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Volumn 6, Issue , 2005, Pages

Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes

Author keywords

[No Author keywords available]

Indexed keywords

CHROMATIN ASSEMBLY; COMPARATIVE ANALYSIS; CONTROL OF GENE EXPRESSION; HOUSEKEEPING GENE; NUCLEOSOME FORMATION; REGULATORY MECHANISM; REGULATORY REGIONS; TISSUE-SPECIFIC GENES;

EID: 25444499171     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-126     Document Type: Article
Times cited : (49)

References (42)
  • 1
    • 0034667792 scopus 로고    scopus 로고
    • Orchestrated response: A symphony of transcription factors for gene control
    • Lemon B, Tjian R: Orchestrated response: a symphony of transcription factors for gene control. Genes Dev 2000, 14:2551-2569.
    • (2000) Genes Dev. , vol.14 , pp. 2551-2569
    • Lemon, B.1    Tjian, R.2
  • 2
  • 3
    • 0034103927 scopus 로고    scopus 로고
    • Transcriptional augmentation: Modulation of gene expression by scaffold/matrix-attached regions (S/MAR elements)
    • Bode J, Benham C, Knopp A, Mielke C: Transcriptional augmentation: modulation of gene expression by scaffold/matrix-attached regions (S/MAR elements). Crit Rev Eukaryot Gene Expr 2000, 10:73-90.
    • (2000) Crit. Rev. Eukaryot. Gene Expr. , vol.10 , pp. 73-90
    • Bode, J.1    Benham, C.2    Knopp, A.3    Mielke, C.4
  • 4
    • 0042528729 scopus 로고    scopus 로고
    • Heterochromatin and epigenetic control of gene expression
    • Grewal SI, Moazed D: Heterochromatin and epigenetic control of gene expression. Science 2003, 301:798-802.
    • (2003) Science , vol.301 , pp. 798-802
    • Grewal, S.I.1    Moazed, D.2
  • 5
    • 0038094501 scopus 로고    scopus 로고
    • Nucleosomes unfold completely at a transcriptionally active promoter
    • Boeger H, Griesenbeck J, Strattan JS, Kornberg RD: Nucleosomes unfold completely at a transcriptionally active promoter. Mol Cell 2003, 11:1587-1598.
    • (2003) Mol. Cell. , vol.11 , pp. 1587-1598
    • Boeger, H.1    Griesenbeck, J.2    Strattan, J.S.3    Kornberg, R.D.4
  • 6
    • 0028445339 scopus 로고
    • Transcriptional activation. Switched-on chromatin
    • Wolffe AP: Transcriptional activation. Switched-on chromatin. Curr Biol 1994, 4:525-528.
    • (1994) Curr. Biol. , vol.4 , pp. 525-528
    • Wolffe, A.P.1
  • 7
    • 0035895841 scopus 로고    scopus 로고
    • Comparative study and prediction of DNA fragments associated with various elements of the nuclear matrix
    • Glazko GV, Rogozin IB, Glazkov MV: Comparative study and prediction of DNA fragments associated with various elements of the nuclear matrix. Biochim Biophys Acta 2001, 1517:351-364.
    • (2001) Biochim. Biophys. Acta , vol.1517 , pp. 351-364
    • Glazko, G.V.1    Rogozin, I.B.2    Glazkov, M.V.3
  • 8
    • 0037372327 scopus 로고    scopus 로고
    • A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions
    • Glazko GV, Koonin EV, Rogozin IB, Shabalina SA: A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions. Trends Genet 2003, 19:119-124.
    • (2003) Trends Genet. , vol.19 , pp. 119-124
    • Glazko, G.V.1    Koonin, E.V.2    Rogozin, I.B.3    Shabalina, S.A.4
  • 9
    • 0141854009 scopus 로고    scopus 로고
    • The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes
    • Versteeg R, van Schaik BD, van Batenburg MF, Roos M, Monajemi R, Caron H, Bussemaker HJ, van Kampen AH: The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. Genome Res 2003, 13:1998-2004.
    • (2003) Genome Res. , vol.13 , pp. 1998-2004
    • Versteeg, R.1    van Schaik, B.D.2    van Batenburg, M.F.3    Roos, M.4    Monajemi, R.5    Caron, H.6    Bussemaker, H.J.7    van Kampen, A.H.8
  • 10
    • 0036613754 scopus 로고    scopus 로고
    • Clustering of housekeeping genes provides a unified model of gene order in the human genome
