Identification of SUMO-dependent chromatin-associated transcriptional repression components by a genome-wide RNA interference screen

2008 ◽  
Vol 2008 (Spring) ◽  
Author(s):  
Guntram Suske ◽  
Bastian Stielow ◽  
Alexandra Sapetschnig ◽  
Imme Krüger ◽  
Michael Boutros
Keyword(s):  
Rna Interference ◽  
Transcriptional Repression ◽  
Genome Wide ◽  
A Genome

scholarly journals A Genome-Wide RNA Interference Screen Identifies a Differential Role of the Mediator CDK8 Module Subunits for GATA/ RUNX-Activated Transcription in Drosophila

2010 ◽  
Vol 30 (11) ◽  
pp. 2837-2848 ◽  
Author(s):  
Vanessa Gobert ◽  
Dani Osman ◽  
Stéphanie Bras ◽  
Benoit Augé ◽  
Muriel Boube ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
Rna Interference ◽  
Cell Fate ◽  
Gata Factor ◽  
Hematopoietic System ◽  
Crystal Cell ◽  
Genome Wide ◽  
A Genome

ABSTRACT Transcription factors of the RUNX and GATA families play key roles in the control of cell fate choice and differentiation, notably in the hematopoietic system. During Drosophila hematopoiesis, the RUNX factor Lozenge and the GATA factor Serpent cooperate to induce crystal cell differentiation. We used Serpent/Lozenge-activated transcription as a paradigm to identify modulators of GATA/RUNX activity by a genome-wide RNA interference screen in cultured Drosophila blood cells. Among the 129 factors identified, several belong to the Mediator complex. Mediator is organized in three modules plus a regulatory “CDK8 module,” composed of Med12, Med13, CycC, and Cdk8, which has long been thought to behave as a single functional entity. Interestingly, our data demonstrate that Med12 and Med13 but not CycC or Cdk8 are essential for Serpent/Lozenge-induced transactivation in cell culture. Furthermore, our in vivo analysis of crystal cell development show that, while the four CDK8 module subunits control the emergence and the proliferation of this lineage, only Med12 and Med13 regulate its differentiation. We thus propose that Med12/Med13 acts as a coactivator for Serpent/Lozenge during crystal cell differentiation independently of CycC/Cdk8. More generally, we suggest that the set of conserved factors identified herein may regulate GATA/RUNX activity in mammals.

scholarly journals An inducible CRISPR interference library for genetic interrogation of Saccharomyces cerevisiae biology

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Amir Momen-Roknabadi ◽  
Panos Oikonomou ◽  
Maxwell Zegans ◽  
Saeed Tavazoie
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcriptional Repression ◽  
Nucleosome Occupancy ◽  
Design Parameters ◽  
Experimental Conditions ◽  
Crispr Interference ◽  
Cellular Processes ◽  
Genome Wide ◽  
Reliable Assessment ◽  
A Genome

AbstractGenome-scale CRISPR interference (CRISPRi) is widely utilized to study cellular processes in a variety of organisms. Despite the dominance of Saccharomyces cerevisiae as a model eukaryote, an inducible genome-wide CRISPRi library in yeast has not yet been presented. Here, we present a genome-wide, inducible CRISPRi library, based on spacer design rules optimized for S. cerevisiae. We have validated this library for genome-wide interrogation of gene function across a variety of applications, including accurate discovery of haploinsufficient genes and identification of enzymatic and regulatory genes involved in adenine and arginine biosynthesis. The comprehensive nature of the library also revealed refined spacer design parameters for transcriptional repression, including location, nucleosome occupancy and nucleotide features. CRISPRi screens using this library can identify genes and pathways with high precision and a low false discovery rate across a variety of experimental conditions, enabling rapid and reliable assessment of genetic function and interactions in S. cerevisiae.

scholarly journals A genome-wide RNA interference screen identifies new regulators of androgen receptor function in prostate cancer cells

2013 ◽  
Vol 23 (4) ◽  
pp. 581-591 ◽  
Author(s):  
K. Imberg-Kazdan ◽  
S. Ha ◽  
A. Greenfield ◽  
C. S. Poultney ◽  
R. Bonneau ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Androgen Receptor ◽  
Rna Interference ◽  
Cancer Cells ◽  
Receptor Function ◽  
Prostate Cancer Cells ◽  
Genome Wide ◽  
A Genome ◽  
Androgen Receptor Function

scholarly journals A Genome-wide RNA Interference Screen Reveals that Variant Histones Are Necessary for Replication-Dependent Histone Pre-mRNA Processing

2007 ◽  
Vol 28 (4) ◽  
pp. 692-699 ◽  
Author(s):  
Eric J. Wagner ◽  
Brandon D. Burch ◽  
Ashley C. Godfrey ◽  
Harmony R. Salzler ◽  
Robert J. Duronio ◽  
...  
Keyword(s):  
Rna Interference ◽  
Mrna Processing ◽  
Genome Wide ◽  
A Genome

scholarly journals A Genome-Wide RNA Interference Screen Identifies a Role for Wnt/β-Catenin Signaling during Rift Valley Fever Virus Infection

