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For: Glazko GV, Koonin EV, Rogozin IB, Shabalina SA. A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions. Trends Genet 2003;19:119-24. [PMID: 12615002 DOI: 10.1016/s0168-9525(03)00016-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Number Cited by Other Article(s)
1
Pathak RU, Phanindhar K, Mishra RK. Transposable elements as scaffold/matrix attachment regions: shaping organization and functions in genomes. Front Mol Biosci 2024;10:1326933. [PMID: 38455359 PMCID: PMC10918478 DOI: 10.3389/fmolb.2023.1326933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/27/2023] [Indexed: 03/09/2024]  Open
2
Dynamics of nuclear matrix attachment regions during 5th instar posterior silk gland development in Bombyx mori. BMC Genomics 2022;23:247. [PMID: 35361117 PMCID: PMC8973518 DOI: 10.1186/s12864-022-08446-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/06/2022] [Indexed: 12/02/2022]  Open
3
Genome-wide identification, phylogenetic and expression pattern analysis of MADS-box family genes in foxtail millet (Setaria italica). Sci Rep 2022;12:4979. [PMID: 35322041 PMCID: PMC8943164 DOI: 10.1038/s41598-022-07103-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/10/2022] [Indexed: 11/28/2022]  Open
4
Poverennaya IV, Roytberg MA. Spliceosomal Introns: Features, Functions, and Evolution. BIOCHEMISTRY (MOSCOW) 2021;85:725-734. [PMID: 33040717 DOI: 10.1134/s0006297920070019] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
5
Kashevarova AA, Lebedev IN. Genomic architecture of human chromosomal diseases. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416040062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
6
Whitaker JW, Nguyen TT, Zhu Y, Wildberg A, Wang W. Computational schemes for the prediction and annotation of enhancers from epigenomic assays. Methods 2015;72:86-94. [PMID: 25461775 PMCID: PMC4778972 DOI: 10.1016/j.ymeth.2014.10.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 09/14/2014] [Accepted: 10/08/2014] [Indexed: 12/31/2022]  Open
7
Seridi L, Ryu T, Ravasi T. Dynamic epigenetic control of highly conserved noncoding elements. PLoS One 2014;9:e109326. [PMID: 25289637 PMCID: PMC4188601 DOI: 10.1371/journal.pone.0109326] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 09/11/2014] [Indexed: 11/19/2022]  Open
8
Polychronopoulos D, Sellis D, Almirantis Y. Conserved noncoding elements follow power-law-like distributions in several genomes as a result of genome dynamics. PLoS One 2014;9:e95437. [PMID: 24787386 PMCID: PMC4008492 DOI: 10.1371/journal.pone.0095437] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/26/2014] [Indexed: 12/31/2022]  Open
9
Noble LM, Andrianopoulos A. Fungal genes in context: genome architecture reflects regulatory complexity and function. Genome Biol Evol 2013;5:1336-52. [PMID: 23699226 PMCID: PMC3730340 DOI: 10.1093/gbe/evt077] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
10
Matsubara S, Kurihara M, Kimura AP. A long non-coding RNA transcribed from conserved non-coding sequences contributes to the mouse prolyl oligopeptidase gene activation. J Biochem 2013;155:243-56. [PMID: 24369296 DOI: 10.1093/jb/mvt113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
11
Lowe CB, Haussler D. 29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. PLoS One 2012;7:e43128. [PMID: 22952639 PMCID: PMC3428314 DOI: 10.1371/journal.pone.0043128] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 07/17/2012] [Indexed: 11/18/2022]  Open
12
Predicting nucleosome binding motif set and analyzing their distributions around functional sites of human genes. Chromosome Res 2012;20:685-98. [DOI: 10.1007/s10577-012-9305-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 07/13/2012] [Accepted: 07/17/2012] [Indexed: 01/30/2023]
