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Volumn 14, Issue 9, 2015, Pages 3635-3644

Insights from ENCODE on missing proteins: Why β-defensin expression is scarcely detected

Author keywords

CHPP; DHS; ENCODE; histone modification; missing proteins; proteome; TF; defensin

Indexed keywords

BETA DEFENSIN; DNA; MESSENGER RNA; MISSING PROTEIN; PROTEIN; UNCLASSIFIED DRUG;

EID: 84941144247     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.5b00565     Document Type: Article
Times cited : (7)

References (39)
  • 1
    • 0029097115 scopus 로고
    • Structure, function, and membrane integration of defensins
    • White, S. H.; Wimley, W. C.; Selsted, M. E. Structure, function, and membrane integration of defensins Curr. Opin. Struct. Biol. 1995, 5, 521-527 10.1016/0959-440X(95)80038-7
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 521-527
    • White, S.H.1    Wimley, W.C.2    Selsted, M.E.3
  • 3
    • 39149127361 scopus 로고    scopus 로고
    • Review: Structure-activity relationships in β-defensin peptides
    • Taylor, K.; Barran, P. E.; Dorin, J. R. Review: Structure-activity relationships in β-defensin peptides Biopolymers 2008, 90, 1-7 10.1002/bip.20900
    • (2008) Biopolymers , vol.90 , pp. 1-7
    • Taylor, K.1    Barran, P.E.2    Dorin, J.R.3
  • 4
    • 33646003552 scopus 로고    scopus 로고
    • β-defensin evolution: Selection complexity and clues for residues of functional importance
    • Semple, C. a M.; Taylor, K.; Eastwood, H.; Barran, P. E.; Dorin, J. R. β-defensin evolution: selection complexity and clues for residues of functional importance Biochem. Soc. Trans. 2006, 34, 257-262 10.1042/BST20060257
    • (2006) Biochem. Soc. Trans. , vol.34 , pp. 257-262
    • Semple, C.A.M.1    Taylor, K.2    Eastwood, H.3    Barran, P.E.4    Dorin, J.R.5
  • 5
    • 84891801560 scopus 로고    scopus 로고
    • Chromosome-8-coded proteome of Chinese Chromosome Proteome Data Set (CCPD) 2.0 with partial immunohistochemical verifications
    • Liu, Y.; Ying, W.; Ren, Z.; Gu, W.; Zhang, Y.; Yan, G.; Yang, P.; Liu, Y.; Yin, X.; Chang, C. et al. Chromosome-8-coded proteome of Chinese Chromosome Proteome Data Set (CCPD) 2.0 with partial immunohistochemical verifications J. Proteome Res. 2014, 13, 126-136 10.1021/pr400902u
    • (2014) J. Proteome Res. , vol.13 , pp. 126-136
    • Liu, Y.1    Ying, W.2    Ren, Z.3    Gu, W.4    Zhang, Y.5    Yan, G.6    Yang, P.7    Liu, Y.8    Yin, X.9    Chang, C.10
  • 6
    • 84874026295 scopus 로고    scopus 로고
    • Qualitative and quantitative expression status of the human chromosome 20 genes in cancer tissues and the representative cell lines
    • Wang, Q.; Wen, B.; Yan, G.; Wei, J.; Xie, L.; Xu, S.; Jiang, D.; Wang, T.; Lin, L.; Zi, J. et al. Qualitative and quantitative expression status of the human chromosome 20 genes in cancer tissues and the representative cell lines J. Proteome Res. 2013, 12, 151-161 10.1021/pr3008336
    • (2013) J. Proteome Res. , vol.12 , pp. 151-161
    • Wang, Q.1    Wen, B.2    Yan, G.3    Wei, J.4    Xie, L.5    Xu, S.6    Jiang, D.7    Wang, T.8    Lin, L.9    Zi, J.10
  • 7
    • 84891799287 scopus 로고    scopus 로고
    • Omics evidence: Single nucleotide variants transmissions on chromosome 20 in liver cancer cell lines
    • Wang, Q.; Wen, B.; Wang, T.; Xu, Z.; Yin, X.; Xu, S.; Ren, Z.; Hou, G.; Zhou, R.; Zhao, H. et al. Omics evidence: Single nucleotide variants transmissions on chromosome 20 in liver cancer cell lines J. Proteome Res. 2014, 13, 200-211 10.1021/pr400899b
    • (2014) J. Proteome Res. , vol.13 , pp. 200-211
    • Wang, Q.1    Wen, B.2    Wang, T.3    Xu, Z.4    Yin, X.5    Xu, S.6    Ren, Z.7    Hou, G.8    Zhou, R.9    Zhao, H.10
  • 8
    • 0032169557 scopus 로고    scopus 로고
    • Human beta-defensin 2 is a salt-sensitive peptide antibiotic expressed in human lung
    • Bals, R.; Wang, X.; Wu, Z.; Freeman, T.; Bafna, V.; Zasloff, M.; Wilson, J. M. Human beta-defensin 2 is a salt-sensitive peptide antibiotic expressed in human lung J. Clin. Invest. 1998, 102, 874-880 10.1172/JCI2410
    • (1998) J. Clin. Invest. , vol.102 , pp. 874-880
