scholarly journals Decision letter: Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation

2013 ◽  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
X Chromosome ◽  
Dosage Compensation

scholarly journals Author response: Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation

2013 ◽  
Author(s):  
William S Kruesi ◽  
Leighton J Core ◽  
Colin T Waters ◽  
John T Lis ◽  
Barbara J Meyer
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Author Response

Chromosomal basis of dosage compensation in Drosophila. X. Assessment of hyperactivity of the male X in situ

1981 ◽  
Vol 47 (1) ◽  
pp. 295-309
Author(s):  
R.N. Chatterjee ◽  
A.S. Mukherjee
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Polytene Chromosomes ◽  
Template Activity ◽  
High Positive Correlation ◽  
Assay Conditions

The results of examination of the template activity of the fixed polytene chromosomes of Drosophila hydei, monitored by 3H-UTP, under in situ assay conditions, upon the use of endogenous Drosophila polymerase, exogenous Escherichia coli RNA polymerase (holoenzyme) and exogenous Drosophila RNA polymerase II (or B) have been presented. Analysis of the data reveals that the transcription patterns with the 3 enzymes are not strictly comparable with the pattern obtained under in vivo conditions. Yet, with each of the 3 conditions of assay, there is a reasonable concordance between the template activity on the single X chromosome of the male and the paired Xs of the female, as observed under in vivo. There is also, in every case, a high positive correlation between the 3H-UMP incorporation into the X chromosome and that into a specific autosome. A site-wise analysis of 3H-UMP labelling under the 3 assay conditions also reveals that for most of the regions, the sites which are highly active in vivo also show high labelling in situ, and the proportionally is maintained in both sexes. These result have been interpreted to have suggested that the hyperactivity of the male X vis-a-vis dosage compensation in Drosophila is primarily a property of the inherent organization of the X chromosome itself and is achieved through modulation in the organization, rather than exclusively through autosomal factor(s), although a secondary level of autosomal regulation has not yet been ruled out.

scholarly journals Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation

eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
William S Kruesi ◽  
Leighton J Core ◽  
Colin T Waters ◽  
John T Lis ◽  
Barbara J Meyer
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Pol Ii ◽  
Transcription Start Sites ◽  
C Elegans ◽  
Mapping Strategy ◽  
Genome Wide ◽  
Mature Mrnas

The X-chromosome gene regulatory process called dosage compensation ensures that males (1X) and females (2X) express equal levels of X-chromosome transcripts. The mechanism in Caenorhabditis elegans has been elusive due to improperly annotated transcription start sites (TSSs). Here we define TSSs and the distribution of transcriptionally engaged RNA polymerase II (Pol II) genome-wide in wild-type and dosage-compensation-defective animals to dissect this regulatory mechanism. Our TSS-mapping strategy integrates GRO-seq, which tracks nascent transcription, with a new derivative of this method, called GRO-cap, which recovers nascent RNAs with 5′ caps prior to their removal by co-transcriptional processing. Our analyses reveal that promoter-proximal pausing is rare, unlike in other metazoans, and promoters are unexpectedly far upstream from the 5′ ends of mature mRNAs. We find that C. elegans equalizes X-chromosome expression between the sexes, to a level equivalent to autosomes, by reducing Pol II recruitment to promoters of hermaphrodite X-linked genes using a chromosome-restructuring condensin complex.

scholarly journals Zinc Finger Protein Zn72D Promotes Productive Splicing of the maleless Transcript

2007 ◽  
Vol 27 (24) ◽  
pp. 8760-8769 ◽  
Author(s):  
Kathleen A. Worringer ◽  
Barbara Panning
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Zinc Finger ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Fluorescent Protein ◽  
Zinc Finger Protein ◽  
General Factor ◽  
Finger Protein ◽  
Msl Complex

