publication . Article . 2017

Computational identification of harmful mutation regions to the activity of transposable elements.

Ian McQuillan; Lingling Jin; Longhai Li;
Open Access
  • Published: 01 Nov 2017 Journal: BMC Genomics, volume 18 (eissn: 1471-2164, Copyright policy)
  • Publisher: Springer Nature
Abstract
Abstract Background Transposable elements (TEs) are interspersed DNA sequences that can move or copy to new positions within a genome. TEs are believed to promote speciation and their activities play a significant role in human disease. In the human genome, the 22 AluY and 6 AluS TE subfamilies have been the most recently active, and their transposition has been implicated in many inherited human diseases and in various forms of cancer. Therefore, understanding their transposition activity is very important and identifying the factors that affect their transpositional activity is of great interest. Recently, there has been some work done to quantify the activity...
Subjects
free text keywords: Research, Transposable elements, Harmful mutation regions, The human genome, Pearson’s coefficient of correlation, Statistical significance test, Multiple testing correction, Biotechnology, TP248.13-248.65, QH426-470, Transposition (music), DNA microarray, Mutation, medicine.disease_cause, medicine, Genome, Consensus sequence, Alu element, Genetics, Human genome, Transposable element, Biology
Related Organizations
Funded by
NSERC
Project
  • Funder: Natural Sciences and Engineering Research Council of Canada (NSERC)
32 references, page 1 of 3

McClintock, B. Chromosome organization and genic expression. Cold Spring Harbor Symposia on Quantitative Biology. 1951 [OpenAIRE]

de Koning, APJ, Gu, W, Castoe, TA, Batzer, MA, Pollock, DD. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 2011; 7 (12): 1002384 [OpenAIRE] [DOI]

Lerat, E. Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity. 2009; 104 (6): 520-33 [OpenAIRE] [PubMed] [DOI]

Finnegan, DJ. Eukaryotic transposable elements and genome evolution. Trends Genet. 1989; 5: 103-7 [OpenAIRE] [PubMed] [DOI]

Wicker, T, Sabot, F, Hua-Van, A, Bennetzen, JL, Capy, P, Chalhoub, B, Flavell, A, Leroy, P, Morgante, M, Panaud, O. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 2007; 8 (12): 973-82 [OpenAIRE] [PubMed] [DOI]

Kazazian, HH. Mobile DNA: Finding Treasure in Junk. 2011

Giordano, J, Ge, Y, Gelfand, Y, Abrusán, G, Benson, G, Warburton, PE. Evolutionary history of mammalian transposons determined by genome-wide defragmentation. PLoS Comput Biol. 2007; 3 (7): 137 [OpenAIRE] [DOI]

Graur, D. Molecular and Genome Evolution. 2016

Jurka, J, Kapitonov, VV, Pavlicek, A, Klonowski, P, Kohany, O, Walichiewicz, J. Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005; 110 (1–4): 462-7 [OpenAIRE] [PubMed] [DOI]

Feschotte, C, Jiang, N, Wessler, SR. Plant transposable elements: where genetics meets genomics. Nat Rev Genet. 2002; 3 (5): 329-41 [OpenAIRE] [PubMed] [DOI]

Khan, H, Smit, A, Boissinot, S. Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res. 2006; 16 (1): 78-87 [OpenAIRE] [PubMed] [DOI]

Mills, RE, Bennett, EA, Iskow, RC, Devine, SE. Which transposable elements are active in the human genome. Trends Genet. 2007; 23 (4): 183-91 [OpenAIRE] [PubMed] [DOI]

Kazazian, HH. An estimated frequency of endogenous insertional mutations in humans. Nat Genet. 1999; 22 (2): 130-130 [OpenAIRE] [PubMed] [DOI]

Li, X, Scaringe, WA, Hill, KA, Roberts, S, Mengos, A, Careri, D, Pinto, MT, Kasper, CK, Sommer, SS. Frequency of recent retrotransposition events in the human factor ix gene. Hum Mutat. 2001; 17 (6): 511-9 [OpenAIRE] [PubMed] [DOI]

