title: Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity.
abstract: A subfamily of Drosophila homeodomain (HD) transcription factors (TFs) controls the identities of individual muscle founder cells (FCs). However, the molecular mechanisms by which these TFs generate unique FC genetic programs remain unknown. To investigate this problem, we first applied genome-wide mRNA expression profiling to identify genes that are activated or repressed by the muscle HD TFs Slouch (Slou) and Muscle segment homeobox (Msh). Next, we used protein-binding microarrays to define the sequences that are bound by Slou, Msh and other HD TFs that have mesodermal expression. These studies revealed that a large class of HDs, including Slou and Msh, predominantly recognize TAAT core sequences but that each HD also binds to unique sites that deviate from this canonical motif. To understand better the regulatory specificity of an individual FC identity HD, we evaluated the functions of atypical binding sites that are preferentially bound by Slou relative to other HDs within muscle enhancers that are either activated or repressed by this TF. These studies showed that Slou regulates the activities of particular myoblast enhancers through Slou-preferred sequences, whereas swapping these sequences for sites that are capable of binding to multiple HD family members does not support the normal regulatory functions of Slou. Moreover, atypical Slou-binding sites are overrepresented in putative enhancers associated with additional Slou-responsive FC genes. Collectively, these studies provide new insights into the roles of individual HD TFs in determining cellular identity, and suggest that the diversity of HD binding preferences can confer regulatory specificity.
authors.affiliation: Laboratory of Developmental Systems Biology, Genetics and Developmental Biology Center, Division of Intramural Research, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Brian W
authors.initials: BW
authors.lastname: Busser
authors.forename: Leila
authors.initials: L
authors.lastname: Shokri
authors.forename: Savina A
authors.initials: SA
authors.lastname: Jaeger
authors.forename: Stephen S
authors.initials: SS
authors.lastname: Gisselbrecht
authors.forename: Aditi
authors.initials: A
authors.lastname: Singhania
authors.forename: Michael F
authors.initials: MF
authors.lastname: Berger
authors.forename: Bo
authors.initials: B
authors.lastname: Zhou
authors.forename: Martha L
authors.initials: ML
authors.lastname: Bulyk
authors.forename: Alan M
authors.initials: AM
authors.lastname: Michelson
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism; D004331:Drosophila melanogaster / Q000196:embryology / Q000235:genetics; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018398:Homeodomain Proteins / Q000235:genetics* / Q000378:metabolism*; D009132:Muscles / Q000196:embryology*; D032446:Myoblasts / Q000502:physiology*; D012333:RNA, Messenger / Q000096:biosynthesis; D012045:Regulatory Sequences, Nucleic Acid; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D018398:Homeodomain Proteins; D012333:RNA, Messenger; D014157:Transcription Factors; C066818:slou protein, Drosophila