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Evidence that most human Alu sequences were inserted in a process that ceased about 30 million years ago

Britten, Roy J. (1994) Evidence that most human Alu sequences were inserted in a process that ceased about 30 million years ago. Proceedings of the National Academy of Sciences of the United States of America, 91 (13). pp. 6148-6150. ISSN 0027-8424. http://resolver.caltech.edu/CaltechAUTHORS:BRIpnas94b

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Abstract

The primate Alu interspersed repeats can be subdivided into classes on the basis of shared nucleotides at a set of diagnostic positions. Each of the classes of Alu sequences is apparently the result of past retrotransposition of transcripts of highly conserved class-specific source genes that differed from each other at the diagnostic positions. The nucleotides at the majority of positions are identical among the source genes and therefore were identical among all of the Alu sequences at the time of their insertion. These CONSBI (conserved before insertion) positions are useful because the changes that have occurred after insertion are recognizable and the divergence resulting from nucleotide substitutions, insertions, and deletions is informative. The divergence of Alu sequences at the CONSBI positions is a measure of the time since a class was inserted. The greatest majority of Alu sequences are in one class (identified as class II), and it is particularly suitable for such examination, since nearly full-length sequences are now known for nearly a thousand members of this class. The average divergence of class II members indicates that the class has an average age of about 40 million years. The distribution in divergence of class II accurately fits a sum of two Poisson distributions. The implication is that class II Alu sequences were derived from two massive past events of insertion of many Alu sequences. In this model the younger subset of class II sequences (corresponding to about 300,000 copies in the genome) has an average divergence of 5% at CONSBI positions. The older set of class II sequences (corresponding to about 150,000 genomic copies) has a 9% average divergence. Based on the drift rate of primate DNA sequences, the events of insertion probably occurred 30-50 million years ago. The goodness of the fit to the Poisson distribution indicates that no significant number of members of class II have been inserted since 30 million years ago.


Item Type:Article
Additional Information:© 1994 by the National Academy of Sciences. Contributed by Roy J. Britten, March 14, 1994. I thank Eric Davidson for useful criticism and Jerzy Jurka and Barbara Rapp for the collection of Alu sequences. This work was supported by National Institutes of Health grants. The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.
Subject Keywords:repeated sequences; evolution; sequence divergence; retroposition
Record Number:CaltechAUTHORS:BRIpnas94b
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:BRIpnas94b
Alternative URL:http://www.pnas.org/cgi/content/abstract/91/13/6148
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:7585
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:09 Mar 2007
Last Modified:14 Nov 2014 19:19

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