TY  - JOUR
A1  - Kimura, Kouichi
A1  - Wakamatsu, Ai
A1  - Suzuki, Yutaka
A1  - Ota, Toshio
A1  - Nishikawa, Tetsuo
A1  - Yamashita, Riu
A1  - Yamamoto, Jun-ichi
A1  - Sekine, Mitsuo
A1  - Tsuritani, Katsuki
A1  - Wakaguri, Hiroyuki
A1  - Ishii, Shizuko
A1  - Sugiyama, Tomoyasu
A1  - Saito, Kaoru
A1  - Isono, Yuko
A1  - Irie, Ryotaro
A1  - Kushida, Norihiro
A1  - Yoneyama, Takahiro
A1  - Otsuka, Rie
A1  - Kanda, Katsuhiro
A1  - Yokoi, Takahide
A1  - Kondo, Hiroshi
A1  - Wagatsuma, Masako
A1  - Murakawa, Katsuji
A1  - Ishida, Shinichi
A1  - Ishibashi, Tadashi
A1  - Takahashi-Fujii, Asako
A1  - Tanase, Tomoo
A1  - Nagai, Keiichi
A1  - Kikuchi, Hisashi
A1  - Nakai, Kenta
A1  - Isogai, Takao
A1  - Sugano, Sumio
T1  - Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes
Y1  - 2006/01/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 55 
EP  - 65 
DO  - 10.1101/gr.4039406 
VL  - 16 
IS  - 1 
UR  - http://genome.cshlp.org/content/16/1/55.abstract 
N2  - By analyzing 1,780,295 5′-end sequences of human full-length cDNAs derived from 164 kinds of oligo-cap cDNA libraries, we identified 269,774 independent positions of transcriptional start sites (TSSs) for 14,628 human RefSeq genes. These TSSs were clustered into 30,964 clusters that were separated from each other by more than 500 bp and thus are very likely to constitute mutually distinct alternative promoters. To our surprise, at least 7674 (52%) human RefSeq genes were subject to regulation by putative alternative promoters (PAPs). On average, there were 3.1 PAPs per gene, with the composition of one CpG-island-containing promoter per 2.6 CpG-less promoters. In 17% of the PAP-containing loci, tissue-specific use of the PAPs was observed. The richest tissue sources of the tissue-specific PAPs were testis and brain. It was also intriguing that the PAP-containing promoters were enriched in the genes encoding signal transduction-related proteins and were rarer in the genes encoding extracellular proteins, possibly reflecting the varied functional requirement for and the restricted expression of those categories of genes, respectively. The patterns of the first exons were highly diverse as well. On average, there were 7.7 different splicing types of first exons per locus partly produced by the PAPs, suggesting that a wide variety of transcripts can be achieved by this mechanism. Our findings suggest that use of alternate promoters and consequent alternative use of first exons should play a pivotal role in generating the complexity required for the highly elaborated molecular systems in humans. 
ER  -