Cordaux, R, Hedges, DJ, Herke, SW, Batzer, MA. Estimating the retrotransposition rate of human Alu elements. Gene. 2006; 373: 134-7 [OpenAIRE] [PubMed] [DOI]

32 references, page 1 of 3
Abstract
Abstract Background Transposable elements (TEs) are interspersed DNA sequences that can move or copy to new positions within a genome. TEs are believed to promote speciation and their activities play a significant role in human disease. In the human genome, the 22 AluY and 6 AluS TE subfamilies have been the most recently active, and their transposition has been implicated in many inherited human diseases and in various forms of cancer. Therefore, understanding their transposition activity is very important and identifying the factors that affect their transpositional activity is of great interest. Recently, there has been some work done to quantify the activity...
Subjects
free text keywords: Research, Transposable elements, Harmful mutation regions, The human genome, Pearson’s coefficient of correlation, Statistical significance test, Multiple testing correction, Biotechnology, TP248.13-248.65, QH426-470, Transposition (music), DNA microarray, Mutation, medicine.disease_cause, medicine, Genome, Consensus sequence, Alu element, Genetics, Human genome, Transposable element, Biology
Related Organizations
Funded by
NSERC
Project
  • Funder: Natural Sciences and Engineering Research Council of Canada (NSERC)
32 references, page 1 of 3

McClintock, B. Chromosome organization and genic expression. Cold Spring Harbor Symposia on Quantitative Biology. 1951 [OpenAIRE]

de Koning, APJ, Gu, W, Castoe, TA, Batzer, MA, Pollock, DD. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 2011; 7 (12): 1002384 [OpenAIRE] [DOI]

Lerat, E. Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity. 2009; 104 (6): 520-33 [OpenAIRE] [PubMed] [DOI]

Finnegan, DJ. Eukaryotic transposable elements and genome evolution. Trends Genet. 1989; 5: 103-7 [OpenAIRE] [PubMed] [DOI]

Wicker, T, Sabot, F, Hua-Van, A, Bennetzen, JL, Capy, P, Chalhoub, B, Flavell, A, Leroy, P, Morgante, M, Panaud, O. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 2007; 8 (12): 973-82 [OpenAIRE] [PubMed] [DOI]

Kazazian, HH. Mobile DNA: Finding Treasure in Junk. 2011

Giordano, J, Ge, Y, Gelfand, Y, Abrusán, G, Benson, G, Warburton, PE. Evolutionary history of mammalian transposons determined by genome-wide defragmentation. PLoS Comput Biol. 2007; 3 (7): 137 [OpenAIRE] [DOI]

Graur, D. Molecular and Genome Evolution. 2016

Jurka, J, Kapitonov, VV, Pavlicek, A, Klonowski, P, Kohany, O, Walichiewicz, J. Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005; 110 (1–4): 462-7 [OpenAIRE] [PubMed] [DOI]

Feschotte, C, Jiang, N, Wessler, SR. Plant transposable elements: where genetics meets genomics. Nat Rev Genet. 2002; 3 (5): 329-41 [OpenAIRE] [PubMed] [DOI]

Khan, H, Smit, A, Boissinot, S. Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res. 2006; 16 (1): 78-87 [OpenAIRE] [PubMed] [DOI]

Mills, RE, Bennett, EA, Iskow, RC, Devine, SE. Which transposable elements are active in the human genome. Trends Genet. 2007; 23 (4): 183-91 [OpenAIRE] [PubMed] [DOI]

Kazazian, HH. An estimated frequency of endogenous insertional mutations in humans. Nat Genet. 1999; 22 (2): 130-130 [OpenAIRE] [PubMed] [DOI]

Li, X, Scaringe, WA, Hill, KA, Roberts, S, Mengos, A, Careri, D, Pinto, MT, Kasper, CK, Sommer, SS. Frequency of recent retrotransposition events in the human factor ix gene. Hum Mutat. 2001; 17 (6): 511-9 [OpenAIRE] [PubMed] [DOI]

Cordaux, R, Hedges, DJ, Herke, SW, Batzer, MA. Estimating the retrotransposition rate of human Alu elements. Gene. 2006; 373: 134-7 [OpenAIRE] [PubMed] [DOI]

32 references, page 1 of 3
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