GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update

Gilsdorf, Moritz; Horn, Thomas; Arziman, Zeynep; Pelz, Oliver; Kiner, Evgeny; Boutros, Michael

doi:10.1093/nar/gkp1038

Cited by 35 publications

(28 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…RNA interference (RNAi) knockdowns were achieved by incubating S2 cells with gene-specific double-strand RNA (dsRNA) as previously described (8,12). The dsRNA probes were selected from the previously tested fragments listed in GenomeRNAi (http://rnai2.dkfz.de/GenomeRNAi/) (15). DNA fragments were PCR amplified from S2 cell genomic DNA.…”

Section: Methodsmentioning

confidence: 99%

Poly(A) Signals Located near the 5′ End of Genes Are Silenced by a General Mechanism That Prevents Premature 3′-End Processing

Guo

Garrett

Micklem

et al. 2011

Molecular and Cellular Biology

View full text Add to dashboard Cite

Poly(A) signals located at the 3 end of eukaryotic genes drive cleavage and polyadenylation at the same end of pre-mRNA. Although these sequences are expected only at the 3 end of genes, we found that strong poly(A) signals are also predicted within the 5 untranslated regions (UTRs) of many Drosophila melanogaster mRNAs. Most of these 5 poly(A) signals have little influence on the processing of the endogenous transcripts, but they are very active when placed at the 3 end of reporter genes. In investigating these unexpected observations, we discovered that both these novel poly(A) signals and standard poly(A) signals become functionally silent when they are positioned close to transcription start sites in either Drosophila or human cells. This indicates that the stage when the poly(A) signal emerges from the polymerase II (Pol II) transcription complex determines whether a putative poly(A) signal is recognized as functional. The data suggest that this mechanism, which probably prevents cryptic poly(A) signals from causing premature transcription termination, depends on low Ser2 phosphorylation of the C-terminal domain of Pol II and inefficient recruitment of processing factors.

show abstract

Section: Methodsmentioning

confidence: 99%

Poly(A) Signals Located near the 5′ End of Genes Are Silenced by a General Mechanism That Prevents Premature 3′-End Processing

Guo

Garrett

Micklem

et al. 2011

Molecular and Cellular Biology

View full text Add to dashboard Cite

show abstract

“…Data were retrieved both from the recently developed database GenomeRNAi [29] and from additional data curated by our group. Thus, for 172 of 313 phosphatases and regulatory subunits the phenotype observed upon gene downregulation was annotated together with the cell type where the phenotype has been observed.…”

Section: 'Sirna Experiment' Tabmentioning

confidence: 99%

HUPHO: the human phosphatase portal

et al. 2012

View full text Add to dashboard Cite

Phosphatases and kinases contribute to the regulation of protein phosphorylation homeostasis in the cell. Phosphorylation is a key post-translational modification underlying the regulation of many cellular processes. Thus, a comprehensive picture of phosphatase function and the identification of their target substrates would aid a systematic approach to a mechanistic description of cell signalling. Here we present a website designed to facilitate the retrieval of information about human protein phosphatases. To this end we developed a search engine to recover and integrate information annotated in several publicly available web resources. In addition we present a text-mining-assisted annotation effort aimed at extracting phosphatase related data reported in the scientific literature. The HuPho (human phosphatases) website can be accessed at http://hupho.uniroma2.it.

show abstract

“…The screen was performed in duplicate. Sequence information about the BKN dsRNA library are deposited in a database that can be accessed at http://www.genomernai.org (32). For the retests, the same procedure was employed to test the selected candidates in quadruplicate.…”

Section: Plasmidsmentioning

confidence: 99%

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

Gobert

Osman

Bras

et al. 2010

Molecular and Cellular Biology

Self Cite

View full text Add to dashboard Cite

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 genomewide 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.During hematopoiesis, multipotent progenitors or stem cells generate a large spectrum of specialized cell types through the progressive deployment of cell-specific gene expression programs (59). In that respect, it is of particular interest to understand how combinatorial inputs from general and lineage-specific transcription factors converge to modulate RNA polymerase II machinery and establish the gene expression programs intrinsic to cell diversification. Over the last decade, cross-species conservation has shown that Drosophila is a valuable model system to gain insights into the mechanisms controlling blood cell fate choice and differentiation at the transcriptional level (36). Indeed, several key transcription factors and cofactors regulating blood cell development in vertebrates also participate in hematopoiesis in Drosophila.Reminiscent of the situation in vertebrates, hematopoiesis in the fruit fly occurs in two temporally and spatially distinct waves: blood cell progenitors (prohemocytes) arise first from the head mesoderm in the early embryo and then from a specialized organ, the lymph gland, in the larva (36). These progenitors differentiate into two main cell types, most closely related to vertebrate myeloid lineages: plasmatocytes, which function as macrophages, and crystal cells, which participate in melanization and clotting (53). So far, we have a better understanding of the transcriptional network controlling blood cell development in the embryo. In particular, it appears that transcription factors of the GATA and RUNX families, which regulate several steps of hematopoiesis in vertebrates, act together to control Drosophila blood cell fate choice and...

show abstract

GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update

Cited by 35 publications

References 20 publications

Poly(A) Signals Located near the 5′ End of Genes Are Silenced by a General Mechanism That Prevents Premature 3′-End Processing

Poly(A) Signals Located near the 5′ End of Genes Are Silenced by a General Mechanism That Prevents Premature 3′-End Processing

HUPHO: the human phosphatase portal

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

Contact Info

Product

Resources

About