    • Lercher MJ, Urrutia AO, Hurst LD: Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet 2002, 31:180-183.
    • (2002) Nat. Genet. , vol.31 , pp. 180-183
    • Lercher, M.J.1    Urrutia, A.O.2    Hurst, L.D.3
  • 11
    • 0042880630 scopus 로고    scopus 로고
    • Spatial organisation of gene expression: The active chromatin hub
    • de Laat W, Grosveld F: Spatial organisation of gene expression: the active chromatin hub. Chromosome Res 2003, 11:447-459.
    • (2003) Chromosome Res. , vol.11 , pp. 447-459
    • de Laat, W.1    Grosveld, F.2
  • 12
    • 0042978644 scopus 로고    scopus 로고
    • Visualization of chromatin domains created by the gypsy insulator of Drosophila
    • Byrd K, Corces VG: Visualization of chromatin domains created by the gypsy insulator of Drosophila. J Cell Biol 2003, 162:565-574.
    • (2003) J. Cell Biol. , vol.162 , pp. 565-574
    • Byrd, K.1    Corces, V.G.2
  • 13
    • 0031915974 scopus 로고    scopus 로고
    • A nuclear matrix/scaffold attachment region co-localizes with the gypsy retrotransposon insulator sequence
    • Nabirochkin S, Ossokina M, Heidmann T: A nuclear matrix/scaffold attachment region co-localizes with the gypsy retrotransposon insulator sequence. J Biol Chem 1998, 273:2473-2479.
    • (1998) J. Biol. Chem. , vol.273 , pp. 2473-2479
    • Nabirochkin, S.1    Ossokina, M.2    Heidmann, T.3
  • 14
  • 15
    • 0028138645 scopus 로고
    • Dissection of the locus control function located on the chicken lysozyme gene domain in transgenic mice
    • Bonifer C, Yannoutsos N, Kruger G, Grosveld F, Sippel AE: Dissection of the locus control function located on the chicken lysozyme gene domain in transgenic mice. Nucleic Acids Res 1994, 22:4202-4210.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4202-4210
    • Bonifer, C.1    Yannoutsos, N.2    Kruger, G.3    Grosveld, F.4    Sippel, A.E.5
  • 16
    • 2942537834 scopus 로고    scopus 로고
    • The 5′-HS4 chicken beta-globin insulator is a CTCF-dependent nuclear matrix-associated element
    • Yusufzai TM, Felsenfeld G: The 5′-HS4 chicken beta-globin insulator is a CTCF-dependent nuclear matrix-associated element. Proc Natl Acad Sci U S A 2004, 101:8620-8624.
    • (2004) Proc. Natl. Acad. Sci. U. S. A. , vol.101 , pp. 8620-8624
    • Yusufzai, T.M.1    Felsenfeld, G.2
  • 17
    • 0842324785 scopus 로고    scopus 로고
    • The nucleosome: From genomic organisation to genomic regulation
    • Khorasanizadeh S: The nucleosome: from genomic organisation to genomic regulation. Cell 2004, 116:259-272.
    • (2004) Cell , vol.116 , pp. 259-272
    • Khorasanizadeh, S.1
  • 18
    • 0034310723 scopus 로고    scopus 로고
    • Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo
    • Suter B, Schnappauf G, Thoma F: Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo. Nucleic Acids Res 2000, 28:4083-4089.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 4083-4089
    • Suter, B.1    Schnappauf, G.2    Thoma, F.3
  • 19
    • 0033588084 scopus 로고    scopus 로고
    • Functional analysis of a homopolymeric (dA-dT) element that provides nucleosomal access to yeast and mammalian transcription factors
    • Koch KA, Thiele DJ: Functional analysis of a homopolymeric (dA-dT) element that provides nucleosomal access to yeast and mammalian transcription factors. J Biol Chem 1999, 274:23752-23760.
    • (1999) J. Biol. Chem. , vol.274 , pp. 23752-23760
    • Koch, K.A.1    Thiele, D.J.2
  • 20
    • 0029664913 scopus 로고    scopus 로고
    • The [(G/C)3NN]n motif: A common DNA repeat that excludes nucleosomes
    • Wang YH, Griffith JD: The [(G/C)3NN]n motif: a common DNA repeat that excludes nucleosomes. Proc Natl Acad Sci U S A 1996, 93:8863-8867.
    • (1996) Proc. Natl. Acad. Sci. U. S. A. , vol.93 , pp. 8863-8867