    • Bals, R.1    Wang, X.2    Wu, Z.3    Freeman, T.4    Bafna, V.5    Zasloff, M.6    Wilson, J.M.7
  • 10
    • 0032731116 scopus 로고    scopus 로고
    • Ocular surface epithelia express mRNA for human beta defensin-2
    • Mcnamara, N. A.; Van, R.; Tuchin, O. S.; Fleiszig, S. M. Ocular surface epithelia express mRNA for human beta defensin-2 Exp. Eye Res. 1999, 69, 483-490 10.1006/exer.1999.0722
    • (1999) Exp. Eye Res. , vol.69 , pp. 483-490
    • McNamara, N.A.1    Van, R.2    Tuchin, O.S.3    Fleiszig, S.M.4
  • 11
    • 39549109127 scopus 로고    scopus 로고
    • A novel antimicrobial peptide on the ocular surface shows decreased expression in inflammation and infection
    • Abedin, A.; Mohammed, I.; Hopkinson, A.; Dua, H. S. A novel antimicrobial peptide on the ocular surface shows decreased expression in inflammation and infection Invest. Ophthalmol. Visual Sci. 2008, 49, 28-33 10.1167/iovs.07-0645
    • (2008) Invest. Ophthalmol. Visual Sci. , vol.49 , pp. 28-33
    • Abedin, A.1    Mohammed, I.2    Hopkinson, A.3    Dua, H.S.4
  • 12
    • 7444260846 scopus 로고    scopus 로고
    • The ENCODE (Encyclopedia of DNA Elements) Project
    • ENCODE Consortium
    • ENCODE Consortium The ENCODE (Encyclopedia of DNA Elements) Project Nature 2004, 306, 636-640
    • (2004) Nature , vol.306 , pp. 636-640
  • 17
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Dunham, I.; Kundaje, A.; Aldred, S. F.; Collins, P. J.; Davis, C. A.; Doyle, F. et al. An integrated encyclopedia of DNA elements in the human genome Nature 2012, 489, 57-74 10.1038/nature11247
    • (2012) Nature , vol.489 , pp. 57-74
    • Dunham, I.1    Kundaje, A.2    Aldred, S.F.3    Collins, P.J.4    Davis, C.A.5    Doyle, F.6
  • 19
    • 84875149194 scopus 로고    scopus 로고
    • Regulation of nucleosome dynamics by histone modifications
    • Zentner, G. E.; Henikoff, S. Regulation of nucleosome dynamics by histone modifications Nat. Struct. Mol. Biol. 2013, 20, 259-266
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 259-266
    • Zentner, G.E.1    Henikoff, S.2
  • 23
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte, J.; Doolittle, R. F. A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 1982, 157, 105-132 10.1016/0022-2836(82)90515-0
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 24
    • 84891818310 scopus 로고    scopus 로고
    • Metrics for the human proteome project 2013-2014 and strategies for finding missing proteins
    • Lane, L.; Bairoch, A.; Beavis, R. C.; Deutsch, E. W.; Gaudet, P.; Lundberg, E.; Omenn, G. S. Metrics for the human proteome project 2013-2014 and strategies for finding missing proteins J. Proteome Res. 2014, 13, 15-20 10.1021/pr401144x
    • (2014) J. Proteome Res. , vol.13 , pp. 15-20
    • Lane, L.1    Bairoch, A.2    Beavis, R.C.3    Deutsch, E.W.4    Gaudet, P.5    Lundberg, E.6    Omenn, G.S.7
  • 25
    • 79955970571 scopus 로고    scopus 로고
    • Comprehensive assessment of sequence variation within the copy number variable defensin cluster on 8p23 by target enriched in-depth 454 sequencing
    • Taudien, S.; Szafranski, K.; Felder, M.; Groth, M.; Huse, K.; Raffaelli, F.; Petzold, A.; Zhang, X.; Rosenstiel, P.; Hampe, J. et al. Comprehensive assessment of sequence variation within the copy number variable defensin cluster on 8p23 by target enriched in-depth 454 sequencing BMC Genomics 2011, 12, 243 10.1186/1471-2164-12-243
    • (2011) BMC Genomics , vol.12 , pp. 243
    • Taudien, S.1    Szafranski, K.2    Felder, M.3    Groth, M.4    Huse, K.5    Raffaelli, F.6    Petzold, A.7    Zhang, X.8    Rosenstiel, P.9    Hampe, J.10
  • 27
    • 77949786295 scopus 로고    scopus 로고
    • Value of using multiple proteases for large-scale mass spectrometry-based proteomics
    • Swaney, D. L.; Wenger, C. D.; Coon, J. J. Value of using multiple proteases for large-scale mass spectrometry-based proteomics J. Proteome Res. 2010, 9, 1323-1329 10.1021/pr900863u
    • (2010) J. Proteome Res. , vol.9 , pp. 1323-1329
    • Swaney, D.L.1    Wenger, C.D.2    Coon, J.J.3
  • 31
    • 79952534189 scopus 로고    scopus 로고
    • Regulation of chromatin by histone modifications
