Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.

@article{citeulike:117784, abstract = {Using high-density oligonucleotide arrays representing essentially all nonrepetitive sequences on human chromosomes 21 and 22, we map the binding sites in vivo for three DNA binding transcription factors, Sp1, cMyc, and p53, in an unbiased manner. This mapping reveals an unexpectedly large number of transcription factor binding site (TFBS) regions, with a minimal estimate of 12,000 for Sp1, 25,000 for cMyc, and 1600 for p53 when extrapolated to the full genome. Only 22\% of these TFBS regions are located at the 5' termini of protein-coding genes while 36\% lie within or immediately 3' to well-characterized genes and are significantly correlated with noncoding RNAs. A significant number of these noncoding RNAs are regulated in response to retinoic acid, and overlapping pairs of protein-coding and noncoding RNAs are often coregulated. Thus, the human genome contains roughly comparable numbers of protein-coding and noncoding genes that are bound by common transcription factors and regulated by common environmental signals.}, address = {Affymetrix, 3380 Central Expressway, Santa Clara, CA 95051, USA.}, author = {Cawley, S. and Bekiranov, S. and Ng, H. H. and Kapranov, P. and Sekinger, E. A. and Kampa, D. and Piccolboni, A. and Sementchenko, V. and Cheng, J. and Williams, A. J. and Wheeler, R. and Wong, B. and Drenkow, J. and Yamanaka, M. and Patel, S. and Brubaker, S. and Tammana, H. and Helt, G. and Struhl, K. and Gingeras, T. R. }, citeulike-article-id = {117784}, issn = {0092-8674}, journal = {Cell}, keywords = {affymetrix, encode, microarray, noncoding, rna}, month = {February}, number = {4}, pages = {499--509}, posted-at = {2008-06-04 23:08:03}, priority = {2}, title = {Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/14980218}, volume = {116}, year = {2004} }

TY - JOUR ID - citeulike:117784 L3 - citeulike-article-id:117784 TI - Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. JF - Cell VL - 116 IS - 4 SP - 499 EP - 509 AD - Affymetrix, 3380 Central Expressway, Santa Clara, CA 95051, USA. SN - 0092-8674 N2 - Using high-density oligonucleotide arrays representing essentially all nonrepetitive sequences on human chromosomes 21 and 22, we map the binding sites in vivo for three DNA binding transcription factors, Sp1, cMyc, and p53, in an unbiased manner. This mapping reveals an unexpectedly large number of transcription factor binding site (TFBS) regions, with a minimal estimate of 12,000 for Sp1, 25,000 for cMyc, and 1600 for p53 when extrapolated to the full genome. Only 22% of these TFBS regions are located at the 5' termini of protein-coding genes while 36% lie within or immediately 3' to well-characterized genes and are significantly correlated with noncoding RNAs. A significant number of these noncoding RNAs are regulated in response to retinoic acid, and overlapping pairs of protein-coding and noncoding RNAs are often coregulated. Thus, the human genome contains roughly comparable numbers of protein-coding and noncoding genes that are bound by common transcription factors and regulated by common environmental signals. KW - affymetrix KW - encode KW - microarray KW - noncoding KW - rna AU - Cawley, S AU - Bekiranov, S AU - Ng, HH AU - Kapranov, P AU - Sekinger, EA AU - Kampa, D AU - Piccolboni, A AU - Sementchenko, V AU - Cheng, J AU - Williams, AJ AU - Wheeler, R AU - Wong, B AU - Drenkow, J AU - Yamanaka, M AU - Patel, S AU - Brubaker, S AU - Tammana, H AU - Helt, G AU - Struhl, K AU - Gingeras, TR PY - 2004/02/20/ UR - http://view.ncbi.nlm.nih.gov/pubmed/14980218 ER -