Our primary goal is to comprehensively identify the functional transcribed sequences, both protein coding and non-protein coding in the model organism Drosophila melanogaster. We will provide a description of the complete gene structures with transcription start sites, polyadenylation sites, and all detectable alternative transcripts. We plan to survey representative time points throughout development, a wide-variety of tissue types and well-characterized and novel cell lines. RNAs from these samples will be used for high-resolution expression profiling of the transcriptome using whole-genome tiling arrays, RNA ligase mediated Rapid Amplification of cDNA ends, RT-PCR and cDNA library construction. RT-PCR will be used to identify and isolate transcripts for rarely expressed genes of small to medium size. The cDNA libraries will be screened using a targeted approach to identify and isolate medium to large transcripts. Characterization of small RNAs (<100 bp) requires innovative strategies and we will use high-resolution (5bp) whole-genome tiling arrays and 454 sequencing. Concurrent with these studies will be a bioinformatic analysis to identify novel unannotated genes that for the first time utilizes algorithms that synthesize expression, comparative sequence and gene prediction. Further, we plan to characterize and annotate the extent of splice variation used to generate protein isoforms and identify the sequences necessary for regulated alternative splicing utilizing in vivo splicing reporter assays, RNAi and computational analysis. Finally, ncRNAs will be validated using in vivo tissue culture assays for expression and function. The scope of these studies is unprecedented and will provide the most comprehensive set of experimental evidence of transcription for any organism. As a public resource, these studies are a prerequisite for understanding normal growth and differentiation and that will aid in understanding these processes in other organisms, including humans. Drosophila models have been developed for Alzheimers, neurodegenerative diseases and cancer. In addition, genes first identified to play a role in Drosophila development are often components of conserved regulatory networks that play important roles during animal development and have been found, in humans, to contribute to the development of a variety of human cancers.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project--Cooperative Agreements (U01)
Project #
5U01HG004271-04
Application #
7799364
Study Section
Special Emphasis Panel (ZHG1-HGR-P (J1))
Program Officer
Feingold, Elise A
Project Start
2007-05-04
Project End
2013-03-31
Budget Start
2010-04-01
Budget End
2013-03-31
Support Year
4
Fiscal Year
2010
Total Cost
$3,529,155
Indirect Cost
Name
Lawrence Berkeley National Laboratory
Department
Genetics
Type
Organized Research Units
DUNS #
078576738
City
Berkeley
State
CA
Country
United States
Zip Code
94720
Stoiber, Marcus; Celniker, Susan; Cherbas, Lucy et al. (2016) Diverse Hormone Response Networks in 41 Independent Drosophila Cell Lines. G3 (Bethesda) 6:683-94
Stoiber, Marcus H; Olson, Sara; May, Gemma E et al. (2015) Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila. Genome Res 25:1692-702
Brooks, Angela N; Duff, Michael O; May, Gemma et al. (2015) Regulation of alternative splicing in Drosophila by 56 RNA binding proteins. Genome Res 25:1771-80
Xiong, Xiao-Peng; Vogler, Georg; Kurthkoti, Krishna et al. (2015) SmD1 Modulates the miRNA Pathway Independently of Its Pre-mRNA Splicing Function. PLoS Genet 11:e1005475
Brown, James B; Celniker, Susan E (2015) Lessons from modENCODE. Annu Rev Genomics Hum Genet 16:31-53
Lee, Hangnoh; McManus, C Joel; Cho, Dong-Yeon et al. (2014) DNA copy number evolution in Drosophila cell lines. Genome Biol 15:R70
Boley, Nathan; Stoiber, Marcus H; Booth, Benjamin W et al. (2014) Genome-guided transcript assembly by integrative analysis of RNA sequence data. Nat Biotechnol 32:341-6
Li, Jingyi Jessica; Huang, Haiyan; Bickel, Peter J et al. (2014) Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data. Genome Res 24:1086-101
Gerstein, Mark B; Rozowsky, Joel; Yan, Koon-Kiu et al. (2014) Comparative analysis of the transcriptome across distant species. Nature 512:445-8
Brown, James B; Boley, Nathan; Eisman, Robert et al. (2014) Diversity and dynamics of the Drosophila transcriptome. Nature 512:393-9

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