title: Regulation of Drosophila eye development by the transcription factor Sine oculis.
abstract: 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-mediated transcriptional regulation in the developing Drosophila eye using ChIP-seq to map So binding regions throughout the genome. We find 7,566 So enriched regions (peaks), estimated to map to 5,952 genes. Using overlap between the So ChIP-seq peak set and genes that are differentially regulated in response to loss or gain of so, we identify putative direct targets of So. We find So binding enrichment in genes not previously known to be regulated by So, including genes that encode cell junction proteins and signaling pathway components. In addition, we analyze a subset of So-bound novel genes in the eye, and find eight genes that have previously uncharacterized eye phenotypes and may be novel direct targets of So. Our study presents a greatly expanded list of candidate So targets and serves as basis for future studies of So-mediated gene regulation in the eye.
authors.affiliation: Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America.
authors.forename: Barbara
authors.initials: B
authors.lastname: Jusiak
authors.affiliation: Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America.
authors.forename: Umesh C
authors.initials: UC
authors.lastname: Karandikar
authors.affiliation: Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America.
authors.forename: Su-Jin
authors.initials: SJ
authors.lastname: Kwak
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America ; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America.
authors.forename: Feng
authors.initials: F
authors.lastname: Wang
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America ; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America.
authors.forename: Hui
authors.initials: H
authors.lastname: Wang
authors.affiliation: Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America ; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America ; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America.
authors.forename: Rui
authors.initials: R
authors.lastname: Chen
authors.affiliation: Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America ; Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America ; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America ; Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America ; Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States of America ; Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America.
authors.forename: Graeme
authors.initials: G
authors.lastname: Mardon
mesh_terms: D000818:Animals; D004331:Drosophila melanogaster / Q000235:genetics; D005123:Eye / Q000254:growth & development; D018507:Gene Expression Regulation, Developmental; D018398:Homeodomain Proteins / Q000235:genetics / Q000502:physiology*; D009898:Optic Disk / Q000254:growth & development / Q000378:metabolism; D038081:Organogenesis / Q000235:genetics; D014157:Transcription Factors / Q000502:physiology*
chemical_list: D018398:Homeodomain Proteins; D014157:Transcription Factors