Sequence composition similarities with the 7SL RNA are highly predictive of functional genomic features.
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.
Paquet
Yanick
Y
Centre de recherche en cancérologie de l'Université Laval, L'Hôtel-Dieu de Québec, Centre hospitalier universitaire de Québec, Québec, Canada.
Anderson
Alan
A
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*
C115990:7SL RNA; D020733:RNA, Small Cytoplasmic; D018271:Signal Recognition Particle; D003850:Deoxyribonuclease I
Proc Natl Acad Sci U S A. 2004 Jan 27;101(4):992-7
14732688
Annu Rev Biochem. 1988;57:159-97
3052270
Trends Genet. 2006 Jan;22(1):38-45
16309780
Genome Res. 2005 Aug;15(8):1073-8
16024818
J Biomed Biotechnol. 2006;2006(1):13569
16877810
Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2740-5
16477033
BMC Bioinformatics. 2006 Oct 25;7:474
17064419
Am J Hematol. 2007 Nov;82(11):1005-9
17654503
Chromosome Res. 2008;16(1):203-15
18293113
Cell. 2007 Nov 30;131(5):844-6
18045531
Proc Natl Acad Sci U S A. 1994 Dec 20;91(26):12832-6
7809130
Genome Res. 2006 Oct;16(10):1310-9
16963707
Mol Cell. 2004 Apr 23;14(2):221-31
15099521
Semin Cell Dev Biol. 2007 Feb;18(1):140-52
17276707
PLoS Comput Biol. 2006 Nov 3;2(11):e150
17083273
Nature. 2003 Jul 10;424(6945):147-51
12853946
Nat Struct Mol Biol. 2006 Sep;13(9):763-71
16936727
Virology. 1985 Dec;147(2):449-58
3840930
Nucleic Acids Res. 2007;35(8):e56
17389645
Mol Cell Biol. 2005 Jun;25(12):5215-25
15923636
Nature. 2006 Nov 23;444(7118):499-502
17086198
Nucleic Acids Res. 2006 Jul 19;34(12):3585-98
16855295
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W512-5
15980524
Trends Genet. 2003 Feb;19(2):68-72
12547512
Blood. 1991 Nov 1;78(9):2165-77
1932737
J Comput Biol. 2005 Jun;12(5):545-53
15952877
Nat Rev Genet. 2008 May;9(5):397-405
18368054
BMC Genomics. 2008 May 17;9:226
18485226
J Cell Biochem. 2007 Nov 1;102(4):801-10
17910027
Science. 2003 Oct 17;302(5644):413
14563999
Blood. 1997 Jul 1;90(1):421-7
9207479
Genome Res. 2008 Sep;18(9):1403-14
18550801
Genome Biol. 2008;9(9):R141
18811936
Trends Genet. 1995 Jul;11(7):283-90
7482779
Genome Res. 2006 Jan;16(1):123-31
16344561
Biol Direct. 2006 Jul 20;1:20
16857058
Nature. 2007 May 10;447(7141):167-77
17495919
Gene. 2002 Jan 23;283(1-2):185-97
11867225
Nat Genet. 2006 Jun;38(6):626-35
16645617
Cytogenet Genome Res. 2005;110(1-4):457-61
16093698
Nucleic Acids Res. 2007 Jan;35(Database issue):D88-92
17130149
Nature. 2009 May 7;459(7243):108-12
19295514
Trends Genet. 2004 Dec;20(12):611-6
15522456
Cytogenet Genome Res. 2005;110(1-4):333-41
16093685
Bioinformatics. 2002 Oct;18(10):1374-81
12376382
Int Rev Cytol. 2005;247:165-221
16344113
Genome Res. 2007 Feb;17(2):201-11
17210927
Nature. 2001 Feb 15;409(6822):860-921
11237011
Proc Int Conf Intell Syst Mol Biol. 2000;8:269-78
10977088
Genome Dyn. 2007;3:163-174
18753791
Genome Dyn. 2007;3:147-162
18753790
Cell. 1982 Aug;30(1):173-83
6290076
Proc Natl Acad Sci U S A. 2005 Jul 12;102(28):9830-5
15998734