    • Bannister, A. J.; Kouzarides, T. Regulation of chromatin by histone modifications Cell Res. 2011, 21, 381-395 10.1038/cr.2011.22
    • (2011) Cell Res. , vol.21 , pp. 381-395
    • Bannister, A.J.1    Kouzarides, T.2
  • 32
    • 84861889354 scopus 로고    scopus 로고
    • Differential DNase i hypersensitivity reveals factor-dependent chromatin dynamics
    • He, H. H.; Meyer, C. A.; Chen, M. W.; Jordan, V. C.; Brown, M.; Liu, X. S. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics Genome Res. 2012, 22, 1015-1025 10.1101/gr.133280.111
    • (2012) Genome Res. , vol.22 , pp. 1015-1025
    • He, H.H.1    Meyer, C.A.2    Chen, M.W.3    Jordan, V.C.4    Brown, M.5    Liu, X.S.6
  • 33
    • 84865754452 scopus 로고    scopus 로고
    • Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
    • Yip, K. Y.; Cheng, C.; Bhardwaj, N.; Brown, J. B.; Leng, J.; Kundaje, A.; Rozowsky, J.; Birney, E.; Bickel, P.; Snyder, M. et al. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors Genome Biol. 2012, 13, R48 10.1186/gb-2012-13-9-r48
    • (2012) Genome Biol. , vol.13 , pp. 48
    • Yip, K.Y.1    Cheng, C.2    Bhardwaj, N.3    Brown, J.B.4    Leng, J.5    Kundaje, A.6    Rozowsky, J.7    Birney, E.8    Bickel, P.9    Snyder, M.10
  • 34
    • 64549139803 scopus 로고    scopus 로고
    • Reversible acetylation of chromatin: Implication in regulation of gene expression, disease and therapeutics
    • Selvi, B. R.; Kundu, T. K. Reversible acetylation of chromatin: Implication in regulation of gene expression, disease and therapeutics Biotechnol. J. 2009, 4, 375-390 10.1002/biot.200900032
    • (2009) Biotechnol. J. , vol.4 , pp. 375-390
    • Selvi, B.R.1    Kundu, T.K.2
  • 35
    • 79960469576 scopus 로고    scopus 로고
    • Increased expression of beta-defensin 1 (DEFB1) in chronic obstructive pulmonary disease
    • Andresen, E.; Günther, G.; Bullwinkel, J.; Lange, C.; Heine, H. Increased expression of beta-defensin 1 (DEFB1) in chronic obstructive pulmonary disease PLoS One 2011, 6, e21898 10.1371/journal.pone.0021898
    • (2011) PLoS One , vol.6 , pp. 21898
    • Andresen, E.1    Günther, G.2    Bullwinkel, J.3    Lange, C.4    Heine, H.5
  • 36
    • 84865852567 scopus 로고    scopus 로고
    • Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
    • Wang, J.; Zhuang, J.; Iyer, S.; Lin, X.; Whitfield, T. W.; Greven, M. C.; Pierce, B. G.; Dong, X.; Kundaje, A.; Cheng, Y. et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors Genome Res. 2012, 22, 1798-1812 10.1101/gr.139105.112
    • (2012) Genome Res. , vol.22 , pp. 1798-1812
    • Wang, J.1    Zhuang, J.2    Iyer, S.3    Lin, X.4    Whitfield, T.W.5    Greven, M.C.6    Pierce, B.G.7    Dong, X.8    Kundaje, A.9    Cheng, Y.10
  • 37
    • 62549128139 scopus 로고    scopus 로고
    • A census of human transcription factors: Function, expression and evolution
    • Vaquerizas, J. M.; Kummerfeld, S. K.; Teichmann, S. a; Luscombe, N. M. A census of human transcription factors: function, expression and evolution Nat. Rev. Genet. 2009, 10, 252-263 10.1038/nrg2538
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 252-263
    • Vaquerizas, J.M.1    Kummerfeld, S.K.2    Teichmann, S.A.3    Luscombe, N.M.4
  • 38
    • 84865049521 scopus 로고    scopus 로고
    • HTRIdb: An open-access database for experimentally verified human transcriptional regulation interactions
    • Bovolenta, L.; Acencio, M. L.; Lemke, N. HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions BMC Genomics 2012, 13, 405 10.1186/1471-2164-13-405
    • (2012) BMC Genomics , vol.13 , pp. 405
    • Bovolenta, L.1    Acencio, M.L.2    Lemke, N.3
  • 39
    • 77950954883 scopus 로고    scopus 로고
    • Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing
    • Taudien, S.; Groth, M.; Huse, K.; Petzold, A.; Szafranski, K.; Hampe, J.; Rosenstiel, P.; Schreiber, S.; Platzer, M. Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing BMC Genomics 2010, 11, 252 10.1186/1471-2164-11-252
    • (2010) BMC Genomics , vol.11 , pp. 252
    • Taudien, S.1    Groth, M.2    Huse, K.3    Petzold, A.4    Szafranski, K.5    Hampe, J.6    Rosenstiel, P.7    Schreiber, S.8    Platzer, M.9


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.