title: Drosophila polypyrimidine tract-binding protein (DmPTB) regulates dorso-ventral patterning genes in embryos.
abstract: The Drosophila polypyrimidine tract-binding protein (dmPTB or hephaestus) plays an important role during embryogenesis. A loss of function mutation, heph(03429), results in varied defects in embryonic developmental processes, leading to embryonic lethality. However, the suite of molecular functions that are disrupted in the mutant remains unknown. We have used an unbiased high throughput sequencing approach to identify transcripts that are misregulated in this mutant. Misregulated transcripts show evidence of significantly altered patterns of splicing (exon skipping, 5' and 3' splice site switching), alternative 5' ends, and mRNA level changes (up and down regulation). These findings are independently supported by reverse-transcription-polymerase chain reaction (RT-PCR) analysis and in situ hybridization. We show that a group of genes, such as Zerknüllt, z600 and screw are among the most upregulated in the mutant and have been functionally linked to dorso-ventral patterning and/or dorsal closure processes. Thus, loss of dmPTB function results in specific misregulated transcripts, including those that provide the missing link between the loss of dmPTB function and observed developmental defects in embryogenesis. This study provides the first comprehensive repertoire of genes affected in vivo in the heph mutant in Drosophila and offers insight into the role of dmPTB during embryonic development.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America.
authors.forename: Joseph
authors.initials: J
authors.lastname: Heimiller
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America.
authors.forename: Vinod
authors.initials: V
authors.lastname: Sridharan
authors.affiliation: BioFrontiers Next-Gen Sequencing Facility, University of Colorado, Boulder, Colorado, United States of America.
authors.forename: Jim
authors.initials: J
authors.lastname: Huntley
authors.affiliation: Departments of Genetics and Medical Genetics, University of Wisconsin, Madison, Wisconsin, United States of America.
authors.forename: Cedric S
authors.initials: CS
authors.lastname: Wesley
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America.
authors.forename: Ravinder
authors.initials: R
authors.lastname: Singh
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D019521:Body Patterning / Q000235:genetics*; D029721:Drosophila Proteins / Q000172:deficiency / Q000235:genetics* / Q000378:metabolism; D004331:Drosophila melanogaster / Q000196:embryology / Q000235:genetics* / Q000378:metabolism; D004625:Embryo, Nonmammalian; D018507:Gene Expression Regulation, Developmental; D059014:High-Throughput Nucleotide Sequencing; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D017403:In Situ Hybridization; D009154:Mutation; D038941:Polypyrimidine Tract-Binding Protein / Q000172:deficiency / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015398:Signal Transduction; D016212:Transforming Growth Factor beta / Q000235:genetics / Q000378:metabolism
chemical_list: D029721:Drosophila Proteins; C588105:Heph protein, Drosophila; D018398:Homeodomain Proteins; D012333:RNA, Messenger; D012097:Repressor Proteins; C090409:SCW protein, Drosophila; D016212:Transforming Growth Factor beta; C085607:Zen protein, Drosophila; D038941:Polypyrimidine Tract-Binding Protein