Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genome-wide binding of the homeodomain transcription factor Sine oculis (So) in the Drosophila eye imaginal disc

ABSTRACT: We report genome-wide binding of the highly conserved TF Sine oculis (So), which is necessary for Drosophila eye development and has few previously known direct transcriptional targets. Our data identify novel putative targets of So-mediated regulation, including genes involved in multiple aspects of development. 2 biological replicates of ChIP-seq with anti-So antibody on chromatin from D. melanogaster third instar eye-antennal imaginal discs; negative control - same sample and ChIP-seq protocol without anti-So antibody

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Feng Wang

PROVIDER: E-GEOD-52943 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Regulation of Drosophila eye development by the transcription factor Sine oculis.

Jusiak Barbara B Karandikar Umesh C UC Kwak Su-Jin SJ Wang Feng F Wang Hui H Chen Rui R Mardon Graeme G

PloS one 20140225 2

Homeodomain transcription factors of the Sine oculis (SIX) family direct multiple regulatory processes throughout the metazoans. Sine oculis (So) was first characterized in the fruit fly Drosophila melanogaster, where it is both necessary and sufficient for eye development, regulating cell survival, proliferation, and differentiation. Despite its key role in development, only a few direct targets of So have been described previously. In the current study, we aim to expand our knowledge of So-med ...[more]

PMID: 24586968

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Project description:Contemporary high throughput technologies permit the rapid identification of transcription factor (TF) target genes on a genome-wide scale, yet the functional significance of TFs requires knowledge of target gene expression patterns, cooperating TFs and cis-regulatory element (CRE) structures. Here we investigated the myogenic regulatory network downstream of the Drosophila zinc finger TF Lame duck (Lmd) by combining both previously published and newly performed genomic data sets, including chromatin immunoprecipitation sequencing (ChIP-seq), genome-wide mRNA profiling, cell-specific expression patterns of putative transcriptional targets, analysis of histone mark signatures, studies of TF co-occupancy by additional mesodermal regulators, TF binding site determination using protein binding microarrays (PBMs), and machine learning of candidate CRE motif compositions. Our findings suggest that Lmd orchestrates an extensive myogenic regulatory network, a conclusion supported by the identification of Lmd-dependent genes, histone signatures of Lmd-bound genomic regions, and the relationship of these features to cell-specific gene expression patterns. The heterogeneous co-occupancy of Lmd-bound regions with additional mesodermal regulators revealed that different transcriptional inputs are used to mediate similar myogenic gene expression patterns. Machine learning further demonstrated diverse combinatorial motif patterns within tissue-specific Lmd-bound regions. PBM analysis established the complete spectrum of Lmd DNA binding specificities, and site-directed mutagenesis of Lmd and additional, newly discovered motifs in known enhancers demonstrated the critical role of these TF binding sites in supporting full enhancer activity. Collectively, these findings provide new insights into the transcriptional codes regulating muscle gene expression, and offer a generalizable approach for similar studies in other systems. Examination of Lmd occupancy to genomic DNA from sorted mesodermal cells

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Dataset Information

Genome-wide binding of the homeodomain transcription factor Sine oculis (So) in the Drosophila eye imaginal disc

Publications

Regulation of Drosophila eye development by the transcription factor Sine oculis.

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