Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Chromatin immunoprecipitation of Drosophila melanogaster transcription factors BCD, HB, KR, KNI, GT, CAD, HKB, TLL, D, FTZ, HRY, PRD, RUN, SLP1, DA, DL, MAD, MED, SHN, SNA, TWI, TFIIB and RNA polII

ABSTRACT: ChIP-chip was performed using chromatin isolated from formaldehyde crosslinked, staged embryos, and affinity purified antibodies against 21 transcription factors (including: BCD, HB, KR, KNI, GT, CAD, HKB, TLL, D, FTZ, HRY, PRD, RUN, SLP1, DA, DL, MAD, MED, SHN, SNA, TWI) that belong to 11 DNA binding domain families, specify distinct developmental fates; as well as the general transcription factor TFIIB, and RNA POLII. Affinity purification of the antibodies was performed with E.coli expressed His-tag fusions of the whole protein (designated as 3, e.g. anti-DL 3), the N-terminal portion of the full length protein (designiated as 1, e.g. anti-BCD 1), or the C-terminal portion of the protein (designated as 2, e.g. anti-BCD 2). While for most factors, we only used one antibody in the ChIP-chip study, for some factors, two or more antibodies that recognize non-overlapping parts of each of the proteins were used. The chromatin immunoprecitation and hybridization for each antibody were carried out in duplicates, and in each chromatin immunoprecitation and hybridization series, two mock IP controls and two input DNA controls were also generated. The microarray used in this study is the Affymetrix Drosophila genomic DNA tiling array, which has about 3 million oligo pairs (perfect match-mismatch), covering the whole euchromatic sequences of the fly genome at a resolution of about 35 bp.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Mark Eisen

PROVIDER: E-TABM-736 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions.

MacArthur Stewart S Li Xiao-Yong XY Li Jingyi J Brown James B JB Chu Hou Cheng HC Zeng Lucy L Grondona Brandi P BP Hechmer Aaron A Simirenko Lisa L Keränen Soile V E SV Knowles David W DW Stapleton Mark M Bickel Peter P Biggin Mark D MD Eisen Michael B MB

Genome biology 20090723 7

<h4>Background</h4>We previously established that six sequence-specific transcription factors that initiate anterior/posterior patterning in Drosophila bind to overlapping sets of thousands of genomic regions in blastoderm embryos. While regions bound at high levels include known and probable functional targets, more poorly bound regions are preferentially associated with housekeeping genes and/or genes not transcribed in the blastoderm, and are frequently found in protein coding sequences or in ...[more]

PMID: 19627575

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Project description:In Caenorhabditis elegans, the dosage compensation complex (DCC) specifically binds to and represses transcription from both X chromosomes in hermaphrodites. The DCC is composed of an X-specific condensin complex that interacts with several proteins. During embryogenesis, DCC starts localizing to the X chromosomes around the 40-cell stage, and is followed by X-enrichment of H4K20me1 between 100-cell to comma stage. Here, we analyzed dosage compensation of the X chromosome between sexes, and the roles of dpy-27 (condensin subunit), dpy-21 (non-condensin DCC member), set-1 (H4K20 monomethylase) and set-4 (H4K20 di-/tri-methylase) in X chromosome repression using mRNA-seq and ChIP-seq analyses across several developmental time points. We found that the DCC starts repressing the X chromosomes by the 40-cell stage, but X-linked transcript levels remain significantly higher in hermaphrodites compared to males through the comma stage of embryogenesis. Dpy-27 and dpy-21 are required for X chromosome repression throughout development, but particularly in early embryos dpy-27 and dpy-21 mutations produced distinct expression changes, suggesting a DCC independent role for dpy-21. We previously hypothesized that the DCC increases H4K20me1 by reducing set-4 activity on the X chromosomes. Accordingly, in the set-4 mutant, H4K20me1 increased more from the autosomes compared to the X, equalizing H4K20me1 level between X and autosomes. H4K20me1 increase on the autosomes led to a slight repression, resulting in a relative effect of X derepression. H4K20me1 depletion in the set-1 mutant showed greater X derepression compared to equalization of H4K20me1 levels between X and autosomes in the set-4 mutant, indicating that H4K20me1 level is important, but X to autosomal balance of H4K20me1 contributes only slightly to X-repression. Thus H4K20me1 by itself is not a downstream effector of the DCC. In summary, X chromosome dosage compensation starts in early embryos as the DCC localizes to the X, and is strengthened in later embryogenesis by H4K20me1. RNA-Seq profiles of C. elegans wild type hermaphrodite, mixed sex, at 5 time points and dpy-27, set-4, dpy-21, set-1 and RNAi at 2-3 time points with 3-4 replicates each. RNA-Seq profiles of C. elegans. Strains are N2 (wild type), BS553 fog-2(oz40) V, CB428 dpy-21(e428) V, MK4 dpy-27(y56) III, MT14911 set-4 (n4600) II, SS1075 set-1(tm1821)/hT2g[bli-4(e937) let-?(q782) qIs48] (I;III). Set-1 collections made as heterozygotes and dpy-27(y56) homozygotes. Spike in RNA-seq libraries have AF16 wild type C. briggsae L1s added at a 1:10 ratio. Timepoints are early embryos (synchronized collection, <40 cells), comma embryos (synchronized early embryos aged for 4 hours), mixed embryos (mixed stage embryos from unsynchronized population), L1 (synchronized L1 larvae), L3 (synchronized L3 larvae), and YA (synchronized young adults, collected before embryos present in hermaphrodite gonad). Biological replicates for each strain/stage listed separately. ChIP-seq profiles of C. elegans DCC subunit dpy-27, H4K20me1 histone modification and RNA pol II large subunit ama-1 in 3-6 replicates from mixed stage (unsynchronized) embryos and synchronized L3 larvae. Corresponding inputs are labelled with "Input_" plus ChIP name.

Dataset Information

Chromatin immunoprecipitation of Drosophila melanogaster transcription factors BCD, HB, KR, KNI, GT, CAD, HKB, TLL, D, FTZ, HRY, PRD, RUN, SLP1, DA, DL, MAD, MED, SHN, SNA, TWI, TFIIB and RNA polII

Publications

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions.

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