2016 ◽  
Vol 90 (16) ◽  
pp. 7084-7097 ◽  
Author(s):  
Brooke Harmon ◽  
Sara W. Bird ◽  
Benjamin R. Schudel ◽  
Anson V. Hatch ◽  
Amy Rasley ◽  
...  
Keyword(s):  
Rna Interference ◽  
Wnt Signaling ◽  
Rift Valley ◽  
Rift Valley Fever ◽  
Rift Valley Fever Virus ◽  
Fever Virus ◽  
Valley Fever ◽  
Rnai Screening ◽  
Genome Wide ◽  
A Genome

ABSTRACTRift Valley fever virus (RVFV) is an arbovirus within theBunyaviridaefamily capable of causing serious morbidity and mortality in humans and livestock. To identify host factors involved in bunyavirus replication, we employed genome-wide RNA interference (RNAi) screening and identified 381 genes whose knockdown reduced infection. The Wnt pathway was the most represented pathway when gene hits were functionally clustered. With further investigation, we found that RVFV infection activated Wnt signaling, was enhanced when Wnt signaling was preactivated, was reduced with knockdown of β-catenin, and was blocked using Wnt signaling inhibitors. Similar results were found using distantly related bunyaviruses La Crosse virus and California encephalitis virus, suggesting a conserved role for Wnt signaling in bunyaviral infection. We propose a model where bunyaviruses activate Wnt-responsive genes to regulate optimal cell cycle conditions needed to promote efficient viral replication. The findings in this study should aid in the design of efficacious host-directed antiviral therapeutics.IMPORTANCERVFV is a mosquito-borne bunyavirus that is endemic to Africa but has demonstrated a capacity for emergence in new territories (e.g., the Arabian Peninsula). As a zoonotic pathogen that primarily affects livestock, RVFV can also cause lethal hemorrhagic fever and encephalitis in humans. Currently, there are no treatments or fully licensed vaccines for this virus. Using high-throughput RNAi screening, we identified canonical Wnt signaling as an important host pathway regulating RVFV infection. The beneficial role of Wnt signaling was observed for RVFV, along with other disparate bunyaviruses, indicating a conserved bunyaviral replication mechanism involving Wnt signaling. These studies supplement our knowledge of the fundamental mechanisms of bunyavirus infection and provide new avenues for countermeasure development against pathogenic bunyaviruses.

scholarly journals Induction of theCandida albicansFilamentous Growth Program by Relief of Transcriptional Repression: A Genome-wide Analysis

2005 ◽  
Vol 16 (6) ◽  
pp. 2903-2912 ◽  
Author(s):  
David Kadosh ◽  
Alexander D. Johnson
Keyword(s):  
Candida Albicans ◽  
Transcriptional Repression ◽  
Fungal Pathogen ◽  
Morphological Transition ◽  
Whole Genome ◽  
Transcriptional Repressors ◽  
Genome Wide Analysis ◽  
Human Fungal Pathogen ◽  
Genome Wide ◽  
A Genome

Candida albicans, the major human fungal pathogen, undergoes a reversible morphological transition from blastospores (round budding cells) to filaments (elongated cells attached end-to-end). This transition, which is induced upon exposure of C. albicans cells to a number of host conditions, including serum and body temperature (37°C), is required for virulence. Using whole-genome DNA microarray analysis, we describe 61 genes that are significantly induced (≥2-fold) during the blastospore to filament transition that takes place in response to exposure to serum and 37°C. We next show that approximately half of these genes are transcriptionally repressed in the blastospore state by three transcriptional repressors, Rfg1, Nrg1, and Tup1. We conclude that the relief of this transcriptional repression plays a key role in bringing the C. albicans filamentous growth program into play, and we describe the framework of this transcriptional circuit.

scholarly journals Identification of Drosophila Zfh2 as a Mediator of Hypercapnic Immune Regulation by a Genome-Wide RNA Interference Screen

2015 ◽  
Vol 196 (2) ◽  
pp. 655-667 ◽  
Author(s):  
Iiro Taneli Helenius ◽  
Ryan J. Haake ◽  
Yong-Jae Kwon ◽  
Jennifer A. Hu ◽  
Thomas Krupinski ◽  
...  
Keyword(s):  
Rna Interference ◽  
Immune Regulation ◽  
Genome Wide ◽  
A Genome

scholarly journals A genome-wide RNA interference screen identifies putative chromatin regulators essential for E2F repression

2007 ◽  
Vol 104 (22) ◽  
pp. 9381-9386 ◽  
Author(s):  
J. Lu ◽  
M.-L. Ruhf ◽  
N. Perrimon ◽  
P. Leder
Keyword(s):  
Rna Interference ◽  
Chromatin Regulators ◽  
Genome Wide ◽  
A Genome
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