Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome

@article{citeulike:1388724, abstract = {The regulation of transcriptional initiation in the human genome is a critical component of global gene regulation, but a complete catalog of human promoters currently does not exist. In order to identify regulatory regions, we developed four computational methods to integrate 129 sets of ENCODE-wide chromatin immunoprecipitation data. They collectively predicted 1393 regions. Roughly 47\% of the regions were unique to one method, as each method makes different assumptions about the data. Overall, predicted regions tend to localize to highly conserved, DNase I hypersensitive, and actively transcribed regions in the genome. Interestingly, a significant portion of the regions overlaps with annotated 3'-UTRs, suggesting that some of them might regulate anti-sense transcription. The majority of the predicted regions are >2 kb away from the 5'-ends of previously annotated human cDNAs and hence are novel. These novel regions may regulate unannotated transcripts or may represent new alternative transcription start sites of known genes. We tested 163 such regions for promoter activity in four cell lines using transient transfection assays, and 25\% of them showed transcriptional activity above background in at least one cell line. We also performed 5'-RACE experiments on 62 novel regions, and 76\% of the regions were associated with the 5'-ends of at least two RACE products. Our results suggest that there are at least 35\% more functional promoters in the human genome than currently annotated.}, author = {Trinklein, Nathan D. and Karaoz, Ulas and Wu, Jiaqian and Halees, Anason and Force and Collins, Patrick J. and Zheng, Deyou and Zhang, Zhengdong D. and Gerstein, Mark B. and Snyder, Michael and Myers, Richard M. and Weng, Zhiping }, citeulike-article-id = {1388724}, doi = {10.1101/gr.5716607}, journal = {Genome Res.}, keywords = {tez}, month = {June}, number = {6}, pages = {720--731}, posted-at = {2007-11-26 22:28:32}, priority = {2}, title = {Integrated analysis of experimental data sets reveals many novel promoters in 1\% of the human genome}, url = {http://dx.doi.org/10.1101/gr.5716607}, volume = {17}, year = {2007} }

TY - JOUR ID - citeulike:1388724 L3 - citeulike-article-id:1388724 TI - Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome JF - Genome Res. VL - 17 IS - 6 SP - 720 EP - 731 N2 - The regulation of transcriptional initiation in the human genome is a critical component of global gene regulation, but a complete catalog of human promoters currently does not exist. In order to identify regulatory regions, we developed four computational methods to integrate 129 sets of ENCODE-wide chromatin immunoprecipitation data. They collectively predicted 1393 regions. Roughly 47% of the regions were unique to one method, as each method makes different assumptions about the data. Overall, predicted regions tend to localize to highly conserved, DNase I hypersensitive, and actively transcribed regions in the genome. Interestingly, a significant portion of the regions overlaps with annotated 3'-UTRs, suggesting that some of them might regulate anti-sense transcription. The majority of the predicted regions are >2 kb away from the 5'-ends of previously annotated human cDNAs and hence are novel. These novel regions may regulate unannotated transcripts or may represent new alternative transcription start sites of known genes. We tested 163 such regions for promoter activity in four cell lines using transient transfection assays, and 25% of them showed transcriptional activity above background in at least one cell line. We also performed 5'-RACE experiments on 62 novel regions, and 76% of the regions were associated with the 5'-ends of at least two RACE products. Our results suggest that there are at least 35% more functional promoters in the human genome than currently annotated. KW - tez AU - Trinklein, Nathan AU - Karaoz, Ulas AU - Wu, Jiaqian AU - Halees, Anason AU - Force AU - Collins, Patrick AU - Zheng, Deyou AU - Zhang, Zhengdong AU - Gerstein, Mark AU - Snyder, Michael AU - Myers, Richard AU - Weng, Zhiping PY - 2007/06/01/ UR - http://dx.doi.org/10.1101/gr.5716607 ER -