title: Metastasis-associated protein ribosomal RNA processing 1 homolog B (RRP1B) modulates metastasis through regulation of histone methylation.
abstract: Overexpression of ribosomal RNA processing 1 homolog B (RRP1B) induces a transcriptional profile that accurately predicts patient outcome in breast cancer. However, the mechanism by which RRP1B modulates transcription is unclear. Here, the chromatin-binding properties of RRP1B were examined to define how it regulates metastasis-associated transcription. To identify genome-wide RRP1B-binding sites, high-throughput ChIP-seq was performed in the human breast cancer cell line MDA-MB-231 and HeLa cells using antibodies against endogenous RRP1B. Global changes in repressive marks such as histone H3 lysine 9 trimethylation (H3K9me3) were also examined by ChIP-seq. Analysis of these samples identified 339 binding regions in MDA-MB-231 cells and 689 RRP1B-binding regions in HeLa cells. Among these, 136 regions were common to both cell lines. Gene expression analyses of these RRP1B-binding regions revealed that transcriptional repression is the primary result of RRP1B binding to chromatin. ChIP-reChIP assays demonstrated that RRP1B co-occupies loci with decreased gene expression with the heterochromatin-associated proteins, tripartite motif-containing protein 28 (TRIM28/KAP1), and heterochromatin protein 1-α (CBX5/HP1α). RRP1B occupancy at these loci was also associated with higher H3K9me3 levels, indicative of heterochromatinization mediated by the TRIM28/HP1α complex. In addition, RRP1B upregulation, which is associated with metastasis suppression, induced global changes in histone methylation.
  
  
  CONCLUSIONS
  RRP1B, a breast cancer metastasis suppressor, regulates gene expression through heterochromatinization and transcriptional repression, which helps our understanding of mechanisms that drive prognostic gene expression in human breast cancer.
authors.affiliation: Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland.
authors.forename: Minnkyong
authors.initials: M
authors.lastname: Lee
authors.affiliation: Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland.
authors.forename: Amy M
authors.initials: AM
authors.lastname: Dworkin
authors.affiliation: Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland.
authors.forename: Jens
authors.initials: J
authors.lastname: Lichtenberg
authors.affiliation: Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland.
authors.forename: Shashank J
authors.initials: SJ
authors.lastname: Patel
authors.affiliation: Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland.
authors.forename: Niraj S
authors.initials: NS
authors.lastname: Trivedi
authors.affiliation: Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland.
authors.forename: Derek
authors.initials: D
authors.lastname: Gildea
authors.affiliation: Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland.
authors.forename: David M
authors.initials: DM
authors.lastname: Bodine
authors.affiliation: Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland. crawforn@mail.nih.gov.
authors.forename: Nigel P S
authors.initials: NP
authors.lastname: Crawford
mesh_terms: D000818:Animals; D051017:Apoptosis Regulatory Proteins / Q000737:chemistry / Q000378:metabolism*; D001665:Binding Sites; D001943:Breast Neoplasms / Q000235:genetics / Q000473:pathology*; D045744:Cell Line, Tumor; D002843:Chromatin / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D000090266:Chromobox Protein Homolog 5; D002868:Chromosomal Proteins, Non-Histone / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D044127:Epigenesis, Genetic; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D006367:HeLa Cells; D006657:Histones / Q000378:metabolism; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics* / Q000473:pathology / Q000556:secondary*; D008745:Methylation; D051379:Mice; D009374:Neoplasms, Experimental; D012097:Repressor Proteins / Q000235:genetics*; D014158:Transcription, Genetic; D000076183:Tripartite Motif-Containing Protein 28
chemical_list: D051017:Apoptosis Regulatory Proteins; C000715594:CBX5 protein, human; C000715595:CBX5 protein, mouse; D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D006657:Histones; C574722:RRP1B protein, human; D012097:Repressor Proteins; D000090266:Chromobox Protein Homolog 5; C101116:TRIM28 protein, human; D000076183:Tripartite Motif-Containing Protein 28
references.citation: Breast. 2011 Oct;20 Suppl 3:S87-91
references.pmid: 22015300
references.citation: Genome Biol. 2009;10(3):R25
references.pmid: 19261174
references.citation: Mol Cell Biol. 1999 Jun;19(6):4366-78
references.pmid: 10330177
references.citation: Mol Biol Cell. 2010 Dec;21(23):4212-26
references.pmid: 20926688
references.citation: Mol Cell Biol. 2011 May;31(9):1833-47
references.pmid: 21343339
references.citation: Int J Dev Biol. 2009;53(2-3):335-54
references.pmid: 19412890
references.citation: Oncogene. 2014 Apr 3;33(14):1818-27
references.pmid: 23604122
references.citation: Breast Cancer Res. 2009;11(5):R75
references.pmid: 19825179
references.citation: PLoS Genet. 2007 Jun;3(6):e89
references.pmid: 17542650
references.citation: Cancer Genomics Proteomics. 2012 Sep-Oct;9(5):311-20
references.pmid: 22990110
references.citation: PLoS Genet. 2010 Sep 23;6(9):e1001134
references.pmid: 20885785
references.citation: Proc Natl Acad Sci U S A. 2008 Dec 2;105(48):18794-9
references.pmid: 19033198
references.citation: CA Cancer J Clin. 2013 Jan;63(1):11-30
references.pmid: 23335087
references.citation: J Biol Chem. 2009 Oct 16;284(42):28660-73
references.pmid: 19710015
references.citation: Nature. 2003 Apr 17;422(6933):735-8
references.pmid: 12700765
references.citation: Annu Rev Genet. 2008;42:131-41
references.pmid: 18759635
references.citation: PLoS Genet. 2007 Nov;3(11):e214
references.pmid: 18081427
references.citation: Mol Cell Biol. 2006 Nov;26(22):8623-38
references.pmid: 16954381
references.citation: J Biol Chem. 2011 Jul 29;286(30):26267-76
references.pmid: 21652716
references.citation: Nature. 2007 Sep 6;449(7158):105-8
references.pmid: 17805299
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D876-82
references.pmid: 20959295
references.citation: Nat Genet. 2003 Jan;33(1):49-54
references.pmid: 12469122
references.citation: Genes Dev. 2002 Apr 15;16(8):919-32
references.pmid: 11959841
references.citation: Nature. 2002 Jan 31;415(6871):530-6
references.pmid: 11823860
references.citation: Cell. 2013 Jan 31;152(3):633-41
references.pmid: 23374354
references.citation: Cytogenet Genome Res. 2005;110(1-4):462-7
references.pmid: 16093699
references.citation: EMBO J. 1999 Nov 15;18(22):6385-95
references.pmid: 10562550
references.citation: Cancer Res. 2011 Apr 15;71(8):3121-31
references.pmid: 21389092
references.citation: Genes Dev. 2001 Feb 15;15(4):428-43
references.pmid: 11230151
references.citation: Proc Natl Acad Sci U S A. 2008 Apr 29;105(17):6380-5
references.pmid: 18427120
references.citation: PLoS One. 2010 Dec 08;5(12):e15082
references.pmid: 21170338
references.citation: Nat Rev Drug Discov. 2006 Jan;5(1):37-50
references.pmid: 16485345
references.citation: Science. 2002 May 10;296(5570):1132-6
references.pmid: 12004135
references.citation: J Biol Chem. 2009 Aug 28;284(35):23622-35
references.pmid: 19581307
references.citation: N Engl J Med. 2002 Dec 19;347(25):1999-2009
references.pmid: 12490681
references.citation: Science. 2008 Feb 8;319(5864):819-21
references.pmid: 18258916