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Expansion of GA dinucleotide repeats increases the density of CLAMP binding sites on the X-chromosome to promote Drosophila dosage compensation [ChIP-Seq]

ABSTRACT: ChIP-seq was performed to compare binding the genome-wide binding profile of the CLAMP transcription factor in two different Drosophila species. ChIP seq experiments compare the binding profile of CLAMP in female larvae to identify conservation of its binding sequence.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Michael Tolstorukov

PROVIDER: E-GEOD-83435 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Synergistic interactions between CLAMP and MSL complex facilitate Drosophila dosage compensation

Project description:ChIP-seq and mRNA-seq experiments were performed to understand the role of the CLAMP protein in dosage compensation ChIP-seq experiments compared the binding profiles of CLAMP in male and female cells and mRNA-seq data to define the role of CLAMP in regulating genes on the X-chromosome

2013-07-15 | E-GEOD-39271 | biostudies-arrayexpress

ChIP-seq study of inheritence of Myc in Drosophila

Project description:Myc is an important oncogene. It is considered as a transcription factor, but the function of Myc in normal or cancer cells have not been fully understood. In addition, Myc plays a role in cell proliferation and differentiation. It is also important for cell identity and stay on chromatin throughout the cell cycle. However, the inheritance of Myc is still a mystery. Here we study the function and inheritance of Myc in D. melanogaster by mapping the binding sites of Myc during interphase and mitosis using ChIP-seq. DNA sample of ChIP for Myc are collected from Kc cells in interphase or mitosis. Input sequences from previous study in the same cell type (GSM762848, GSM762849) are used as control.

2013-01-21 | E-GEOD-39521 | biostudies-arrayexpress

Expansion of GA dinucleotide repeats increases the density of CLAMP binding sites on the X-chromosome to promote Drosophila dosage compensation

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-07-17 | E-GEOD-83444 | biostudies-arrayexpress

Su(H) early embryonic ChIP-seq

Project description:This submission data was generated in Angela Stathopoulos's lab. Project goal was to map Su(H) associated regions on Drosophila melanogaster genome. In Drosophila embryos, a nuclear gradient of Dorsal (Dl) directs differential gene expression along the dorsoventral (DV) axis, translating it into distinct domains separated by sharp boundaries between future mesodermal, neural and ectodermal territories. However, the mechanisms used to differentially position gene expression boundaries along this axis are not fully understood. Here, we show that the transcription factor Suppressor of Hairless [Su(H)] influences the positioning of dorsal boundaries for many genes expressed along the DV axis. Synthetic reporter constructs provide molecular evidence that Su(H) binding sites support repression and act to counterbalance activation through Dl and the ubiquitous activator Zelda. Overall, our study highlights a role for broadly expressed repressors, like Su(H), and organization of transcription factor binding sites within cis-regulatory modules as important elements controlling spatial domains of gene expression, to facilitate flexible positioning of boundaries across the entire DV axis. 1 g of 2-4 hour yw embryos were used. Two replicate ChIP-seq samples were analyzed using goat (Santa cruz goat polyclonal #sc-15813), and rabbit (Santa cruz rabbit polyclonal #sc-25761) antibodies.

2014-10-13 | E-GEOD-59726 | biostudies-arrayexpress

Transcription profiling of human slow flow venous malformations and normal saphenous veins

Project description:Objective: Vascular malformations affect 3% of neonates. Venous malformations (VMs) are the largest group representing more than 50 % of cases. In hereditary forms of VMs gene mutations have been identified, but for the large group of spontaneous forms the primary cause and downstream dysregulated genes are unknown. Methods and Results: We have performed a global comparison of gene; expression in slow-flow VMs and normal saphenous veins using human whole genome micro-arrays. Genes of interest were validated with qRT-PCR. Gene expression in the tunica media was studied after laser micro-dissection of small pieces of tissue. Protein expression in endothelial cells (ECs) was studied with antibodies. We detected 511 genes more than 4-fold down- and 112 genes more than 4-fold up-regulated. Notably, chemokines, growth factors, transcription factors and regulators of extra-cellular matrix (ECM) turnover were regulated. We observed activation and arterialization of ECs of the VM proper, whereas ECs of vasa vasorum exhibited up-regulation of inflammation markers. In the tunica media, an altered ECM turnover and composition was found. Conclusions: Our studies demonstrate dysregulated gene expression in tunica interna, media and externa of VMs, and show that each of the three layers represents a reactive compartment. The dysregulated genes may serve as therapeutic targets. Experiment Overall Design: - 4 samples Experiment Overall Design: - samples are replicates with dye swap

2008-06-15 | E-GEOD-7190 | biostudies-arrayexpress

Heat-shock protein 90 globally targets paused promoters and regulates environment-induced gene expression

Project description:In this study we provide evidence that Hsp90 binds chromatin at specific sites close to several TSS in Drosophila S2 cell line. In addition of finding a preference for stalled promoter regions of annotated genes, we uncover many intergenic Hsp90 binding sites coinciding with non-annotated transcription start sites. Interestingly, this set includes promoters for primary transcripts of microRNA genes, thereby expanding the scope of Hsp90 to transcriptional control of many genes. We finally conclude that Hsp90 contacts NelfE and thus regulates pol II pausing. Our Dataset comprises of 1 ChIP-seq sample using chromatin from S2 cells which was immunoprecipitated, using antibodies against Drosophila Hsp90. The two biological replicates are submitted along with the input replicates.