13
Hemberg M, Gray JM, Cloonan N, Kuersten S, Grimmond S, Greenberg ME, Kreiman G. Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites. Nucleic Acids Res 2012;40:7858-69. [PMID: 22684627 PMCID: PMC3439890 DOI: 10.1093/nar/gks477] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]  Open
14
Rogozin IB, Carmel L, Csuros M, Koonin EV. Origin and evolution of spliceosomal introns. Biol Direct 2012;7:11. [PMID: 22507701 PMCID: PMC3488318 DOI: 10.1186/1745-6150-7-11] [Citation(s) in RCA: 224] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 03/15/2012] [Indexed: 12/31/2022]  Open
15
Vissers LELM, Stankiewicz P. Microdeletion and microduplication syndromes. Methods Mol Biol 2012;838:29-75. [PMID: 22228006 DOI: 10.1007/978-1-61779-507-7_2] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
16
Abnizova I, Walter K, Te Boekhorst R, Elgar G, Gilks WR. STATISTICAL INFORMATION CHARACTERIZATION OF CONSERVED NON-CODING ELEMENTS IN VERTEBRATES. J Bioinform Comput Biol 2011;5:533-47. [PMID: 17636860 DOI: 10.1142/s0219720007002898] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Revised: 02/23/2007] [Accepted: 02/23/2007] [Indexed: 01/28/2023]
17
Ponting CP, Nellåker C, Meader S. Rapid turnover of functional sequence in human and other genomes. Annu Rev Genomics Hum Genet 2011;12:275-99. [PMID: 21721940 DOI: 10.1146/annurev-genom-090810-183115] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
18
Chatterjee S, Bourque G, Lufkin T. Conserved and non-conserved enhancers direct tissue specific transcription in ancient germ layer specific developmental control genes. BMC DEVELOPMENTAL BIOLOGY 2011;11:63. [PMID: 22011226 PMCID: PMC3210094 DOI: 10.1186/1471-213x-11-63] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 10/20/2011] [Indexed: 01/29/2023]
19
Characterization of a new ARID family transcription factor (Brightlike/ARID3C) that co-activates Bright/ARID3A-mediated immunoglobulin gene transcription. Mol Immunol 2011;49:260-72. [PMID: 21955986 DOI: 10.1016/j.molimm.2011.08.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 08/27/2011] [Indexed: 11/21/2022]
20
Tattermusch A, Brockdorff N. A scaffold for X chromosome inactivation. Hum Genet 2011;130:247-53. [PMID: 21660507 DOI: 10.1007/s00439-011-1027-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 05/27/2011] [Indexed: 11/30/2022]
21
Chavali PL, Funa K, Chavali S. Cis-regulation of microRNA expression by scaffold/matrix-attachment regions. Nucleic Acids Res 2011;39:6908-18. [PMID: 21586588 PMCID: PMC3167628 DOI: 10.1093/nar/gkr303] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
22
Künstner A, Nabholz B, Ellegren H. Evolutionary constraint in flanking regions of avian genes. Mol Biol Evol 2011;28:2481-9. [PMID: 21393603 DOI: 10.1093/molbev/msr066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
23
Robyr D, Friedli M, Gehrig C, Arcangeli M, Marin M, Guipponi M, Farinelli L, Barde I, Verp S, Trono D, Antonarakis SE. Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences. PLoS One 2011;6:e17634. [PMID: 21408183 PMCID: PMC3049788 DOI: 10.1371/journal.pone.0017634] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 02/04/2011] [Indexed: 02/02/2023]  Open
24
George JW, Dille EA, Heckert LL. Current concepts of follicle-stimulating hormone receptor gene regulation. Biol Reprod 2011;84:7-17. [PMID: 20739665 PMCID: PMC4480823 DOI: 10.1095/biolreprod.110.085043] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 05/04/2010] [Accepted: 08/16/2010] [Indexed: 12/25/2022]  Open
25
Conte I, Marco-Ferreres R, Beccari L, Cisneros E, Ruiz JM, Tabanera N, Bovolenta P. Proper differentiation of photoreceptors and amacrine cells depends on a regulatory loop between NeuroD and Six6. Development 2010;137:2307-17. [PMID: 20534668 DOI: 10.1242/dev.045294] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
