title: Sequence composition similarities with the 7SL RNA are highly predictive of functional genomic features.
abstract: Transposable elements derived from the 7SL RNA gene, such as Alu elements in primates, have had remarkable success in several mammalian lineages. The results presented here show a broad spectrum of functions for genomic segments that display sequence composition similarities with the 7SL RNA gene. Using thoroughly documented loci, we report that DNaseI-hypersensitive sites can be singled out in large genomic sequences by an assessment of sequence composition similarities with the 7SL RNA gene. We apply a root word frequency approach to illustrate a distinctive relationship between the sequence of the 7SL RNA gene and several classes of functional genomic features that are not presumed to be of transposable origin. Transposable elements that show noticeable similarities with the 7SL sequence include Alu sequences, as expected, but also long terminal repeats and the 5'-untranslated regions of long interspersed repetitive elements. In sequences masked for repeated elements, we find, when using the 7SL RNA gene as query sequence, distinctive similarities with promoters, exons and distal gene regulatory regions. The latter being the most notoriously difficult to detect, this approach may be useful for finding genomic segments that have regulatory functions and that may have escaped detection by existing methods.
authors.affiliation: Centre de recherche en cancérologie de l'Université Laval, L'Hôtel-Dieu de Québec, Centre hospitalier universitaire de Québec, Québec, Canada.
authors.forename: Yanick
authors.initials: Y
authors.lastname: Paquet
authors.forename: Alan
authors.initials: A
authors.lastname: Anderson
mesh_terms: D001482:Base Composition; D003850:Deoxyribonuclease I; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D020071:Interspersed Repetitive Sequences; D020733:RNA, Small Cytoplasmic / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D018271:Signal Recognition Particle / Q000235:genetics*
chemical_list: C115990:7SL RNA; D020733:RNA, Small Cytoplasmic; D018271:Signal Recognition Particle; D003850:Deoxyribonuclease I
references.citation: Proc Natl Acad Sci U S A. 2004 Jan 27;101(4):992-7
references.pmid: 14732688
references.citation: Annu Rev Biochem. 1988;57:159-97
references.pmid: 3052270
references.citation: Trends Genet. 2006 Jan;22(1):38-45
references.pmid: 16309780
references.citation: Genome Res. 2005 Aug;15(8):1073-8
references.pmid: 16024818
references.citation: J Biomed Biotechnol. 2006;2006(1):13569
references.pmid: 16877810
references.citation: Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2740-5
references.pmid: 16477033
references.citation: BMC Bioinformatics. 2006 Oct 25;7:474
references.pmid: 17064419
references.citation: Am J Hematol. 2007 Nov;82(11):1005-9
references.pmid: 17654503
references.citation: Chromosome Res. 2008;16(1):203-15
references.pmid: 18293113
references.citation: Cell. 2007 Nov 30;131(5):844-6
references.pmid: 18045531
references.citation: Proc Natl Acad Sci U S A. 1994 Dec 20;91(26):12832-6
references.pmid: 7809130
references.citation: Genome Res. 2006 Oct;16(10):1310-9
references.pmid: 16963707
references.citation: Mol Cell. 2004 Apr 23;14(2):221-31
references.pmid: 15099521
references.citation: Semin Cell Dev Biol. 2007 Feb;18(1):140-52
references.pmid: 17276707
references.citation: PLoS Comput Biol. 2006 Nov 3;2(11):e150
references.pmid: 17083273
references.citation: Nature. 2003 Jul 10;424(6945):147-51
references.pmid: 12853946
references.citation: Nat Struct Mol Biol. 2006 Sep;13(9):763-71
references.pmid: 16936727
references.citation: Virology. 1985 Dec;147(2):449-58
references.pmid: 3840930
references.citation: Nucleic Acids Res. 2007;35(8):e56
references.pmid: 17389645
references.citation: Mol Cell Biol. 2005 Jun;25(12):5215-25
references.pmid: 15923636
references.citation: Nature. 2006 Nov 23;444(7118):499-502
references.pmid: 17086198
references.citation: Nucleic Acids Res. 2006 Jul 19;34(12):3585-98
references.pmid: 16855295
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W512-5
references.pmid: 15980524
references.citation: Trends Genet. 2003 Feb;19(2):68-72
references.pmid: 12547512
references.citation: Blood. 1991 Nov 1;78(9):2165-77
references.pmid: 1932737
references.citation: J Comput Biol. 2005 Jun;12(5):545-53
references.pmid: 15952877
references.citation: Nat Rev Genet. 2008 May;9(5):397-405
references.pmid: 18368054
references.citation: BMC Genomics. 2008 May 17;9:226
references.pmid: 18485226
references.citation: J Cell Biochem. 2007 Nov 1;102(4):801-10
references.pmid: 17910027
references.citation: Science. 2003 Oct 17;302(5644):413
references.pmid: 14563999
references.citation: Blood. 1997 Jul 1;90(1):421-7
references.pmid: 9207479
references.citation: Genome Res. 2008 Sep;18(9):1403-14
references.pmid: 18550801
references.citation: Genome Biol. 2008;9(9):R141
references.pmid: 18811936
references.citation: Trends Genet. 1995 Jul;11(7):283-90
references.pmid: 7482779
references.citation: Genome Res. 2006 Jan;16(1):123-31
references.pmid: 16344561
references.citation: Biol Direct. 2006 Jul 20;1:20
references.pmid: 16857058
references.citation: Nature. 2007 May 10;447(7141):167-77
references.pmid: 17495919
references.citation: Gene. 2002 Jan 23;283(1-2):185-97
references.pmid: 11867225
references.citation: Nat Genet. 2006 Jun;38(6):626-35
references.pmid: 16645617
references.citation: Cytogenet Genome Res. 2005;110(1-4):457-61
references.pmid: 16093698
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D88-92
references.pmid: 17130149
references.citation: Nature. 2009 May 7;459(7243):108-12
references.pmid: 19295514
references.citation: Trends Genet. 2004 Dec;20(12):611-6
references.pmid: 15522456
references.citation: Cytogenet Genome Res. 2005;110(1-4):333-41
references.pmid: 16093685
references.citation: Bioinformatics. 2002 Oct;18(10):1374-81
references.pmid: 12376382
references.citation: Int Rev Cytol. 2005;247:165-221
references.pmid: 16344113
references.citation: Genome Res. 2007 Feb;17(2):201-11
references.pmid: 17210927
references.citation: Nature. 2001 Feb 15;409(6822):860-921
references.pmid: 11237011
references.citation: Proc Int Conf Intell Syst Mol Biol. 2000;8:269-78
references.pmid: 10977088
references.citation: Genome Dyn. 2007;3:163-174
references.pmid: 18753791
references.citation: Genome Dyn. 2007;3:147-162
references.pmid: 18753790
references.citation: Cell. 1982 Aug;30(1):173-83
references.pmid: 6290076
references.citation: Proc Natl Acad Sci U S A. 2005 Jul 12;102(28):9830-5
references.pmid: 15998734