메뉴 건너뛰기




Volumn 9, Issue 3, 2014, Pages 996-1006

Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver

Author keywords

[No Author keywords available]

Indexed keywords

HEPATOCYTE NUCLEAR FACTOR 3BETA; HISTONE DEACETYLASE 3; LIVER X RECEPTOR ALPHA; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR ALPHA; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA; SERUM RESPONSE FACTOR; DNA BINDING PROTEIN; FOXA2 PROTEIN, MOUSE; HISTONE DEACETYLASE; NUCLEOSOME; PROTEIN BINDING; TRANSCRIPTION FACTOR; ZFP67 PROTEIN, MOUSE;

EID: 84919712381     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2014.09.048     Document Type: Article
Times cited : (65)

References (57)
  • 4
    • 49149090637 scopus 로고    scopus 로고
    • Hepatocyte-specific ablation of Foxa2 alters bile acid homeostasis and results in endoplasmic reticulum stress
    • Bochkis, I.M., Rubins, N.E., White, P., Furth, E.E., Friedman, J.R., and Kaestner, K.H. (2008). Hepatocyte-specific ablation of Foxa2 alters bile acid homeostasis and results in endoplasmic reticulum stress. Nat. Med. 14, 828-836.
    • (2008) Nat. Med. , vol.14 , pp. 828-836
    • Bochkis, I.M.1    Rubins, N.E.2    White, P.3    Furth, E.E.4    Friedman, J.R.5    Kaestner, K.H.6
  • 5
    • 84864041695 scopus 로고    scopus 로고
    • Genome-wide location analysis reveals distinct transcriptional circuitry by paralogous regulators Foxa1 and Foxa2
    • Bochkis, I.M., Schug, J., Ye, D.Z., Kurinna, S., Stratton, S.A., Barton, M.C., and Kaestner, K.H. (2012). Genome-wide location analysis reveals distinct transcriptional circuitry by paralogous regulators Foxa1 and Foxa2. PLoS Genet. 8, e1002770.
    • (2012) PLoS Genet. , vol.8
    • Bochkis, I.M.1    Schug, J.2    Ye, D.Z.3    Kurinna, S.4    Stratton, S.A.5    Barton, M.C.6    Kaestner, K.H.7
  • 6
    • 84889082596 scopus 로고    scopus 로고
    • Bile acid-induced inflammatory signaling in mice lacking Foxa2 in the liver leads to activation of mTOR and age-onset obesity
    • Bochkis, I.M., Shin, S., and Kaestner, K.H. (2013). Bile acid-induced inflammatory signaling in mice lacking Foxa2 in the liver leads to activation of mTOR and age-onset obesity. Mol Metab 2, 447-456.
    • (2013) Mol Metab , vol.2 , pp. 447-456
    • Bochkis, I.M.1    Shin, S.2    Kaestner, K.H.3
  • 7
    • 84856777771 scopus 로고    scopus 로고
    • Genome-wide profiling of liver X receptor, retinoid X receptor, and peroxisome proliferator-activated receptor α in mouse liver reveals extensive sharing of binding sites
    • Boergesen, M., Pedersen, T.A., Gross, B., van Heeringen, S.J., Hagenbeek, D., Bindesbøll, C., Caron, S., Lalloyer, F., Steffensen, K.R., Nebb, H.I., et al. (2012). Genome-wide profiling of liver X receptor, retinoid X receptor, and peroxisome proliferator-activated receptor α in mouse liver reveals extensive sharing of binding sites. Mol. Cell. Biol. 32, 852-867.
    • (2012) Mol. Cell. Biol. , vol.32 , pp. 852-867
    • Boergesen, M.1    Pedersen, T.A.2    Gross, B.3    van Heeringen, S.J.4    Hagenbeek, D.5    Bindesbøll, C.6    Caron, S.7    Lalloyer, F.8    Steffensen, K.R.9    Nebb, H.I.10
  • 9
  • 10
    • 84873351389 scopus 로고    scopus 로고
    • DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing
    • Chen, K., Xi, Y., Pan, X., Li, Z., Kaestner, K., Tyler, J., Dent, S., He, X., and Li, W. (2013). DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res. 23, 341-351.
    • (2013) Genome Res. , vol.23 , pp. 341-351
    • Chen, K.1    Xi, Y.2    Pan, X.3    Li, Z.4    Kaestner, K.5    Tyler, J.6    Dent, S.7    He, X.8    Li, W.9
  • 11
    • 0035057611 scopus 로고    scopus 로고
    • Senescence represses the nuclear localization of the serum response factor and differentiation regulates its nuclear localization with lineage specificity
    • Ding, W., Gao, S., and Scott, R.E. (2001). Senescence represses the nuclear localization of the serum response factor and differentiation regulates its nuclear localization with lineage specificity. J. Cell Sci. 114, 1011-1018.
    • (2001) J. Cell Sci. , vol.114 , pp. 1011-1018
    • Ding, W.1    Gao, S.2    Scott, R.E.3
  • 13
    • 73349117487 scopus 로고    scopus 로고
    • Toll-like receptor signaling links dietary fatty acids to the metabolic syndrome
