메뉴 건너뛰기




Volumn 108, Issue 1, 2009, Pages 22-34

Stability of histone modifications across mammalian genomes: Implications for 'epigenetic' marking

Author keywords

Chromatin in mammalian genomes; Histone modifications in mammals; Quantitation of ChIP assays

Indexed keywords

HISTONE; HISTONE H3;

EID: 69249154260     PISSN: 07302312     EISSN: 10974644     Source Type: Journal    
DOI: 10.1002/jcb.22250     Document Type: Review
Times cited : (69)

References (71)
  • 1
    • 0023660740 scopus 로고
    • Affinity chromatographic purification of nucleosomes containing transcriptionally active DNA sequences
    • Allegra P, Sterner R, Clayton DF, Allfrey VG. 1987. Affinity chromatographic purification of nucleosomes containing transcriptionally active DNA sequences. J Mol Biol 196:379-388.
    • (1987) J Mol Biol , vol.196 , pp. 379-388
    • Allegra, P.1    Sterner, R.2    Clayton, D.F.3    Allfrey, V.G.4
  • 2
    • 78651162036 scopus 로고
    • Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis
    • Allfrey VG, Faulkner R, Mirsky AE. 1964. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci USA 51:786-794.
    • (1964) Proc Natl Acad Sci USA , vol.51 , pp. 786-794
    • Allfrey, V.G.1    Faulkner, R.2    Mirsky, A.E.3
  • 4
    • 66149186985 scopus 로고    scopus 로고
    • Genomic location analysis by ChIP-Seq
    • Barski A, Zhao K. 2009. Genomic location analysis by ChIP-Seq. J Cell Biochem 107:11-18.
    • (2009) J Cell Biochem , vol.107 , pp. 11-18
    • Barski, A.1    Zhao, K.2
  • 9
    • 34249337761 scopus 로고    scopus 로고
    • Perceptions of epigenetics
    • Bird A. 2007. Perceptions of epigenetics. Nature 447:396-398.
    • (2007) Nature , vol.447 , pp. 396-398
    • Bird, A.1
  • 11
    • 1242316281 scopus 로고    scopus 로고
    • ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
    • Buck MJ, Lieb JD. 2004. ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83:349-360.
    • (2004) Genomics , vol.83 , pp. 349-360
    • Buck, M.J.1    Lieb, J.D.2
  • 12
    • 0023395729 scopus 로고
    • Rapid and reversible changes in nucleosome structure accompany the activation, repression, and superinduction of murine fibroblast protooncogenes c-fos and c-myc
    • Chen TA, Allfrey VG. 1987. Rapid and reversible changes in nucleosome structure accompany the activation, repression, and superinduction of murine fibroblast protooncogenes c-fos and c-myc. Proc Natl Acad Sci USA 84:5252-5256.
    • (1987) Proc Natl Acad Sci USA , vol.84 , pp. 5252-5256
    • Chen, T.A.1    Allfrey, V.G.2
  • 15
    • 33746457753 scopus 로고    scopus 로고
    • Enhanced histone acetylation and transcription: A dynamic perspective
    • Clayton AL, Hazzalin CA, Mahadevan LC. 2006. Enhanced histone acetylation and transcription: A dynamic perspective. Mol Cell 23:289-296.
    • (2006) Mol Cell , vol.23 , pp. 289-296
    • Clayton, A.L.1    Hazzalin, C.A.2    Mahadevan, L.C.3
  • 16
    • 57849109058 scopus 로고    scopus 로고
    • Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    • Core LJ, Waterfall JJ, Lis JT. 2008. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322:1845-1848.
    • (2008) Science , vol.322 , pp. 1845-1848
    • Core, L.J.1    Waterfall, J.J.2    Lis, J.T.3
  • 17
    • 58049191558 scopus 로고    scopus 로고
    • Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation
    • Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W, Zhao K. 2009. Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell 4:80-93.
    • (2009) Cell Stem Cell , vol.4 , pp. 80-93
    • Cui, K.1    Zang, C.2    Roh, T.Y.3    Schones, D.E.4    Childs, R.W.5    Peng, W.6    Zhao, K.7
  • 18
    • 33846972618 scopus 로고    scopus 로고
    • Differential histone modifications mark mouse imprinting control regions during spermatogenesis
    • Delaval K, Govin J, Cerqueira F, Rousseaux S, Khochbin S, Feil R. 2007. Differential histone modifications mark mouse imprinting control regions during spermatogenesis. EMBO J 26:720-729.
    • (2007) EMBO J , vol.26 , pp. 720-729