2012-05-14 | E-GEOD-31226 | biostudies-arrayexpress

Heterochromatin remodeling by CDK12 contributes to learning in Drosophila

Project description:We describe the epigenetic profiling of the H3K9me2 and HP1a in Drosophila third instar larvae before and after CDK12 depletion by RNA interference (RNAi). Here we show that CDK12 regulates heterochromatin dynamics in Drosophila chromosomes. Depletion of CDK12 induces the increased HP1a and H3K9me2 binding profile on the coding region of euchromatic genes, with the X chromosome being the most affected. These results are consistent with the polytene chromosome immunostaining pattern of HP1a and H3K9me2 after CDK12 knockdown in our initial cytological observations, which show that CDK12 depletion induce heterochromatin spreading on euchromatic arms, especially on the X chromosome. This study describes a novel role of the CDK12 complex in controlling the epigenetic transition between euchromatin and heterochromatin. Examination of the genome-wide H3K9me2 and HP1a binding profile in wildtype larvae (WT) and CDK12-depleted larvae (CDK12-KD). Examination of the genome-wide CDK12 binding profile in wildtype larvae (WT). Twelve independent immunoprecipitations were conducted for each antibody. Two biological replicates were performed.

2015-11-02 | E-GEOD-63011 | biostudies-arrayexpress

RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins

Project description:Background: Sm proteins are multimeric RNA-binding factors, found in all three domains of life. Eukaryotic Sm proteins, together with their associated RNAs, form small ribonucleoprotein (RNP) complexes important in multiple aspects of gene regulation. Comprehensive knowledge of the RNA components of Sm RNPs is critical for understanding their functions. Results: We developed a multi-targeting RNA-immunoprecipitation sequencing (RIP-seq) strategy to reliably identify Sm-associated RNAs from Drosophila ovaries and cultured human cells. Using this method, we discovered three major categories of Sm-associated transcripts: small nuclear (sn)RNAs, small Cajal body (sca)RNAs and mRNAs. Additional RIP-PCR analysis showed both ubiquitous and tissue-specific interactions. We provide evidence that the mRNA-Sm interactions are mediated by snRNPs, and that one of the mechanisms of interaction is via base pairing. Moreover, the Sm-associated mRNAs are mature, indicating a splicing-independent function for Sm RNPs. Conclusions: This study represents the first comprehensive analysis of eukaryotic Sm-containing RNPs, and provides a basis for additional functional analyses of Sm proteins and their associated snRNPs outside of the context of pre-mRNA splicing. Our findings expand the repertoire of eukaryotic Sm-containing RNPs and suggest new functions for snRNPs in mRNA metabolism. RNA-Immunoprecipitation sequencing of RNA-Sm protein complexes.

2013-12-01 | E-GEOD-35842 | biostudies-arrayexpress

ChIP-Seq of ORC2 bound to third instar salivary gland DNA in WT and mutant Drosophila, analyzed by Illumina sequencing

Project description:We analyzed ORC2 ChIP-Seq from hand dissected salivary glands of wandering third instar larvae from OrR or SuUR Drosophila. Goals were to ascertain the difference in binding profile between salivary glands expressing and not expressing the Supressor of UnderReplication protein. One replicate is included for each of OrR (WT) or SuUR salivary glands.

2011-10-18 | E-GEOD-31899 | biostudies-arrayexpress

Identification of transcription factor binding sites from ChIP-seq data at high-resolution

Project description:Genome-wide mapping of proteinM-bM-^@M-^SDNA interactions is essential for a full understanding of transcriptional regulation. A precise map of binding sites for transcription factors, core transcriptional machinery is vital for deciphering the gene regulatory networks that underlie various biological processes. Chromatin immunoprecipitation followed by sequencing (ChIPM-bM-^@M-^Sseq) is a technique for genome-wide profiling of DNA-binding proteins. However, our conventional ChIPM-bM-^@M-^Sseq occasionally gives wider peaks which might be due to overlapping binding sites of two or more transcription factors. Therefore, to improve the resolution of our conventional ChIPM-bM-^@M-^Sseq which have DNA-protein footprint of ~100 bp, we decreased the size of DNA-protein footprint to ~ 50 bp by DNaseI digestion of whole cell extract (WCE). ChIP-seq for Twist transcription factor in Drosophila embryos

2014-02-06 | E-GEOD-40664 | biostudies-arrayexpress

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