Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity

Marion L. Carroll, Astrid M. Roy-Engel, Son V. Nguyen, Abdel Halim Salem, Erika Vogel, Bethaney Vincent, Jeremy Myers, Zahid Ahmad, Lan Nguyen, Mimi Sammarco, W. Scott Watkins, Jurgen Henke, Wojciech Makalowski, Lynn B. Jorde, Prescott L. Deininger, Mark A. Batzer

Research output: Contribution to journalArticle

132 Citations (Scopus)

Abstract

We have utilized computational biology to screen GenBank for the presence of recently integrated Ya5 and Yb8 Alu family members. Our analysis identified 2640 Ya5 Alu family members and 1852 Yb8 Alu family members from the draff sequence of the human genome. We selected a set of 475 of these elements for detailed analyses. Analysis of the DNA sequences from the individual Alu elements revealed a low level of random mutations within both subfamilies consistent with the recent origin of these elements within the human genome. Polymerase chain reaction assays were used to determine the phylogenetic distribution and human genomic variation associated with each Alu repeat. Over 99% of the Ya5 and Yb8 Alu family members were restricted to the human genome and absent from orthologous positions within the genomes of several non-human primates, confirming the recent origin of these Alu subfamilies in the human genome. Approximately 1% of the analyzed Ya5 and Yb8 Alu family members had integrated into previously undefined repeated regions of the human genome. Analysis of mosaic Yb8 elements suggests gene conversion played an important role in generating sequence diversity among these elements. Of the 475 evaluated elements, a total of 106 of the Ya5 and Yb8 Alu family members were polymorphic for insertion presence/absence within the genomes of a diverse array of human populations. The newly identified Alu insertion polymorphisms will be useful tools for the study of human genomic diversity.

Original languageEnglish (US)
Pages (from-to)17-40
Number of pages24
JournalJournal of Molecular Biology
Volume311
Issue number1
DOIs
StatePublished - Aug 3 2001

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Alu Elements
Human Genome
Genome
Gene Conversion
Nucleic Acid Databases
Computational Biology
DNA Sequence Analysis
Primates
Polymerase Chain Reaction
Mutation

Keywords

  • Alu insertion polymorphism
  • Computational biology
  • Gene conversion

ASJC Scopus subject areas

  • Virology

Cite this

Carroll, M. L., Roy-Engel, A. M., Nguyen, S. V., Salem, A. H., Vogel, E., Vincent, B., ... Batzer, M. A. (2001). Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. Journal of Molecular Biology, 311(1), 17-40. https://doi.org/10.1006/jmbi.2001.4847

Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. / Carroll, Marion L.; Roy-Engel, Astrid M.; Nguyen, Son V.; Salem, Abdel Halim; Vogel, Erika; Vincent, Bethaney; Myers, Jeremy; Ahmad, Zahid; Nguyen, Lan; Sammarco, Mimi; Watkins, W. Scott; Henke, Jurgen; Makalowski, Wojciech; Jorde, Lynn B.; Deininger, Prescott L.; Batzer, Mark A.

In: Journal of Molecular Biology, Vol. 311, No. 1, 03.08.2001, p. 17-40.

Research output: Contribution to journalArticle

Carroll, ML, Roy-Engel, AM, Nguyen, SV, Salem, AH, Vogel, E, Vincent, B, Myers, J, Ahmad, Z, Nguyen, L, Sammarco, M, Watkins, WS, Henke, J, Makalowski, W, Jorde, LB, Deininger, PL & Batzer, MA 2001, 'Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity', Journal of Molecular Biology, vol. 311, no. 1, pp. 17-40. https://doi.org/10.1006/jmbi.2001.4847
Carroll, Marion L. ; Roy-Engel, Astrid M. ; Nguyen, Son V. ; Salem, Abdel Halim ; Vogel, Erika ; Vincent, Bethaney ; Myers, Jeremy ; Ahmad, Zahid ; Nguyen, Lan ; Sammarco, Mimi ; Watkins, W. Scott ; Henke, Jurgen ; Makalowski, Wojciech ; Jorde, Lynn B. ; Deininger, Prescott L. ; Batzer, Mark A. / Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. In: Journal of Molecular Biology. 2001 ; Vol. 311, No. 1. pp. 17-40.
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