    • Delaval, K.1    Govin, J.2    Cerqueira, F.3    Rousseaux, S.4    Khochbin, S.5    Feil, R.6
  • 20
    • 21044450362 scopus 로고    scopus 로고
    • MAP kinase-mediated phosphorylation of distinct pools of histone H3 at S10 or S28 via mitogen- and stress-activated kinase 1/2
    • Dyson MH, Thomson S, Inagaki M, Goto H, Arthur SJ, Nightingale K, Iborra FJ, Mahadevan LC. 2005. MAP kinase-mediated phosphorylation of distinct pools of histone H3 at S10 or S28 via mitogen- and stress-activated kinase 1/2. J Cell Sci 118:2247-2259.
    • (2005) J Cell Sci , vol.118 , pp. 2247-2259
    • Dyson, M.H.1    Thomson, S.2    Inagaki, M.3    Goto, H.4    Arthur, S.J.5    Nightingale, K.6    Iborra, F.J.7    Mahadevan, L.C.8
  • 22
    • 38549139593 scopus 로고    scopus 로고
    • Dynamic histone H3 methylation during gene induction: HYPB/Setd2 mediates all H3K36 trimethylation
    • Edmunds JW, Mahadevan LC, Clayton AL. 2008. Dynamic histone H3 methylation during gene induction: HYPB/Setd2 mediates all H3K36 trimethylation. EMBO J 27:406-420.
    • (2008) EMBO J , vol.27 , pp. 406-420
    • Edmunds, J.W.1    Mahadevan, L.C.2    Clayton, A.L.3
  • 23
    • 33747453473 scopus 로고    scopus 로고
    • Insulators: Exploiting transcriptional and epigenetic mechanisms
    • Gaszner M, Felsenfeld G. 2006. Insulators: Exploiting transcriptional and epigenetic mechanisms. Nat Rev Genet 7:703-713.
    • (2006) Nat Rev Genet , vol.7 , pp. 703-713
    • Gaszner, M.1    Felsenfeld, G.2
  • 24
    • 54949110207 scopus 로고    scopus 로고
    • Heterogeneity of embryonic and adult stem cells
    • Graf T, Stadtfeld M. 2008. Heterogeneity of embryonic and adult stem cells. Cell Stem Cell 3:480-483.
    • (2008) Cell Stem Cell , vol.3 , pp. 480-483
    • Graf, T.1    Stadtfeld, M.2
  • 26
    • 34447098370 scopus 로고    scopus 로고
    • A chromatin landmark and transcription initiation at most promoters in human cells
    • Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA. 2007. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130:77-88.
    • (2007) Cell , vol.130 , pp. 77-88
    • Guenther, M.G.1    Levine, S.S.2    Boyer, L.A.3    Jaenisch, R.4    Young, R.A.5
  • 28
    • 0036358038 scopus 로고    scopus 로고
    • MAPK-regulated transcription: A continuously variable gene switch?
    • Hazzalin CA, Mahadevan LC. 2002. MAPK-regulated transcription: A continuously variable gene switch? Nat Rev Mol Cell Biol 3:30-40.
    • (2002) Nat Rev Mol Cell Biol , vol.3 , pp. 30-40
    • Hazzalin, C.A.1    Mahadevan, L.C.2
  • 29
    • 29144463657 scopus 로고    scopus 로고
    • Dynamic acetylation of all lysine 4-methylated histone H3 in the mouse nucleus: Analysis at c-fos and c-jun
    • Hazzalin CA, Mahadevan LC. 2005. Dynamic acetylation of all lysine 4-methylated histone H3 in the mouse nucleus: Analysis at c-fos and c-jun. PLoS Biol 3:e393.
    • (2005) PLoS Biol , vol.3
    • Hazzalin, C.A.1    Mahadevan, L.C.2
  • 30
    • 0024003456 scopus 로고
    • A direct link between core histone acetylation and transcriptionally active chromatin
    • Hebbes TR, Thorne AW, Crane-Robinson C. 1988. A direct link between core histone acetylation and transcriptionally active chromatin. EMBO J 7:1395-1402.
    • (1988) EMBO J , vol.7 , pp. 1395-1402
    • Hebbes, T.R.1    Thorne, A.W.2    Crane-Robinson, C.3
  • 34
    • 33846905189 scopus 로고    scopus 로고
    • Distinctive signatures of histone methylation in transcribed coding and noncoding human beta-globin sequences
    • Kim A, Kiefer CM, Dean A. 2007. Distinctive signatures of histone methylation in transcribed coding and noncoding human beta-globin sequences. Mol Cell Biol 27:1271-1279.
    • (2007) Mol Cell Biol , vol.27 , pp. 1271-1279
    • Kim, A.1    Kiefer, C.M.2    Dean, A.3
  • 35
    • 32344450824 scopus 로고    scopus 로고
    • Genomic DNA methylation: The mark and its mediators
    • Klose RJ, Bird AP. 2006. Genomic DNA methylation: The mark and its mediators. Trends Biochem Sci 31:89-97.
    • (2006) Trends Biochem Sci , vol.31 , pp. 89-97
    • Klose, R.J.1    Bird, A.P.2
  • 38
    • 33847076849 scopus 로고    scopus 로고
