Transcriptional regulation is extremely important and highly complex in humans. In this project, we focus on the transcriptional regulation of alternative first exons in a tissue specific manner. First exons are often poorly characterized in eukaryotic genomes. Furthermore, alternative first exons can reside in genomic locations that are far apart from each other, leading to distinct usage of proximal promoters. There are numerous examples in the literature on widely separated alternative promoters that are responsible for tissue specific expression. The central hypothesis of this proposal is that alternative splicing of first exons is indicative of alternative proximal promoter usage, which will be an important factor in our identification of functional cis-element clusters that regulate differential tissue-specific gene expressions. ? ? The project tightly couples the computational expertise in Weng's laboratory with the extremely sensitive and quantitative gene expression technique recently developed by Ding and Cantor at Boston University. We will computationally characterize all genes in the 30 Mb of human sequence selected by the ENCODE project, identify ~ 100 genes with alternative first exon splicing, study the expression levels of splicing variants in major tissue types, and investigate the cis-elements in the promoters of these genes that could account for their transcriptional regulation. ? ? The project has four specific aims: 1) Computationally analyze the ENCODE sequences and select ~100 genes that exhibit both alternative first exon usage and tissue specific expression patterns; 2) Experimentally validate first exon usage for all genes identified in Aim 1 and measure their expression levels in ten major tissue types; 3) Computationally predict cis-element clusters in the alternative proximal promoters of the genes and select ~40 most confident predictions that may account for tissue-specific expressions; and 4) Experimentally test the ~40 computational predictions using transfection assays in five cell lines. ? ?

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
7R01HG003110-04
Application #
7613126
Study Section
Special Emphasis Panel (ZHG1-HGR-P (02))
Program Officer
Good, Peter J
Project Start
2003-09-30
Project End
2008-06-30
Budget Start
2008-01-01
Budget End
2008-06-30
Support Year
4
Fiscal Year
2005
Total Cost
$161,200
Indirect Cost
Name
University of Massachusetts Medical School Worcester
Department
Biochemistry
Type
Schools of Medicine
DUNS #
603847393
City
Worcester
State
MA
Country
United States
Zip Code
01655
Moqtaderi, Zarmik; Wang, Jie; Raha, Debasish et al. (2010) Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat Struct Mol Biol 17:635-40
Fu, Yutao; Sinha, Manisha; Peterson, Craig L et al. (2008) The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet 4:e1000138
(2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816
Peckham, Heather E; Thurman, Robert E; Fu, Yutao et al. (2007) Nucleosome positioning signals in genomic DNA. Genome Res 17:1170-7
Xi, Hualin; Shulha, Hennady P; Lin, Jane M et al. (2007) Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet 3:e136
Koch, Christoph M; Andrews, Robert M; Flicek, Paul et al. (2007) The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res 17:691-707
Xi, Hualin; Yu, Yong; Fu, Yutao et al. (2007) Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1. Genome Res 17:798-806
Lin, Jane M; Collins, Patrick J; Trinklein, Nathan D et al. (2007) Transcription factor binding and modified histones in human bidirectional promoters. Genome Res 17:818-27
Trinklein, Nathan D; Karaoz, Ulas; Wu, Jiaqian et al. (2007) Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res 17:720-31
Zhang, Zhengdong D; Paccanaro, Alberto; Fu, Yutao et al. (2007) Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Res 17:787-97

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