Integrative analysis of the caenorhabditis elegans genome by the modENCODE project
- Gerstein, M.B.
- Lu, Z.J.
- Van Nostrand, E.L.
- Cheng, C.
- Arshinoff, B.I.
- Liu, T.
- Yip, K.Y.
- Robilotto, R.
- Rechtsteiner, A.
- Ikegami, K.
- Alves, P.
- Chateigner, A.
- Perry, M.
- Morris, M.
- Auerbach, R.K.
- Feng, X.
- Leng, J.
- Vielle, A.
- Niu, W.
- Rhrissorrakrai, K.
- Agarwal, A.
- Alexander, R.P.
- Barber, G.
- Brdlik, C.M.
- Brennan, J.
- Brouillet, J.J.
- Carr, A.
- Cheung, M.S.
- Clawson, H.
- Contrino, S.
- Dannenberg, L.O.
- Dernburg, A.F.
- Desai, A.
- Dick, L.
- Dose, A.C.
- Du, J.
- Egelhofer, T.
- Ercan, S.
- Euskirchen, G.
- Ewing, B.
- Feingold, E.A.
- Gassmann, R.
- Good, P.J.
- Green, P.
- Gullier, F.
- Gutwein, M.
- Guyer, M.S.
- Habegger, L.
- Han, T.
- Henikoff, J.G.
- Henz, S.R.
- Hinrichs, A.
- Holster, H.
- Hyman, T.
- Iniguez, A.L.
- Janette, J.
- Jensen, M.
- Kato, M.
- Kent, W.J.
- Kephart, E.
- Khivansara, V.
- Khurana, E.
- Kim, J.K.
- Kolasinska-Zwierz, P.
- Lai, E.C.
- Latorre, I.
- Leahey, A.
- Lewis, S.
- Lloyd, P.
- Lochovsky, L.
- Lowdon, R.F.
- Lubling, Y.
- Lyne, R.
- Maccoss, M.
- Mackowiak, S.D.
- Mangone, M.
- McKay, S.
- Mecenas, D.
- Merrihew, G.
- Miller, D.M.
- Muroyama, A.
- Murray, J.I.
- Ooi, S.L.
- Pham, H.
- Phippen, T.
- Preston, E.A.
- Rajewsky, N.
- Raetsch, G.
- Rosenbaum, H.
- Rozowsky, J.
- Rutherford, K.
- Ruzanov, P.
- Sarov, M.
- Sasidharan, R.
- Sboner, A.
- Scheid, P.
- Segal, E.
- Shin, H.
- Shou, C.
- Slack, F.J.
- Slightam, C.
- Smith, R.
- Spencer, W.C.
- Stinson, E.O.
- Taing, S.
- Takasaki, T.
- Vafeados, D.
- Voronina, K.
- Wang, G.
- Washington, N.L.
- Whittle, C.M.
- Wu, B.
- Yan, K.K.
- Zeller, G.
- Zha, Z.
- Zhong, M.
- Zhou, X.
- Ahringer, J.
- Strome, S.
- Gunsalus, K.C.
- Micklem, G.
- Liu, X.S.
- Reinke, V.
- Kim, S.K.
- Hillier, L.W.
- Henikoff, S.
- Piano, F.
- Snyder, M.
- Stein, L.
- Lieb, J.D.
- Waterston, R.H.
DOIAbstract
We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome ...
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