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Post-transcription initiation function of the ubiquitous SAGA complex in tissue-specific gene activation (ChIP-seq)

ABSTRACT: SAGA is a highly conserved transcriptional co-activator complex involved in multiple steps of transcription with activities that function both pre and post initiation. Loss of individual subunits results in developmental defects, suggesting a role in development. To better understand the roles of SAGA functions in developmental gene expression and it's relationship with RNA polymerase II, we examined its composition, binding profile, and the effects of subunit loss on gene expression in two distinct cell types in late stage Drosophila embryos: muscle and neurons.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE29513 | GEO | 2011/08/22

SECONDARY ACCESSION(S): PRJNA153999

REPOSITORIES: GEO

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Post-transcription initiation function of the ubiquitous SAGA complex in tissue-specific gene activation (ChIP-seq)

Project description:SAGA is a highly conserved transcriptional co-activator complex involved in multiple steps of transcription with activities that function both pre and post initiation. Loss of individual subunits results in developmental defects, suggesting a role in development. To better understand the roles of SAGA functions in developmental gene expression and it's relationship with RNA polymerase II, we examined its composition, binding profile, and the effects of subunit loss on gene expression in two distinct cell types in late stage Drosophila embryos: muscle and neurons. Chromatin IP of FLAG-tagged SAGA subunit Ada2b, and RNA polymerase II (antibody 4H8), was performed in neuronal (elav+) or muscle (mef2+) cells isolated by FACS from late stage embryos, and compared to whole cell extracts (input). The control constists of an IP performed in neuronal cells from a non-tagged strain.

2011-08-22 | E-GEOD-29513 | biostudies-arrayexpress

Post-transcription initiation function of the ubiquitous SAGA complex in tissue-specific gene activation (gene expression)

Project description:SAGA is a highly conserved transcriptional co-activator complex involved in multiple steps of transcription with activities that function both pre and post initiation. Loss of individual subunits results in developmental defects, suggesting a role in development. In particular, SAGA contains a ubiquitin protease activity involved in the transition from transcription initiation to elongation. Loss of the Sgf11 SAGA subunit causes loss of deubiquitination activity, and leads to defects in axon targeting and embryonic lethality. To better understand the roles of SAGA functions in developmental gene expression we examined its composition, binding profile, and the effects of subunit loss on gene expression in two distinct cell types in late stage Drosophila embryos: muscle and neurons.

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Conserved and unique features of the SAGA complex in plants [ChIP-seq]

Project description:The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex is an evolutionarily conserved, multifunctional co-activator complex, which has a critical role in histone acetylation, gene expression, and various developmental processes in eukaryotes. However, little is known about the composition and function of the SAGA complex in plants. Here, we found that the SAGA complex in Arabidopsis thaliana contains not only conserved subunits and but also four plant-specific subunits, including three homologous subunits, SCS1, SCS2A, and SCS2B (SCS1/2A/2B), and a TAF-like subunit, TAFL. We also found that a series of SAGA subunits are shared in yeast and/or metazoans but are absent in Arabidopsis. Mutations in the unique SAGA subunits SCS1/2A/2B lead to defective phenotypes similar to those caused by mutations in the conserved SAGA subunits HAG1 and ADA2B; these defective phenotypes include delayed juvenile-to-adult phase transition, late flowering, and increased trichome density. SCS1/2A/2B function in the SAGA complex to promote the transcription of development-related genes by facilitating histone H3 acetylation. The results suggest that, compared to SAGA complexes in other eukaryotes, the SAGA complex in plants has evolved unique features that are necessary for normal growth and development.

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Conserved and unique features of the SAGA complex in plants [RNA-seq]

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Post-transcription initiation function of the ubiquitous SAGA complex in tissue-specific gene activation.

