title: Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network.
abstract: 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 ChIP sequencing (ChIP-seq), genome-wide mRNA profiling, cell-specific expression patterns of putative transcriptional targets, analysis of histone mark signatures, studies of TF cooccupancy 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 cooccupancy 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 insights into the transcriptional codes regulating muscle gene expression and offer a generalizable approach for similar studies in other systems.
authors.affiliation: Laboratory of Developmental Systems Biology, National Heart Lung and Blood Institute, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Brian W
authors.initials: BW
authors.lastname: Busser
authors.forename: Di
authors.initials: D
authors.lastname: Huang
authors.forename: Kevin R
authors.initials: KR
authors.lastname: Rogacki
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Lane
authors.forename: Leila
authors.initials: L
authors.lastname: Shokri
authors.forename: Ting
authors.initials: T
authors.lastname: Ni
authors.forename: Caitlin E
authors.initials: CE
authors.lastname: Gamble
authors.forename: Stephen S
authors.initials: SS
authors.lastname: Gisselbrecht
authors.forename: Jun
authors.initials: J
authors.lastname: Zhu
authors.forename: Martha L
authors.initials: ML
authors.lastname: Bulyk
authors.forename: Ivan
authors.initials: I
authors.lastname: Ovcharenko
authors.forename: Alan M
authors.initials: AM
authors.lastname: Michelson
mesh_terms: D000818:Animals; D030801:Animals, Genetically Modified; D001185:Artificial Intelligence; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D004247:DNA / Q000235:genetics / Q000378:metabolism; D029721:Drosophila Proteins / Q000235:genetics* / Q000378:metabolism; D004331:Drosophila melanogaster / Q000166:cytology / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D018507:Gene Expression Regulation, Developmental; D053263:Gene Regulatory Networks; D049750:Genome, Insect; D008648:Mesoderm / Q000166:cytology / Q000254:growth & development / Q000378:metabolism; D008969:Molecular Sequence Data; D024510:Muscle Development / Q000235:genetics*; D032446:Myoblasts / Q000166:cytology / Q000378:metabolism; D018006:Myogenic Regulatory Factors / Q000235:genetics* / Q000378:metabolism; D049490:Systems Biology; D059467:Transcriptome
chemical_list: D029721:Drosophila Proteins; D018006:Myogenic Regulatory Factors; C442328:lmd protein, Drosophila; D004247:DNA