31
Views
32
CrossRef citations to date
0
Altmetric
Article

Transcriptional Activity Affects the H3K4me3 Level and Distribution in the Coding Region

, &
Pages 2933-2946 | Received 11 Nov 2009, Accepted 05 Apr 2010, Published online: 20 Mar 2023

REFERENCES

  • Allis, C. D., S. L. Berger, J. Cote, S. Dent., T. Jenuwien, T. Kouzarides, L. Pillus, D. Reinberg, Y. Shi, R. Shiekhattar, A. Shilatifard, J. Workman, and Y. Zhang. 2007. New nomenclature for chromatin-modifying enzymes. Cell 131:633–636.
  • Barski, A., S. Cuddapah, K. Cui, T. Y. Roh, D. E. Schones, Z. Wang, G. Wei, I. Chepelev, and K. Zhao. 2007. High-resolution profiling of histone methylations in the human genome. Cell 129:823–837.
  • Bernstein, B. E., M. Kamal, K. Lindblad-Toh, S. Bekiranov, D. K. Bailey, D. J. Huebert, S. McMahon, E. K. Karlsson, E. J. Kulbokas III, T. R. Gingeras, S. L. Schreiber, and E. S. Lander. 2005. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120:169–181.
  • Daury, L., C. Chailleux, J. Bonvallet, and D. Trouche. 2006. Histone H3.3 deposition at E2F-regulated genes is linked to transcription. EMBO Rep. 7:66–71.
  • Han, L., I. G. Lin, and C. L. Hsieh. 2001. Protein binding protects sites on stable episomes and in the chromosome from de novo methylation. Mol. Cell. Biol. 21:3416–3424.
  • Heintzman, N. D., R. K. Stuart, G. Hon, Y. Fu, C. W. Ching, R. D. Hawkins, L. O. Barrera, S. Van Calcar, C. Qu, K. A. Ching, W. Wang, Z. Weng, R. D. Green, G. E. Crawford, and B. Ren. 2007. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39:311–318.
  • Hsieh, C. L. 1994. Dependence of transcriptional repression on CpG methylation density. Mol. Cell. Biol. 14:5487–5494.
  • Irvine, R. A., I. G. Lin, and C. L. Hsieh. 2002. DNA methylation has a local effect on transcription and histone acetylation. Mol. Cell. Biol. 22:6689–6696.
  • Kim, T. H., L. O. Barrera, M. Zheng, C. Qu, M. A. Singer, T. A. Richmond, Y. Wu, R. D. Green, and B. Ren. 2005. A high-resolution map of active promoters in the human genome. Nature 436:876–880.
  • Kimura, H., and P. R. Cook. 2001. Kinetics of core histones in living human cells: little exchange of H3 and H4 and some rapid exchange of H2B. J. Cell Biol. 153:1341–1353.
  • Lee, C. K., Y. Shibata, B. Rao, B. D. Strahl, and J. D. Lieb. 2004. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat. Genet. 36:900–905.
  • Li, B., M. Carey, and J. L. Workman. 2007. The role of chromatin during transcription. Cell 128:707–719.
  • Lin, I. G., and C. L. Hsieh. 2001. Chromosomal DNA demethylation specified by protein binding. EMBO Rep. 2:108–112.
  • Lin, I. G., T. J. Tomzynski, Q. Ou, and C. L. Hsieh. 2000. Modulation of DNA binding protein affinity directly affects target site demethylation. Mol. Cell. Biol. 20:2343–2349.
  • Lorincz, M. C., D. R. Dickerson, M. Schmitt, and M. Groudine. 2004. Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat. Struct. Mol. Biol. 11:1068–1075.
  • Miao, F., and R. Natarajan. 2005. Mapping global histone methylation patterns in the coding regions of human genes. Mol. Cell. Biol. 25:4650–4661.
  • Moran, J. V., S. E. Holmes, T. P. Naas, R. J. DeBerardinis, J. D. Boeke, and H. H. Kazazian, Jr. 1996. High frequency retrotransposition in cultured mammalian cells. Cell 87:917–927.
  • Okitsu, C. Y., and C. L. Hsieh. 2007. DNA methylation dictates histone H3K4 methylation. Mol. Cell. Biol. 27:2746–2757.
  • Ostrowski, M., H. Richard-Foy, R. Wolford, D. Berard, and G. Hager. 1983. Glucocorticoid regulation of transcription at an amplified, episomal promoter. Mol. Cell. Biol. 3:2045–2057.
  • Roh, T. Y., S. Cuddapah, K. Cui, and K. Zhao. 2006. The genomic landscape of histone modifications in human T cells. Proc. Natl. Acad. Sci. U. S. A. 103:15782–15787.
  • Roh, T. Y., S. Cuddapah, and K. Zhao. 2005. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev. 19:542–552.
  • Saunders, A., L. J. Core, and J. T. Lis. 2006. Breaking barriers to transcription elongation. Nat. Rev. Mol. Cell Biol. 7:557–567.
  • Schwabish, M. A., and K. Struhl. 2004. Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA polymerase II. Mol. Cell. Biol. 24:10111–10117.
  • Schwartz, B. E., and K. Ahmad. 2005. Transcriptional activation triggers deposition and removal of the histone variant H3.3. Genes Dev. 19:804–814.
  • Sims, R. J., III, S. Millhouse, C. F. Chen, B. A. Lewis, H. Erdjument-Bromage, P. Tempst, J. L. Manley, and D. Reinberg. 2007. Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing. Mol. Cell 28:665–676.
  • Suganuma, T., and J. L. Workman. 2008. Crosstalk among histone modifications. Cell 135:604–607.
  • Vermeulen, M., K. W. Mulder, S. Denissov, W. W. Pijnappel, F. M. van Schaik, R. A. Varier, M. P. Baltissen, H. G. Stunnenberg, M. Mann, and H. T. Timmers. 2007. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 131:58–69.
  • Wirbelauer, C., O. Bell, and D. Schubeler. 2005. Variant histone H3.3 is deposited at sites of nucleosomal displacement throughout transcribed genes while active histone modifications show a promoter-proximal bias. Genes Dev. 19:1761–1766.
  • Yamasaki-Ishizaki, Y., T. Kayashima, C. K. Mapendano, H. Soejima, T. Ohta, H. Masuzaki, A. Kinoshita, T. Urano, K. I. Yoshiura, N. Matsumoto, T. Ishimaru, T. Mukai, N. Niikawa, and T. Kishino. 2007. Role of DNA methylation and histone H3 lysine 27 methylation in tissue-specific imprinting of mouse Grb10. Mol. Cell. Biol. 27:732–742.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.