ABSTRACT In organisms with sex chromosomes, dosage compensation equalizes gene expression between the sexes. In Drosophila melanogaster males, the male-specific lethal (MSL) complex of proteins and two noncoding roX RNAs coat the X chromosome, resulting in a twofold transcriptional upregulation to equalize gene expression with that of females. How MSL complex enrichment on the X chromosome is regulated is not well understood. We performed an RNA interference screen to identify new factors required for dosage compensation. Using a Drosophila Schneider S2 cell line in which green fluorescent protein (GFP)-tagged MSL2 localizes to the X chromosome, we assayed ∼7,200 knockdowns for their effects on GFP-MSL2 distribution. One factor identified is the zinc finger protein Zn72D. In its absence, the MSL complex no longer coats the X chromosome. We demonstrate that Zn72D is required for productive splicing of the transcript for the MSL protein Maleless, explaining the dosage compensation defect. However, Zn72D is required for the viability of both sexes, indicating its functions are not sex specific. Consistent with this, Zn72D colocalizes with elongating RNA polymerase II, implicating it as a more general factor involved in RNA metabolism.

scholarly journals Multi-step regulation of transcription kinetics explains the non-linear relation between RNA polymerase II density and mRNA expression in Dosage Compensation

2017 ◽  
Author(s):  
Pouria Dasmeh
Keyword(s):  
Rna Polymerase ◽  
Mrna Expression ◽  
Rna Polymerase Ii ◽  
Dosage Compensation ◽  
Mammalian Cells ◽  
Experimental Studies ◽  
Regulation Of Transcription ◽  
Pol Ii ◽  
Non Linear

AbstractIn heterogametic organisms, expression of unequal number of X chromosomes in males and females is balanced by a process called dosage compensation. In Drosophila and mammals, dosage compensation involves nearly two-fold up-regulation of the X chromosome mediated by dosage compensation complex (DCC). Experimental studies on the role of DCC on RNA polymerase II (Pol II) transcription in mammals disclosed a non-linear relationship between Pol II densities at different transcription steps and mRNA expression. An ~20-30% increase in Pol II densities corresponds to a rough 200% increase in mRNA expression and two-fold up-regulation. Here, using a simple kinetic model of Pol II transcription calibrated by in vivo measured rate constants of different transcription steps in mammalian cells, we demonstrate how this non-linearity can be explained by multi-step transcriptional regulation. Moreover, we show how multi-step enhancement of Pol II transcription can increase mRNA production while leaving Pol II densities unaffected. Our theoretical analysis not only recapitulates experimentally observed Pol II densities upon two-fold up-regulation but also points to a limitation of inferences based on Pol II profiles from chromatin immunoprecipitation sequencing (ChIP-seq) or global run-on assays.

scholarly journals RNA polymerase II depletion from the inactive X chromosome territory is not mediated by physical compartmentalization.

2021 ◽  
Author(s):  
Samuel Collombet ◽  
Isabell Rall ◽  
Claire Dugast-Darzacq ◽  
Alec Heckert ◽  
Aliaksandr Halavatyi ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
X Chromosome ◽  
Dense Body ◽  
Chromosome Territory ◽  
Single Particle Tracking ◽  
Transcription Machinery ◽  
Inactive X Chromosome ◽  
Gene Level ◽  
Nuclear Compartmentalization

Sub-nuclear compartmentalization has been proposed to play an important role in gene regulation by segregating active and inactive parts of the genome in distinct physical and biochemical environments, where transcription and epigenetic factors are either concentrated or depleted. The inactive X chromosome offers a paradigm for studying sub-nuclear compartmentalization. When the non-coding Xist RNA coats the X chromosome, it recruits repressors and chromatin factors that trigger gene silencing, and forms a dense body of heterochromatin from which the transcription machinery appears to be excluded. Phase separation has been proposed to be involved in X-chromosome inactivation (XCI) and might explain exclusion of the transcription machinery by preventing its diffusion into the Xist-coated territory. Here, using quantitative fluorescence microscopy and single particle tracking, we show that RNA polymerase II (RNAPII) freely accesses the Xist territory during initiation of XCI, and that its diffusion is not prevented by biophysical constraints. Instead, the apparent depletion of RNAPII is due to the loss of its chromatin bound fraction. These findings demonstrate that initial exclusion of RNA Pol2 from the inactive X is a consequence of its reduced binding rate at the chromatin and gene level, rather than the biophysical compartmentalization of the inactive X heterochromatin domain. The Xist silent compartment is thus a biochemical rather than a biophysical compartment, at least during initiation of XCI.

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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