The major aims of the Genomic Functional Analysis Section are to identify cis-and trans-acting functional elements in vertebrate genomes. Approaches to find these elements incorporate computational and experimental components including whole-genome comparative analyses, predictions based on machine learning techniques and experimental testing. Major focus areas include identifying bidirectional promoters in the human genome and elucidating their involvement in cancer, understanding the relationship between sequence-based regulatory features and expression patterns from alternative promoters, and developing high throughput assays to identify silencer elements in the human genome. All research avenues converge on the identification of transcription factor binding sites, which are the basic components of gene regulation. Approaches to identify proteins that bind to these regulatory sites are underway for all three of the above research areas. During the course of our work, novel motifs were implicated as silencers and new biological insights were revealed for the genomic structure of alternative promoters. A collaborative effort has been established to define regulatory networks that control gene expression in pathways involved in cancer. These studies will address the methodology of network modeling and identify new targets for cancer diagnostics and testing. These targets are being identified through computational approaches. Experimental follow-up is being done using bisulfite sequencing to assess aberrant methylation of promoter regions, in collaboration with the NIH Sequencing Facility. The analysis aims to study the methylation patterns of promoters in ovarian cancer compared to normal tissue.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Intramural Research (Z01)
Project #
1Z01HG200323-03
Application #
7594332
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
3
Fiscal Year
2007
Total Cost
$1,366,769
Indirect Cost
Name
National Human Genome Research Institute
Department
Type
DUNS #
City
State
Country
United States
Zip Code
Margolin, Gennady; Petrykowska, Hanna M; Jameel, Nader et al. (2016) Robust Detection of DNA Hypermethylation of ZNF154 as a Pan-Cancer Locus with in Silico Modeling for Blood-Based Diagnostic Development. J Mol Diagn 18:283-98
Lichtenberg, Jens; Jacox, Edwin; Welch, Joshua D et al. (2009) Word-based characterization of promoters involved in human DNA repair pathways. BMC Genomics 10 Suppl 1:S18
Piontkivska, Helen; Yang, Mary Q; Larkin, Denis M et al. (2009) Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts. BMC Genomics 10:189
Jacox, Edwin; Elnitski, Laura (2008) Finding Occurrences of Relevant Functional Elements in Genomic Signatures. Int J Comput Sci 2:599-606
Yang, Mary Qu; Elnitski, Laura L (2008) Prediction-based approaches to characterize bidirectional promoters in the mammalian genome. BMC Genomics 9 Suppl 1:S2
Petrykowska, Hanna M; Vockley, Christopher M; Elnitski, Laura (2008) Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus. Genome Res 18:1238-46
Yang, Mary Qu; Taylor, James; Elnitski, Laura (2008) Comparative analyses of bidirectional promoters in vertebrates. BMC Bioinformatics 9 Suppl 6:S9
Yang, Mary Qu; Elnitski, Laura L (2007) A computational study of bidirectional promoters in the human genome. Lect Notes Comput Sci 4463:361-371
Elnitski, Laura L; Shah, Prachi; Moreland, R Travis et al. (2007) The ENCODEdb portal: simplified access to ENCODE Consortium data. Genome Res 17:954-9
Yang, Mary Q; Koehly, Laura M; Elnitski, Laura L (2007) Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes. PLoS Comput Biol 3:e72

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