26
Programming DNA replication origins and chromosome organization. Chromosome Res 2010;18:137-45. [DOI: 10.1007/s10577-009-9105-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
27
TIAN J, ZHAO ZH, CHEN HP. [Conserved non-coding elements in human genome]. YI CHUAN = HEREDITAS 2009;31:1067-1076. [PMID: 19933086 DOI: 10.3724/sp.j.1005.2009.01067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
28
Koonin EV. Darwinian evolution in the light of genomics. Nucleic Acids Res 2009;37:1011-34. [PMID: 19213802 PMCID: PMC2651812 DOI: 10.1093/nar/gkp089] [Citation(s) in RCA: 171] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]  Open
29
Attanasio C, Reymond A, Humbert R, Lyle R, Kuehn MS, Neph S, Sabo PJ, Goldy J, Weaver M, Haydock A, Lee K, Dorschner M, Dermitzakis ET, Antonarakis SE, Stamatoyannopoulos JA. Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells. Genome Biol 2008;9:R168. [PMID: 19055709 PMCID: PMC2646272 DOI: 10.1186/gb-2008-9-12-r168] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 09/24/2008] [Accepted: 12/02/2008] [Indexed: 01/26/2023]  Open
30
The words of the regulatory code are arranged in a variable manner in highly conserved enhancers. Dev Biol 2008;318:366-77. [PMID: 18455719 DOI: 10.1016/j.ydbio.2008.03.034] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Revised: 03/17/2008] [Accepted: 03/20/2008] [Indexed: 01/29/2023]
31
Hirano Y, Ishii K, Kumeta M, Furukawa K, Takeyasu K, Horigome T. Proteomic and targeted analytical identification of BXDC1 and EBNA1BP2 as dynamic scaffold proteins in the nucleolus. Genes Cells 2008;14:155-66. [PMID: 19170763 DOI: 10.1111/j.1365-2443.2008.01262.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
32
Gluch A, Vidakovic M, Bode J. Scaffold/matrix attachment regions (S/MARs): relevance for disease and therapy. Handb Exp Pharmacol 2008:67-103. [PMID: 18491049 DOI: 10.1007/978-3-540-72843-6_4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
33
Strähle U, Rastegar S. Conserved non-coding sequences and transcriptional regulation. Brain Res Bull 2007;75:225-30. [PMID: 18331875 DOI: 10.1016/j.brainresbull.2007.11.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Revised: 11/12/2007] [Accepted: 11/12/2007] [Indexed: 01/05/2023]
34
Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements. Proc Natl Acad Sci U S A 2007;104:20443-8. [PMID: 18077382 DOI: 10.1073/pnas.0705658104] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
35
Kim MS, Lim HS, Ahn SJ, Jeong YK, Kim CG, Lee HH. Enhanced expression of EGFP gene in CHSE-214 cells by an ARS element from mud loach (Misgurnus mizolepis). Plasmid 2007;58:228-39. [PMID: 17586046 DOI: 10.1016/j.plasmid.2007.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Revised: 04/16/2007] [Accepted: 05/01/2007] [Indexed: 10/23/2022]
36
Sanges R, Kalmar E, Claudiani P, D'Amato M, Muller F, Stupka E. Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage. Genome Biol 2007;7:R56. [PMID: 16859531 PMCID: PMC1779573 DOI: 10.1186/gb-2006-7-7-r56] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2006] [Revised: 04/05/2006] [Accepted: 06/27/2006] [Indexed: 02/06/2023]  Open
37
Linnemann AK, Platts AE, Doggett N, Gluch A, Bode J, Krawetz SA. Genomewide identification of nuclear matrix attachment regions: an analysis of methods. Biochem Soc Trans 2007;35:612-7. [PMID: 17511663 DOI: 10.1042/bst0350612] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
38
Freeling M, Rapaka L, Lyons E, Pedersen B, Thomas BC. G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis. THE PLANT CELL 2007;19:1441-57. [PMID: 17496117 PMCID: PMC1913728 DOI: 10.1105/tpc.107.050419] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Revised: 03/10/2007] [Accepted: 04/19/2007] [Indexed: 05/15/2023]