    • Chromatin modifications and their function
    • Kouzarides T. 2007. Chromatin modifications and their function. Cell 128:693-705.
    • (2007) Cell , vol.128 , pp. 693-705
    • Kouzarides, T.1
  • 39
    • 55449105221 scopus 로고    scopus 로고
    • Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE. 2008. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet 4:e1000242.
    • Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE. 2008. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet 4:e1000242.
  • 40
    • 0035282573 scopus 로고    scopus 로고
    • Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins
    • Lachner M, O'Carroll D, Rea S, Mechtler K, Jenuwein T. 2001. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410:116-120.
    • (2001) Nature , vol.410 , pp. 116-120
    • Lachner, M.1    O'Carroll, D.2    Rea, S.3    Mechtler, K.4    Jenuwein, T.5
  • 41
    • 2042437650 scopus 로고    scopus 로고
    • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, S
    • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
  • 42
    • 48949092575 scopus 로고    scopus 로고
    • A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3′ end RNA polyadenylation
    • Lian Z, Karpikov A, Lian J, Mahajan MC, Hartman S, Gerstein M, Snyder M, Weissman SM. 2008. A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3′ end RNA polyadenylation. Genome Res 18:1224-1237.
    • (2008) Genome Res , vol.18 , pp. 1224-1237
    • Lian, Z.1    Karpikov, A.2    Lian, J.3    Mahajan, M.C.4    Hartman, S.5    Gerstein, M.6    Snyder, M.7    Weissman, S.M.8
  • 43
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 Å resolution
    • Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389:251-260.
    • (1997) Nature , vol.389 , pp. 251-260
    • Luger, K.1    Mader, A.W.2    Richmond, R.K.3    Sargent, D.F.4    Richmond, T.J.5
  • 49
    • 14644406272 scopus 로고    scopus 로고
    • Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping
    • Roh TY, Cuddapah S, Zhao K. 2005. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev 19:542-552.
    • (2005) Genes Dev , vol.19 , pp. 542-552
    • Roh, T.Y.1    Cuddapah, S.2    Zhao, K.3
  • 50
    • 33750488431 scopus 로고    scopus 로고
    • The genomic landscape of histone modifications in human T cells
    • Roh TY, Cuddapah S, Cui K, Zhao K. 2006. The genomic landscape of histone modifications in human T cells. Proc Natl Acad Sci USA 103:15782-15787.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 15782-15787
    • Roh, T.Y.1    Cuddapah, S.2    Cui, K.3    Zhao, K.4
  • 51
    • 64849110610 scopus 로고    scopus 로고
    • Determination of enriched histone modifications in non-genic portions of the human genome
    • Rosenfeld JA, Wang Z, Schones DE, Zhao K, Desalle R, Zhang MQ. 2009. Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics 10:143.
    • (2009) BMC Genomics , vol.10 , pp. 143
    • Rosenfeld, J.A.1    Wang, Z.2    Schones, D.E.3    Zhao, K.4    Desalle, R.5    Zhang, M.Q.6
  • 52
  • 53
    • 0037074010 scopus 로고    scopus 로고
    • Signaling network model of chromatin
    • Schreiber SL, Bernstein BE. 2002. Signaling network model of chromatin. Cell 111:771-778.
    • (2002) Cell , vol.111 , pp. 771-778
    • Schreiber, S.L.1    Bernstein, B.E.2
  • 55
    • 36249027156 scopus 로고    scopus 로고
    • Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing
    • Sims RJ III, Millhouse S, Chen CF, Lewis BA, Erdjument-Bromage H, Tempst P, Manley JL, Reinberg D. 2007. Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing. Mol Cell 28:665-676.
    • (2007) Mol Cell , vol.28 , pp. 665-676
    • Sims III, R.J.1    Millhouse, S.2    Chen, C.F.3    Lewis, B.A.4    Erdjument-Bromage, H.5    Tempst, P.6    Manley, J.L.7    Reinberg, D.8
  • 57
    • 0034610814 scopus 로고    scopus 로고
    • The language of covalent histone modifications
    • Strahl BD, Allis CD. 2000. The language of covalent histone modifications. Nature 403:41-45.
    • (2000) Nature , vol.403 , pp. 41-45
    • Strahl, B.D.1    Allis, C.D.2
  • 58