Project description:The Spt-Ada-Gcn5-acetyltransferase (SAGA) complex was discovered from Saccharomyces cerevisiae and has been well characterized as an important transcriptional coactivator that interacts both with sequence-specific transcription factors and the TATA-binding protein TBP. SAGA contains a histone acetyltransferase and a ubiquitin protease. In metazoans, SAGA is essential for development, yet little is known about the function of SAGA in differentiating tissue. We analyzed the composition, interacting proteins, and genomic distribution of SAGA in muscle and neuronal tissue of late stage Drosophila melanogaster embryos. The subunit composition of SAGA was the same in each tissue; however, SAGA was associated with considerably more transcription factors in muscle compared with neurons. Consistent with this finding, SAGA was found to occupy more genes specifically in muscle than in neurons. Strikingly, SAGA occupancy was not limited to enhancers and promoters but primarily colocalized with RNA polymerase II within transcribed sequences. SAGA binding peaks at the site of RNA polymerase pausing at the 5' end of transcribed sequences. In addition, many tissue-specific SAGA-bound genes required its ubiquitin protease activity for full expression. These data indicate that in metazoans SAGA plays a prominent post-transcription initiation role in tissue-specific gene expression.

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SAGA core module subunits regulate gene expression during oogenesis [ChIP-seq]

Project description:ChIP-nexus performed in Kc167 cells for subunits of the SAGA coactivator complex;ChIP performed in ovary homogenate for subunits of the SAGA coactivator complex

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Genome-wide analysis of SAGA subunits: ada2b, spt3, nonstop, and sgf11, as well as RNA pol II in 1-3 hr embryos of Drosophila melanogaster.

Project description:The Spt-Ada-Gcn5-acetyltransferase (SAGA) chromatin-modifying complex is a transcriptional coactivator that contains four different modules of subunits. The intact SAGA complex has been well characterized for its function in transcription regulation and development. However, little is known about the roles of individual modules within SAGA and if they have any SAGA independent functions. Here we demonstrate that the two enzymatic modules of Drosophila SAGA are differently required in oogenesis. Loss of the HAT activity blocks oogenesis, while loss of the DUB activity does not. However, the DUB module regulates a subset of genes in early embryogenesis and loss of the DUB subunits causes defects in embryogenesis. ChIP-seq analysis of ada2b, spt3, nonstop, and sgf11revealed that both the DUB and HAT modules bind most SAGA target genes even though many of these targets do not require the DUB module for expression. Furthermore, we found that the DUB module can bind to chromatin and regulate transcription independently of the rest of SAGA. Our results suggest that the DUB module has functions within SAGA as well as independent functions.

2017-10-01 | GSE98862 | GEO

Post-transcription initiation function of the ubiquitous SAGA complex in tissue-specific gene activation

Project description:Post-transcription initiation function of the ubiquitous SAGA complex in tissue-specific gene activation

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RNA Seq analysis of whole ovaries following mutation of SAGA subunits: Ada2b, Ataxin-7, or non-stop in Drosophila melanogaster

Project description:The Spt-Ada-Gcn5-acetyltransferase (SAGA) chromatin-modifying complex is a transcriptional coactivator that contains four different modules of subunits. The intact SAGA complex has been well characterized for its function in transcription regulation and development. However, little is known about the roles of individual modules within SAGA and if they have any SAGA independent functions. Here we demonstrate that the two enzymatic modules of Drosophila SAGA are differently required in oogenesis. Ada2b is part of the HAT module (Histone Acetyl Transferase), whereas Ataxin-7 and non-stop are members of the DUB module (Deubiquitinase). Loss of the HAT activity blocks oogenesis, while loss of the DUB activity does not. However, the DUB module regulates a subset of genes in early embryogenesis and loss of the DUB subunits causes defects in embryogenesis. ChIP-seq analysis of ada2b, spt3, nonstop, and sgf11revealed that both the DUB and HAT modules bind most SAGA target genes even though many of these targets do not require the DUB module for expression. Furthermore, we found that the DUB module can bind to chromatin and regulate transcription independently of the rest of SAGA. Our results suggest that the DUB module has functions within SAGA as well as independent functions.

2017-10-01 | GSE98864 | GEO

Genome-wide analysis of SAGA subunit ada2b, and histones ubH2B, H2b, H3, H3K9ac, and H3K14ac in wt and Ataxin 7 mutants of 1-3 hr embryos of Drosophila melanogaster

2017-10-01 | GSE103453 | GEO