Browsing by Subject "Transcription Initiation Site"

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    ItemOpen Access
    Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
    (Nature, 2002-12-05) Okazaki, Y; Furuno, M; Kasukawa, T; Adachi, J; Bono, H; Kondo, S; Nikaido, I; Osato, N; Osato, N; Saito, R; Suzuki, H; Yamanaka, I; Kiyosawa, H; Yagi, K; Tomaru, Y; Hasegawa, Y; Nogami, A; Schönbach, C; Gojobori, T; Baldarelli, R; Hill, DP; Bult, C; Hume, DA; Hume, DA; Quackenbush, J; Schriml, LM; Kanapin, A; Matsuda, H; Batalov, S; Beisel, KW; Blake, JA; Bradt, D; Brusic, V; Chothia, C; Corbani, LE; Cousins, S; Dalla, E; Dragani, TA; Fletcher, CF; Forrest, A; Frazer, KS; Gaasterland, T; Gariboldi, M; Gissi, C; Godzik, A; Gough, J; Grimmond, S; Gustincich, S; Hirokawa, N; Jackson, IJ; Jarvis, ED; Kanai, A; Kawaji, H; Kawasawa, Y; Kedzierski, RM; King, BL; Konagaya, A; Kurochkin, IV; Lee, Y; Lenhard, B; Lyons, PA; Maglott, DR; Maltais, L; Marchionni, L; McKenzie, L; Miki, H; Nagashima, T; Numata, K; Okido, T; Pavan, WJ; Pertea, G; Pesole, G; Petrovsky, N; Pillai, R; Pontius, JU; Qi, D; Ramachandran, S; Ravasi, T; Reed, JC; Reed, DJ; Reid, J; Ring, BZ; Ringwald, M; Sandelin, A; Schneider, C; Semple, CAM; Setou, M; Shimada, K; Sultana, R; Takenaka, Y; Taylor, MS; Teasdale, RD; Tomita, M; Verardo, R; Wagner, L; Wahlestedt, C; Wang, Y; Watanabe, Y; Wells, C; Wilming, LG; Wynshaw-Boris, A; Yanagisawa, M; Yang, I; Yang, L; Yuan, Z; Zavolan, M; Zhu, Y; Zimmer, A; Carninci, P; Hayatsu, N; Hirozane-Kishikawa, T; Konno, H; Nakamura, M; Sakazume, N; Sato, K; Shiraki, T; Waki, K; Kawai, J; Aizawa, K; Arakawa, T; Fukuda, S; Hara, A; Hashizume, W; Imotani, K; Ishii, Y; Itoh, M; Kagawa, I; Miyazaki, A; Sakai, K; Sasaki, D; Shibata, K; Shinagawa, A; Yasunishi, A; Yoshino, M; Waterston, R; Lander, ES; Rogers, J; Birney, E; Hayashizaki, Y; FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team
    Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.
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    ItemOpen Access
    Pol II docking and pausing at growth and stress genes in C. elegans.
    (Cell Rep, 2014-02-13) Maxwell, Colin S; Kruesi, William S; Core, Leighton J; Kurhanewicz, Nicole; Waters, Colin T; Lewarch, Caitlin L; Antoshechkin, Igor; Lis, John T; Meyer, Barbara J; Baugh, L Ryan
    Fluctuations in nutrient availability profoundly impact gene expression. Previous work revealed postrecruitment regulation of RNA polymerase II (Pol II) during starvation and recovery in Caenorhabditis elegans, suggesting that promoter-proximal pausing promotes rapid response to feeding. To test this hypothesis, we measured Pol II elongation genome wide by two complementary approaches and analyzed elongation in conjunction with Pol II binding and expression. We confirmed bona fide pausing during starvation and also discovered Pol II docking. Pausing occurs at active stress-response genes that become downregulated in response to feeding. In contrast, "docked" Pol II accumulates without initiating upstream of inactive growth genes that become rapidly upregulated upon feeding. Beyond differences in function and expression, these two sets of genes have different core promoter motifs, suggesting alternative transcriptional machinery. Our work suggests that growth and stress genes are both regulated postrecruitment during starvation but at initiation and elongation, respectively, coordinating gene expression with nutrient availability.
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    ItemOpen Access
    Promoting developmental transcription.
    (Development, 2010-01) Ohler, Uwe; Wassarman, David A
    Animal growth and development depend on the precise control of gene expression at the level of transcription. A central role in the regulation of developmental transcription is attributed to transcription factors that bind DNA enhancer elements, which are often located far from gene transcription start sites. Here, we review recent studies that have uncovered significant regulatory functions in developmental transcription for the TFIID basal transcription factors and for the DNA core promoter elements that are located close to transcription start sites.