    • 7544227521 scopus 로고    scopus 로고
    • Centromeric chromatin exhibits a histone modification pattern that is distinct from both euchromatin and heterochromatin
    • Sullivan BA, Karpen GH. 2004. Centromeric chromatin exhibits a histone modification pattern that is distinct from both euchromatin and heterochromatin. Nat Struct Mol Biol 11:1076-1083.
    • (2004) Nat Struct Mol Biol , vol.11 , pp. 1076-1083
    • Sullivan, B.A.1    Karpen, G.H.2
  • 59
    • 35848961668 scopus 로고    scopus 로고
    • How chromatin-binding modules interpret histone modifications: Lessons from professional pocket pickers
    • Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ. 2007. How chromatin-binding modules interpret histone modifications: Lessons from professional pocket pickers. Nat Struct Mol Biol 14:1025-1040.
    • (2007) Nat Struct Mol Biol , vol.14 , pp. 1025-1040
    • Taverna, S.D.1    Li, H.2    Ruthenburg, A.J.3    Allis, C.D.4    Patel, D.J.5
  • 60
    • 0033200205 scopus 로고    scopus 로고
    • The nucleosomal response associated with immediate-early gene induction is mediated via alternative MAP kinase cascades: MSK1 as a potential histone H3/HMG-14 kinase
    • Thomson S, Clayton AL, Hazzalin CA, Rose S, Barratt MJ, Mahadevan LC. 1999. The nucleosomal response associated with immediate-early gene induction is mediated via alternative MAP kinase cascades: MSK1 as a potential histone H3/HMG-14 kinase. EMBO J 18:4779-4793.
    • (1999) EMBO J , vol.18 , pp. 4779-4793
    • Thomson, S.1    Clayton, A.L.2    Hazzalin, C.A.3    Rose, S.4    Barratt, M.J.5    Mahadevan, L.C.6
  • 61
    • 0035694785 scopus 로고    scopus 로고
    • Independent dynamic regulation of histone phosphorylation and acetylation during immediate-early gene induction
    • Thomson S, Clayton AL, Mahadevan LC. 2001. Independent dynamic regulation of histone phosphorylation and acetylation during immediate-early gene induction. Mol Cell 8:1231-1241.
    • (2001) Mol Cell , vol.8 , pp. 1231-1241
    • Thomson, S.1    Clayton, A.L.2    Mahadevan, L.C.3
  • 62
    • 15044358494 scopus 로고    scopus 로고
    • Reading signals on the nucleosome with a new nomenclature for modified histones
    • Turner BM. 2005. Reading signals on the nucleosome with a new nomenclature for modified histones. Nat Struct Mol Biol 12:110-112.
    • (2005) Nat Struct Mol Biol , vol.12 , pp. 110-112
    • Turner, B.M.1
  • 63
    • 23044431656 scopus 로고    scopus 로고
    • Histone H3 lysine 9 methylation and HP1gamma are associated with transcription elongation through mammalian chromatin
    • Vakoc CR, Mandat SA, Olenchock BA, Blobel GA. 2005. Histone H3 lysine 9 methylation and HP1gamma are associated with transcription elongation through mammalian chromatin. Mol Cell 19:381-391.
    • (2005) Mol Cell , vol.19 , pp. 381-391
    • Vakoc, C.R.1    Mandat, S.A.2    Olenchock, B.A.3    Blobel, G.A.4
  • 64
    • 33845451555 scopus 로고    scopus 로고
    • Profile of histone lysine methylation across transcribed mammalian chromatin
    • Vakoc CR, Sachdeva MM, Wang H, Blobel GA. 2006. Profile of histone lysine methylation across transcribed mammalian chromatin. Mol Cell Biol 26:9185-9195.
    • (2006) Mol Cell Biol , vol.26 , pp. 9185-9195
    • Vakoc, C.R.1    Sachdeva, M.M.2    Wang, H.3    Blobel, G.A.4
  • 67
    • 59149083658 scopus 로고    scopus 로고
    • Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells
    • Wen B, Wu H, Shinkai Y, Irizarry RA, Feinberg AP. 2009. Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat Genet 41:246-250.
    • (2009) Nat Genet , vol.41 , pp. 246-250
    • Wen, B.1    Wu, H.2    Shinkai, Y.3    Irizarry, R.A.4    Feinberg, A.P.5
  • 69
    • 58049206591 scopus 로고    scopus 로고
    • The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation
    • Yoh SM, Lucas JS, Jones KA. 2008. The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation. Genes Dev 22:3422-3434.
    • (2008) Genes Dev , vol.22 , pp. 3422-3434
    • Yoh, S.M.1    Lucas, J.S.2    Jones, K.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.