The goal of this proposal is to obtain a coordinated and comprehensive picture of the transcribed regions and factors that regulate or affect transcriptional activity in the genomic regions selected as part of the ENCODE project. This proposal builds on our experience in genomic analysis using chromosome 22 tiling arrays. We will first prepare and test several types of genomic DNA arrays that tile the unique sequences of the ENCODE regions. We will then identify transcription coding segments in these regions using several RNA sources. In conjunction with the coding region identification, we will map the binding sites for at least 150 sequence-specific or general transcription factors, chromatin modifying or remodeling factors, and transcription related histone modifications using chromatin immunoprecipiation and probing of the arrays (ChiP chip). In parallel, we will explore the status of DNA methylation through this region. Our results will be made publicly accessible in a comprehensive web database and we will interrelate our genomic annotations with those determined by other groups. We expect these pilot studies of the ENCODE region to be scaleable to the analysis of the entire human genome.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project--Cooperative Agreements (U01)
Project #
5U01HG003156-03
Application #
6942685
Study Section
Special Emphasis Panel (ZHG1-HGR-P (02))
Program Officer
Feingold, Elise A
Project Start
2003-09-30
Project End
2008-07-31
Budget Start
2005-08-01
Budget End
2008-07-31
Support Year
3
Fiscal Year
2005
Total Cost
$1,589,760
Indirect Cost
Name
Yale University
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
043207562
City
New Haven
State
CT
Country
United States
Zip Code
06520
Xie, Dan; Boyle, Alan P; Wu, Linfeng et al. (2013) Dynamic trans-acting factor colocalization in human cells. Cell 155:713-24
(2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816
Zheng, Deyou; Frankish, Adam; Baertsch, Robert et al. (2007) Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res 17:839-51
Gerstein, Mark B; Bruce, Can; Rozowsky, Joel S et al. (2007) What is a gene, post-ENCODE? History and updated definition. Genome Res 17:669-81
Washietl, Stefan; Pedersen, Jakob S; Korbel, Jan O et al. (2007) Structured RNAs in the ENCODE selected regions of the human genome. Genome Res 17:852-64
Euskirchen, Ghia M; Rozowsky, Joel S; Wei, Chia-Lin et al. (2007) Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res 17:898-909
Zheng, Deyou; Gerstein, Mark B (2007) The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they? Trends Genet 23:219-24
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
Emanuelsson, Olof; Nagalakshmi, Ugrappa; Zheng, Deyou et al. (2007) Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. Genome Res 17:886-97

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