    • Fessler, M.B., Rudel, L.L., and Brown, J.M. (2009). Toll-like receptor signaling links dietary fatty acids to the metabolic syndrome. Curr. Opin. Lipidol. 20, 379-385.
    • (2009) Curr. Opin. Lipidol. , vol.20 , pp. 379-385
    • Fessler, M.B.1    Rudel, L.L.2    Brown, J.M.3
  • 14
    • 0141446024 scopus 로고    scopus 로고
    • Liver peroxisome proliferator-activated receptor gamma contributes to hepatic steatosis, triglyceride clearance, and regulation of body fat mass
    • Gavrilova, O., Haluzik, M., Matsusue, K., Cutson, J.J., Johnson, L., Dietz, K.R., Nicol, C.J., Vinson, C., Gonzalez, F.J., and Reitman, M.L. (2003). Liver peroxisome proliferator-activated receptor gamma contributes to hepatic steatosis, triglyceride clearance, and regulation of body fat mass. J. Biol. Chem. 278, 34268-34276.
    • (2003) J. Biol. Chem. , vol.278 , pp. 34268-34276
    • Gavrilova, O.1    Haluzik, M.2    Matsusue, K.3    Cutson, J.J.4    Johnson, L.5    Dietz, K.R.6    Nicol, C.J.7    Vinson, C.8    Gonzalez, F.J.9    Reitman, M.L.10
  • 15
    • 64549137257 scopus 로고    scopus 로고
    • CIDE proteins and metabolic disorders
    • Gong, J., Sun, Z., and Li, P. (2009). CIDE proteins and metabolic disorders. Curr. Opin. Lipidol. 20, 121-126.
    • (2009) Curr. Opin. Lipidol. , vol.20 , pp. 121-126
    • Gong, J.1    Sun, Z.2    Li, P.3
  • 16
    • 0035724413 scopus 로고    scopus 로고
    • The SMRT and N-CoR corepressors are activating cofactors for histone deacetylase 3
    • Guenther, M.G., Barak, O., and Lazar, M.A. (2001). The SMRT and N-CoR corepressors are activating cofactors for histone deacetylase 3. Mol. Cell. Biol. 21, 6091-6101.
    • (2001) Mol. Cell. Biol. , vol.21 , pp. 6091-6101
    • Guenther, M.G.1    Barak, O.2    Lazar, M.A.3
  • 17
    • 37249054901 scopus 로고    scopus 로고
    • Chromatin opening and stable perturbation of core histone:DNA contacts by FoxO1
    • Hatta, M., and Cirillo, L.A. (2007). Chromatin opening and stable perturbation of core histone:DNA contacts by FoxO1. J. Biol. Chem. 282, 35583-35593.
    • (2007) J. Biol. Chem. , vol.282 , pp. 35583-35593
    • Hatta, M.1    Cirillo, L.A.2
  • 20
    • 0038701745 scopus 로고    scopus 로고
    • Regulation of aging and agerelated disease by DAF-16 and heat-shock factor
    • Hsu, A.L., Murphy, C.T., and Kenyon, C. (2003). Regulation of aging and agerelated disease by DAF-16 and heat-shock factor. Science 300, 1142-1145.
    • (2003) Science , vol.300 , pp. 1142-1145
    • Hsu, A.L.1    Murphy, C.T.2    Kenyon, C.3
  • 22
  • 23
    • 80052022281 scopus 로고    scopus 로고
    • The reduction of SIRT1 in livers of old mice leads to impaired body homeostasis and to inhibition of liver proliferation
    • Jin, J., Iakova, P., Jiang, Y., Medrano, E.E., and Timchenko, N.A. (2011). The reduction of SIRT1 in livers of old mice leads to impaired body homeostasis and to inhibition of liver proliferation. Hepatology 54, 989-998.
    • (2011) Hepatology , vol.54 , pp. 989-998
    • Jin, J.1    Iakova, P.2    Jiang, Y.3    Medrano, E.E.4    Timchenko, N.A.5
  • 27
    • 41949120723 scopus 로고    scopus 로고
    • Liver-specific deletion of histone deacetylase 3 disrupts metabolic transcriptional networks
    • Knutson, S.K., Chyla, B.J., Amann, J.M., Bhaskara, S., Huppert, S.S., and Hiebert, S.W. (2008). Liver-specific deletion of histone deacetylase 3 disrupts metabolic transcriptional networks. EMBO J. 27, 1017-1028.
    • (2008) EMBO J. , vol.27 , pp. 1017-1028
    • Knutson, S.K.1    Chyla, B.J.2    Amann, J.M.3    Bhaskara, S.4    Huppert, S.S.5    Hiebert, S.W.6
  • 29
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
    • Li, B., and Dewey, C.N. (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323.
    • (2011) BMC Bioinformatics , vol.12 , pp. 323
    • Li, B.1    Dewey, C.N.2
  • 30
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H., and Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 32
    • 84892440367 scopus 로고    scopus 로고
    • Chromatin modifications as determinants of muscle stem cell quiescence and chronological aging
    • Liu, L., Cheung, T.H., Charville, G.W., Hurgo, B.M., Leavitt, T., Shih, J., Brunet, A., and Rando, T.A. (2013). Chromatin modifications as determinants of muscle stem cell quiescence and chronological aging. Cell Rep 4, 189-204.
