Reciprocal intronic and exonic histone modification regions in humans (original) (raw)
Berger, S.L. The complex language of chromatin regulation during transcription. Nature447, 407–412 (2007). ArticleCAS Google Scholar
Kouzarides, T. Chromatin modifications and their function. Cell128, 693–705 (2007). ArticleCAS Google Scholar
Loyola, A. & Almouzni, G. Marking histone H3 variants: how, when and why? Trends Biochem. Sci.32, 425–433 (2007). ArticleCAS Google Scholar
Lee, B.M. & Mahadevan, L.C. Stability of histone modifications across mammalian genomes: implications for 'epigenetic' marking. J. Cell. Biochem.108, 22–34 (2009). ArticleCAS Google Scholar
Talbert, P.B. & Henikoff, S. Histone variants–ancient wrap artists of the epigenome. Nat. Rev. Mol. Cell Biol.11, 264–275 (2010). ArticleCAS Google Scholar
Vermeulen, M. et al. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell131, 58–69 (2007). ArticleCAS Google Scholar
Perales, R. & Bentley, D. “Cotranscriptionality”: the transcription elongation complex as a nexus for nuclear transactions. Mol. Cell36, 178–191 (2009). ArticleCAS Google Scholar
Zhong, X.Y., Wang, P., Han, J., Rosenfeld, M.G. & Fu, X. SR proteins in vertical integration of gene expression from transcription to RNA processing to translation. Mol. Cell35, 1–10 (2009). ArticleCAS Google Scholar
Brès, V., Yoshida, T., Pickle, L. & Jones, K.A. SKIP interacts with c-Myc and Menin to promote HIV-1 Tat transactivation. Mol. Cell36, 75–87 (2009). Article Google Scholar
Li, B., Carey, M. & Workman, J.L. The role of chromatin during transcription. Cell128, 707–719 (2007). ArticleCAS Google Scholar
Yoh, S.M., Lucas, J.S. & Jones, K.A. The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation. Genes Dev.22, 3422–3434 (2008). ArticleCAS Google Scholar
Luco, R.F. et al. Regulation of alternative splicing by histone modifications. Science327, 996–1000 (2010). ArticleCAS Google Scholar
Andersson, R., Enroth, S., Rada-Iglesias, A., Wadelius, C. & Komorowski, J. Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res.19, 1732–1741 (2009). ArticleCAS Google Scholar
Hon, G., Wang, W. & Ren, B. Discovery and annotation of functional chromatin signatures in the human genome. PLOS Comput. Biol.5, e1000566 (2009). Article Google Scholar
Kolasinska-Zwierz, P. et al. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat. Genet.41, 376–381 (2009). ArticleCAS Google Scholar
Nahkuri, S., Taft, R.J. & Mattick, J.S. Nucleosomes are preferentially positioned at exons in somatic and sperm cells. Cell Cycle8, 3420–3424 (2009). ArticleCAS Google Scholar
Schwartz, S., Meshorer, E. & Ast, G. Chromatin organization marks exon-intron structure. Nat. Struct. Mol. Biol.16, 990–995 (2009). ArticleCAS Google Scholar
Spies, N., Nielsen, C.B., Padgett, R.A. & Burge, C.B. Biased chromatin signatures around polyadenylation sites and exons. Mol. Cell36, 245–254 (2009). ArticleCAS Google Scholar
Tilgner, H. et al. Nucleosome positioning as a determinant of exon recognition. Nat. Struct. Mol. Biol.16, 996–1001 (2009). ArticleCAS Google Scholar
Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell129, 823–837 (2007). ArticleCAS Google Scholar
Schones, D.E. et al. Dynamic regulation of nucleosome positioning in the human genome. Cell132, 887–898 (2008). ArticleCAS Google Scholar
Shema, E. et al. The histone H2B-specific ubiquitin ligase RNF20/hBRE1 acts as a putative tumor suppressor through selective regulation of gene expression. Genes Dev.22, 2664–2676 (2008). ArticleCAS Google Scholar