    • Wang, Y.H.1    Griffith, J.D.2
  • 21
    • 0029026719 scopus 로고
    • Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure
    • Iyer V, Struhl K: Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. Embo J 1995, 14:2570-2579.
    • (1995) Embo J. , vol.14 , pp. 2570-2579
    • Iyer, V.1    Struhl, K.2
  • 22
    • 0032694088 scopus 로고    scopus 로고
    • Control of meiotic recombination and gene expression in yeast by a simple repetitive DNA sequence that excludes nucleosomes
    • Kirkpatrick DT, Wang YH, Dominska M, Griffith JD, Petes TD: Control of meiotic recombination and gene expression in yeast by a simple repetitive DNA sequence that excludes nucleosomes. Mol Cell Biol 1999, 19:7661-7671.
    • (1999) Mol. Cell Biol. , vol.19 , pp. 7661-7671
    • Kirkpatrick, D.T.1    Wang, Y.H.2    Dominska, M.3    Griffith, J.D.4    Petes, T.D.5
  • 23
    • 2342437120 scopus 로고    scopus 로고
    • Alu repeat analysis in the complete human genome: Trends and variations with respect to genomic composition
    • Grover D, Mukerji M, Bhatnagar P, Kannan K, Brahmachari SK: Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition. Bioinformatics 2004, 20:813-817.
    • (2004) Bioinformatics , vol.20 , pp. 813-817
    • Grover, D.1    Mukerji, M.2    Bhatnagar, P.3    Kannan, K.4    Brahmachari, S.K.5
  • 24
    • 0037301560 scopus 로고    scopus 로고
    • Origin of a substantial fraction of human regulatory sequences from transposable elements
    • Jordan IK, Rogozin IB, Glazko GV, Koonin EV: Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet 2003, 19:68-72.
    • (2003) Trends Genet. , vol.19 , pp. 68-72
    • Jordan, I.K.1    Rogozin, I.B.2    Glazko, G.V.3    Koonin, E.V.4
  • 26
    • 0042836785 scopus 로고    scopus 로고
    • Nonrandom distribution of alu elements in genes of various functional categories: Insight from analysis of human chromosomes 21 and 22
    • Grover D, Majumder PP, Rao CB, Brahmachari SK, Mukerji M: Nonrandom distribution of alu elements in genes of various functional categories: insight from analysis of human chromosomes 21 and 22. Mol Biol Evol 2003, 20:1420-1424.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 1420-1424
    • Grover, D.1    Majumder, P.P.2    Rao, C.B.3    Brahmachari, S.K.4    Mukerji, M.5
  • 27
    • 0023038804 scopus 로고
    • Acceptor sites for retroviral integrations map near DNase I-hypersensitive sites in chromatin
    • Vijaya S, Steffen DL, Robinson HL: Acceptor sites for retroviral integrations map near DNase I-hypersensitive sites in chromatin. J Virol 1986, 60:683-692.
    • (1986) J. Virol. , vol.60 , pp. 683-692
    • Vijaya, S.1    Steffen, D.L.2    Robinson, H.L.3
  • 28
    • 0038692119 scopus 로고    scopus 로고
    • Human housekeeping genes are compact
    • Eisenberg E, Levanon EY: Human housekeeping genes are compact. Trends Genet 2003, 19:362-365.
    • (2003) Trends Genet. , vol.19 , pp. 362-365
    • Eisenberg, E.1    Levanon, E.Y.2
  • 29
    • 4744355710 scopus 로고    scopus 로고
    • Compactness of human housekeeping genes: Selection for economy or genomic design?
    • Vinogradov AE: Compactness of human housekeeping genes: selection for economy or genomic design? Trends Genet 2004, 20:248-253.
    • (2004) Trends Genet. , vol.20 , pp. 248-253
    • Vinogradov, A.E.1
  • 30
    • 1842665155 scopus 로고    scopus 로고
    • Clusters of regulatory signals for RNA polymerase II transcription associated with Alu family repeats and CpG islands in human promoters
    • Oei SL, Babich VS, Kazakov VI, Usmanova NM, Kropotov AV, Tomilin NV: Clusters of regulatory signals for RNA polymerase II transcription associated with Alu family repeats and CpG islands in human promoters. Genomics 2004, 83:873-882.
    • (2004) Genomics , vol.83 , pp. 873-882