    • (2013) Cell Rep , vol.4 , pp. 189-204
    • Liu, L.1    Cheung, T.H.2    Charville, G.W.3    Hurgo, B.M.4    Leavitt, T.5    Shih, J.6    Brunet, A.7    Rando, T.A.8
  • 38
    • 78349283454 scopus 로고    scopus 로고
    • Peroxisome proliferator-activated receptor alpha target genes
    • Rakhshandehroo, M., Knoch, B., Müller, M., and Kersten, S. (2010). Peroxisome proliferator-activated receptor alpha target genes. PPAR Res. 2010, 2010.
    • (2010) PPAR Res. , vol.2010 , pp. 2010
    • Rakhshandehroo, M.1    Knoch, B.2    Müller, M.3    Kersten, S.4
  • 39
    • 75249087100 scopus 로고    scopus 로고
    • edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson, M.D., McCarthy, D.J., and Smyth, G.K. (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 43
    • 70549098559 scopus 로고    scopus 로고
    • Mouse models of inherited lipodystrophy
    • Savage, D.B. (2009). Mouse models of inherited lipodystrophy. Dis. Model. Mech. 2, 554-562.
    • (2009) Dis. Model. Mech. , vol.2 , pp. 554-562
    • Savage, D.B.1
  • 44
    • 33646745137 scopus 로고    scopus 로고
    • Lamin A-dependent nuclear defects in human aging
    • Scaffidi, P., and Misteli, T. (2006). Lamin A-dependent nuclear defects in human aging. Science 312, 1059-1063.
    • (2006) Science , vol.312 , pp. 1059-1063
    • Scaffidi, P.1    Misteli, T.2
  • 47
    • 66149117384 scopus 로고    scopus 로고
    • Hepatocyte expression of serum response factor is essential for liver function, hepatocyte proliferation and survival, and postnatal body growth in mice
    • Sun, K., Battle, M.A., Misra, R.P., and Duncan, S.A. (2009). Hepatocyte expression of serum response factor is essential for liver function, hepatocyte proliferation and survival, and postnatal body growth in mice. Hepatology 49, 1645-1654.
    • (2009) Hepatology , vol.49 , pp. 1645-1654
    • Sun, K.1    Battle, M.A.2    Misra, R.P.3    Duncan, S.A.4
  • 50
    • 77949874234 scopus 로고    scopus 로고
    • Histone variants-ancient wrap artists of the epigenome
    • Talbert, P.B., and Henikoff, S. (2010). Histone variants-ancient wrap artists of the epigenome. Nat. Rev. Mol. Cell Biol. 11, 264-275.
    • (2010) Nat. Rev. Mol. Cell Biol. , vol.11 , pp. 264-275
    • Talbert, P.B.1    Henikoff, S.2
  • 51
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq
    • Trapnell, C., Pachter, L., and Salzberg, S.L. (2009). TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 53
    • 5444223019 scopus 로고    scopus 로고
    • Site-specific analysis of histone methylation and acetylation
    • Umlauf, D., Goto, Y., and Feil, R. (2004). Site-specific analysis of histone methylation and acetylation. Methods Mol. Biol. 287, 99-120.
    • (2004) Methods Mol. Biol. , vol.287 , pp. 99-120
    • Umlauf, D.1    Goto, Y.2    Feil, R.3
  • 54
    • 33644875782 scopus 로고    scopus 로고
    • A new generation of JASPAR, the open-access repository for transcription factor binding site profiles
    • Vlieghe, D., Sandelin, A., De Bleser, P.J., Vleminckx, K., Wasserman, W.W., van Roy, F., and Lenhard, B. (2006). A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res. 34 (Database issue), D95-D97.
    • (2006) Nucleic Acids Res , vol.34 , Issue.DATABASE ISSUE , pp. D95-D97
    • Vlieghe, D.1    Sandelin, A.2    De Bleser, P.J.3    Vleminckx, K.4    Wasserman, W.W.5    van Roy, F.6    Lenhard, B.7
  • 56
    • 0027096119 scopus 로고
    • Nucleosome core displacement in vitro via a metastable transcription factor-nucleosome complex
    • Workman, J.L., and Kingston, R.E. (1992). Nucleosome core displacement in vitro via a metastable transcription factor-nucleosome complex. Science 258, 1780-1784.
    • (1992) Science , vol.258 , pp. 1780-1784
    • Workman, J.L.1    Kingston, R.E.2
  • 57
    • 84883587895 scopus 로고    scopus 로고
    • PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments
    • Zambelli, F., Pesole, G., and Pavesi, G. (2013). PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments. Nucleic Acids Res. 41 (Web Server issue), W535-43.
    • (2013) Nucleic Acids Res , vol.41 , Issue.WEB SERVER ISSUE , pp. W535-W543
    • Zambelli, F.1    Pesole, G.2    Pavesi, G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.