Wang, Z. et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet.40, 897–903 (2008). ArticleCAS Google Scholar
Jin, C. et al. H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nat. Genet.41, 941–945 (2009). ArticleCAS Google Scholar
McGhee, J.D. & Felsenfeld, G. Another potential artifact in the study of nucleosome phasing by chromatin digestion with micrococcal nuclease. Cell32, 1205–1215 (1983). ArticleCAS Google Scholar
Dohm, J.C., Lottaz, C., Borodina, T. & Himmelbauer, H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res.36, e105 (2008). Article Google Scholar
Jin, C. & Felsenfeld, G. Nucleosome stability mediated by histone variants H3.3 and H2A.Z. Genes Dev.21, 1519–1529 (2007). ArticleCAS Google Scholar
Wahl, M.C., Will, C.L. & Lührmann, R. The spliceosome: design principles of a dynamic RNP machine. Cell136, 701–718 (2009). ArticleCAS Google Scholar
Chen, M. & Manley, J.L. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat. Rev. Mol. Cell Biol.10, 741–754 (2009). ArticleCAS Google Scholar
Shi, J., Hu, Z., Pabon, K. & Scotto, K.W. Caffeine regulates alternative splicing in a subset of cancer-associated genes: a role for SC35. Mol. Cell. Biol.28, 883–895 (2008). ArticleCAS Google Scholar
Oberdoerffer, S. et al. Regulation of CD45 alternative splicing by heterogeneous ribonucleoprotein, hnRNPLL. Science321, 686–691 (2008). ArticleCAS Google Scholar
Topp, J.D., Jackson, J., Melton, A.A. & Lynch, K.W. A cell-based screen for splicing regulators identifies hnRNP LL as a distinct signal-induced repressor of CD45 variable exon 4. RNA14, 2038–2049 (2008). ArticleCAS Google Scholar
Wu, Z. et al. Memory T cell RNA rearrangement programmed by heterogeneous nuclear ribonucleoprotein hnRNPLL. Immunity29, 863–875 (2008). ArticleCAS Google Scholar
Edmunds, J.W., Mahadevan, L.C. & Clayton, A.L. Dynamic histone H3 methylation during gene induction: HYPB/Setd2 mediates all H3K36 trimethylation. EMBO J.27, 406–420 (2008). ArticleCAS Google Scholar
House, A.E. & Lynch, K.W. An exonic splicing silencer represses spliceosome assembly after ATP-dependent exon recognition. Nat. Struct. Mol. Biol.13, 937–944 (2006). ArticleCAS Google Scholar
Raisner, R.M. et al. Histone variant H2A.Z marks the 5′ ends of both active and inactive genes in euchromatin. Cell123, 233–248 (2005). ArticleCAS Google Scholar
Kouskouti, A. & Talianidis, I. Histone modifications defining active genes persist after transcriptional and mitotic inactivation. EMBO J.24, 347–357 (2005). ArticleCAS Google Scholar
Guenther, M.G., Levine, S.S., Boyer, L.A., Jaenisch, R. & Young, R.A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell130, 77–88 (2007). ArticleCAS Google Scholar
Latham, J.A. & Dent, S.Y.R. Cross-regulation of histone modifications. Nat. Struct. Mol. Biol.14, 1017–1024 (2007). ArticleCAS Google Scholar
Mohan, M. et al. Linking H3K79 trimethylation to Wnt signaling through a novel Dot1-containing complex (DotCom). Genes Dev.24, 574–589 (2010). ArticleCAS Google Scholar
Kim, J., Hake, S.B. & Roeder, R.G. The human homolog of yeast BRE1 functions as a transcriptional coactivator through direct activator interactions. Mol. Cell20, 759–770 (2005). ArticleCAS Google Scholar
Kim, J. et al. RAD6-Mediated transcription-coupled H2B ubiquitylation directly stimulates H3K4 methylation in human cells. Cell137, 459–471 (2009). ArticleCAS Google Scholar
Kim, T. & Buratowski, S. Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 5′ transcribed regions. Cell137, 259–272 (2009). ArticleCAS Google Scholar