39
Thomas BC, Rapaka L, Lyons E, Pedersen B, Freeling M. Arabidopsis intragenomic conserved noncoding sequence. Proc Natl Acad Sci U S A 2007;104:3348-53. [PMID: 17301222 PMCID: PMC1805546 DOI: 10.1073/pnas.0611574104] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Indexed: 11/18/2022]  Open
40
Carlton VEH, Ireland JS, Useche F, Faham M. Functional single nucleotide polymorphism-based association studies. Hum Genomics 2006;2:391-402. [PMID: 16848977 PMCID: PMC3525158 DOI: 10.1186/1479-7364-2-6-391] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
41
Thomas BC, Pedersen B, Freeling M. Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res 2006;16:934-46. [PMID: 16760422 PMCID: PMC1484460 DOI: 10.1101/gr.4708406] [Citation(s) in RCA: 300] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
42
Xie F, Wang X, Cooper DN, Chuzhanova N, Fang Y, Cai X, Wang Z, Wang H. A novel Alu-mediated 61-kb deletion of the von Willebrand factor (VWF) gene whose breakpoints co-locate with putative matrix attachment regions. Blood Cells Mol Dis 2006;36:385-91. [PMID: 16690331 DOI: 10.1016/j.bcmd.2006.03.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2005] [Accepted: 03/07/2006] [Indexed: 11/15/2022]
43
Tetko IV, Haberer G, Rudd S, Meyers B, Mewes HW, Mayer KFX. Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana. PLoS Comput Biol 2006;2:e21. [PMID: 16604187 PMCID: PMC1420657 DOI: 10.1371/journal.pcbi.0020021] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2005] [Accepted: 02/07/2006] [Indexed: 11/18/2022]  Open
44
Vinogradov AE. "Genome design" model: evidence from conserved intronic sequence in human-mouse comparison. Genes Dev 2006;16:347-54. [PMID: 16461636 PMCID: PMC1415212 DOI: 10.1101/gr.4318206] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2005] [Accepted: 12/15/2005] [Indexed: 11/25/2022]
45
Stone EA, Cooper GM, Sidow A. Trade-offs in detecting evolutionarily constrained sequence by comparative genomics. Annu Rev Genomics Hum Genet 2005;6:143-64. [PMID: 16124857 DOI: 10.1146/annurev.genom.6.080604.162146] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
46
Adams MD. Conserved sequences and the evolution of gene regulatory signals. Curr Opin Genet Dev 2005;15:628-33. [PMID: 16185862 DOI: 10.1016/j.gde.2005.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2005] [Accepted: 09/14/2005] [Indexed: 12/26/2022]
47
Bejerano G, Siepel AC, Kent WJ, Haussler D. Computational screening of conserved genomic DNA in search of functional noncoding elements. Nat Methods 2005;2:535-45. [PMID: 16170870 DOI: 10.1038/nmeth0705-535] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
48
Sironi M, Menozzi G, Comi GP, Cagliani R, Bresolin N, Pozzoli U. Analysis of intronic conserved elements indicates that functional complexity might represent a major source of negative selection on non-coding sequences. Hum Mol Genet 2005;14:2533-46. [PMID: 16037065 DOI: 10.1093/hmg/ddi257] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]  Open
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Aloni R, Lancet D. Conservation anchors in the vertebrate genome. Genome Biol 2005;6:115. [PMID: 15998454 PMCID: PMC1175977 DOI: 10.1186/gb-2005-6-7-115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]  Open
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Ganapathi M, Srivastava P, Sutar SKD, Kumar K, Dasgupta D, Pal Singh G, Brahmachari V, Brahmachari SK. Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes. BMC Bioinformatics 2005;6:126. [PMID: 15918906 PMCID: PMC1173084 DOI: 10.1186/1471-2105-6-126] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2004] [Accepted: 05/26/2005] [Indexed: 11/10/2022]  Open
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