermore, we visualize dendritic spines in 70 micrometer thick brain slices with an axial resolution < 200 nm. Finally, we image dynamics of the endoplasmatic reticulum and microtubules in living cells with up to 255 frames/s.

Sign in / Sign up

Export Citation Format

Share Document