Gene Regulation in the Postgenomic Era: Technology Takes the Wheel

Molecular Cell

Volumn 28, Issue 5, 2007, Pages 708-714

  Dunn, Rebecca K ^a,b   Kingston, Robert E ^a,b  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H3; HISTONE H4; RNA POLYMERASE; RNA POLYMERASE II;

ARTICLE; CHROMATIN STRUCTURE; CRYOELECTRON MICROSCOPY; CRYSTAL STRUCTURE; DNA HELIX; DNA MICROARRAY; ESCHERICHIA COLI; EUKARYOTE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOMICS; NONHUMAN; PROMOTER REGION; REGULATORY MECHANISM; TECHNOLOGY; TRANSCRIPTION REGULATION;

EUKARYOTA;

EID: 36749089518     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2007.11.022     Document Type: Note

References (34)

1. Bannister A.J., Zegerman P., Partridge J.F., Miska E.A., Thomas J.O., Allshire R.C., and Kouzarides T. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410 (2001) 120-124
2. Bernstein B.E., Mikkelsen T.S., Xie X., Kamal M., Huebert D.J., Cuff J., Fry B., Meissner A., Wernig M., Plath K., et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125 (2006) 315-326
3. Boyer L.A., Lee T.I., Cole M.F., Johnstone S.E., Levine S.S., Zucker J.P., Guenther M.G., Kumar R.M., Murray H.L., Jenner R.G., et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122 (2005) 947-956
4. Boyer L.A., Plath K., Zeitlinger J., Brambrink T., Medeiros L.A., Lee T.I., Levine S.S., Wernig M., Tajonar A., Ray M.K., et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441 (2006) 349-353
5. Collins S.R., Miller K.M., Maas N.L., Roguev A., Fillingham J., Chu C.S., Schuldiner M., Gebbia M., Recht J., Shales M., et al. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446 (2007) 806-810
6. Daniel J.A., and Grant P.A. Multi-tasking on chromatin with the SAGA coactivator complexes. Mutat. Res. 618 (2007) 135-148
7. Davis J.A., Takagi Y., Kornberg R.D., and Asturias F.A. Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction. Mol. Cell 10 (2002) 409-415
8. Dostie J., Richmond T.A., Arnaout R.A., Selzer R.R., Lee W.L., Honan T.A., Rubio E.D., Krumm A., Lamb J., Nusbaum C., et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 16 (2006) 1299-1309
9. Grewal S.I., and Moazed D. Heterochromatin and epigenetic control of gene expression. Science 301 (2003) 798-802
10. Guenther M.G., Levine S.S., Boyer L.A., Jaenisch R., and Young R.A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130 (2007) 77-88
11. Hansen S.K., Takada S., Jacobson R.H., Lis J.T., and Tjian R. Transcription properties of a cell type-specific TATA-binding protein, TRF. Cell 91 (1997) 71-83
12. Ho Y., Gruhler A., Heilbut A., Bader G.D., Moore L., Adams S.L., Millar A., Taylor P., Bennett K., Boutilier K., et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415 (2002) 180-183
13. Jacobs S.A., and Khorasanizadeh S. Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science 295 (2002) 2080-2083
14. Jacobson R.H., Ladurner A.G., King D.S., and Tjian R. Structure and function of a human TAFII250 double bromodomain module. Science 288 (2000) 1422-1425
15. Kornberg R.D. The molecular basis of eukaryotic transcription. Proc. Natl. Acad. Sci. USA 104 (2007) 12955-12961
16. Krogan N.J., Kim M., Ahn S.H., Zhong G., Kobor M.S., Cagney G., Emili A., Shilatifard A., Buratowski S., and Greenblatt J.F. RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol. Cell. Biol. 22 (2002) 6979-6992
17. Lachner M., O'Carroll D., Rea S., Mechtler K., and Jenuwein T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410 (2001) 116-120
18. Lee T.I., Jenner R.G., Boyer L.A., Guenther M.G., Levine S.S., Kumar R.M., Chevalier B., Johnstone S.E., Cole M.F., Isono K., et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125 (2006) 301-313
19. Luger K., Mader A.W., Richmond R.K., Sargent D.F., and Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389 (1997) 251-260
20. McDonald M.J., and Rosbash M. Microarray analysis and organization of circadian gene expression in Drosophila. Cell 107 (2001) 567-578
21. Mikkelsen T.S., Ku M., Jaffe D.B., Issac B., Lieberman E., Giannoukos G., Alvarez P., Brockman W., Kim T.K., Koche R.P., et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448 (2007) 553-560
22. Raisner R.M., Hartley P.D., Meneghini M.D., Bao M.Z., Liu C.L., Schreiber S.L., Rando O.J., and Madhani H.D. Histone variant H2A.Z marks the 5′ ends of both active and inactive genes in euchromatin. Cell 123 (2005) 233-248
23. Ren B., Robert F., Wyrick J.J., Aparicio O., Jennings E.G., Simon I., Zeitlinger J., Schreiber J., Hannett N., Kanin E., et al. Genome-wide location and function of DNA binding proteins. Science 290 (2000) 2306-2309
24. Rougvie A.E., and Lis J.T. The RNA polymerase II molecule at the 5′ end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged. Cell 54 (1988) 795-804
25. Schena M., Shalon D., Davis R.W., and Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270 (1995) 467-470
26. Shi Y., Lan F., Matson C., Mulligan P., Whetstine J.R., Cole P.A., and Casero R.A. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119 (2004) 941-953
27. Sparmann A., and van Lohuizen M. Polycomb silencers control cell fate, development and cancer. Nat. Rev. Cancer 6 (2006) 846-856
28. Strahl B.D., and Allis C.D. The language of covalent histone modifications. Nature 403 (2000) 41-45
29. Tsukada Y.I., Fang J., Erdjument-Bromage H., Warren M.E., Borchers C.H., Tempst P., and Zhang Y. Histone demethylation by a family of JmjC domain-containing proteins. Nature 439 (2005) 811-816
30. Verdel A., Jia S., Gerber S., Sugiyama T., Gygi S., Grewal S.I., and Moazed D. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303 (2004) 672-676
31. Volpe T.A., Kidner C., Hall I.M., Teng G., Grewal S.I., and Martienssen R.A. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297 (2002) 1833-1837
32. Volpe T., Schramke V., Hamilton G.L., White S.A., Teng G., Martienssen R.A., and Allshire R.C. RNA interference is required for normal centromere function in fission yeast. Chromosome Res. 11 (2003) 137-146
33. Weinmann A.S., Yan P.S., Oberley M.J., Huang T.H., and Farnham P.J. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev. 16 (2002) 235-244
34. Yuan G.C., Liu Y.J., Dion M.F., Slack M.D., Wu L.F., Altschuler S.J., and Rando O.J. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309 (2005) 626-630