    • Oei, S.L.1    Babich, V.S.2    Kazakov, V.I.3    Usmanova, N.M.4    Kropotov, A.V.5    Tomilin, N.V.6
  • 31
    • 18744421874 scopus 로고    scopus 로고
    • Chromatin higher order structure: Opening up chromatin for transcription
    • Nemeth A, Langst G: Chromatin higher order structure: opening up chromatin for transcription. Brief Funct Genomic Proteomic 2004, 2:334-343.
    • (2004) Brief Funct. Genomic Proteomic , vol.2 , pp. 334-343
    • Nemeth, A.1    Langst, G.2
  • 32
    • 0038341719 scopus 로고    scopus 로고
    • Human genome. A low number wins the GeneSweep Pool
    • Pennisi E: Human genome. A low number wins the GeneSweep Pool. Science 2003, 300:1484.
    • (2003) Science , vol.300 , pp. 1484
    • Pennisi, E.1
  • 33
    • 0342314566 scopus 로고
    • Unusual DNA Structures: Sequence Requirements and Role in Transcriptional Control
    • Edited by Sarma RH and Sarma MH. New York: Adenine Press
    • Brahmachari SK, Ramesh N, Shouche YS, Mishra RK, Bagga R and Meera G Unusual DNA Structures: Sequence Requirements and Role in Transcriptional Control. In Structure and Methods. Volume 2. Edited by Sarma RH and Sarma MH. New York: Adenine Press; 1990:33-49.
    • (1990) Structure and Methods , vol.2 , pp. 33-49
    • Brahmachari, S.K.1    Ramesh, N.2    Shouche, Y.S.3    Mishra, R.K.4    Bagga, R.5    Meera, G.6
  • 34
    • 0022496666 scopus 로고
    • DNA structural variability as a factor in gene expression and evolution
    • Conrad M, Brahmachari SK, Sasisekharan V: DNA structural variability as a factor in gene expression and evolution. Biosystems 1986, 19:123-126.
    • (1986) Biosystems , vol.19 , pp. 123-126
    • Conrad, M.1    Brahmachari, S.K.2    Sasisekharan, V.3
  • 35
    • 4444258534 scopus 로고    scopus 로고
    • Chromatin architecture of the human genome: Gene-rich domains are enriched in open chromatin fibers
    • Gilbert N, Boyle S, Fiegler H, Woodfine K, Carter NP, Bickmore WA: Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers. Cell 2004, 118:555-566.
    • (2004) Cell , vol.118 , pp. 555-566
    • Gilbert, N.1    Boyle, S.2    Fiegler, H.3    Woodfine, K.4    Carter, N.P.5    Bickmore, W.A.6
  • 36
    • 84874661856 scopus 로고    scopus 로고
    • List of housekeeping genes
    • List of housekeeping genes [http://www.compugen.co.il/supp_info/Housekeeping_genes.html]
  • 37
    • 0030741634 scopus 로고    scopus 로고
    • Mathematical model to predict regions of chromatin attachment to the nuclear matrix
    • Singh GB, Kramer JA, Krawetz SA: Mathematical model to predict regions of chromatin attachment to the nuclear matrix. Nucleic Acids Res 1997, 25:1419-1425.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 1419-1425
    • Singh, G.B.1    Kramer, J.A.2    Krawetz, S.A.3
  • 38
    • 84874664911 scopus 로고    scopus 로고
    • MAR Finder
    • MAR Finder [http://futuresoft.org/MAR-Wiz/]
  • 39
    • 0034139621 scopus 로고    scopus 로고
    • Computer prediction of sites associated with various elements of the nuclear matrix
    • Rogozin IB, Glazko GV, Glazkov MV: Computer prediction of sites associated with various elements of the nuclear matrix. Brief Bioinform 2000, 1:33-44.
    • (2000) Brief Bioinform. , vol.1 , pp. 33-44
    • Rogozin, I.B.1    Glazko, G.V.2    Glazkov, M.V.3
  • 40
    • 84874660111 scopus 로고    scopus 로고
    • ChrClass [ftp.ncbi.nih.gov/pub/kondrashov/MAR/Chrclass.zip]
    • ChrClass [ftp.ncbi.nih.gov/pub/kondrashov/MAR/Chrclass.zip]
  • 41
    • 84874645356 scopus 로고    scopus 로고
    • Recon
    • Recon [http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/]
  • 42
    • 84874659339 scopus 로고    scopus 로고
    • RepeatMasker
    • RepeatMasker [http://www.repeatmasker.org/]


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.