Characterization of Alu repeats that are associated with trinucleotide and tetranucleotide repeat microsatellites

Chandri N Yandava; Julie M Gastier; Jacqueline C Pulido; Tom Brody; Val  Sheffield; Jeffrey Murray; Kenneth  Buetow; Geoffrey M Duyk

doi:10.1101/gr.7.7.716

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Characterization of Alu repeats that are associated with trinucleotide and tetranucleotide repeat microsatellites

Journal article

Open access

Peer reviewed

Characterization of Alu repeats that are associated with trinucleotide and tetranucleotide repeat microsatellites

Chandri N Yandava, Julie M Gastier, Jacqueline C Pulido, Tom Brody, Val Sheffield, Jeffrey Murray, Kenneth Buetow and Geoffrey M Duyk

Genome research, Vol.7(7), pp.716-724

07/1997

DOI: 10.1101/gr.7.7.716

PMID: 9253600

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Abstract

The association of subclasses of Alu repetitive elements with various classes of trinucleotide and tetranucleotide microsatellites was characterized as a first step toward advancing our understanding of the evolution of microsatellite repeats. In addition, information regarding the association of specific classes of microsatellites with families of Alu elements was used to facilitate the development of genetic markers. Sequences containing Alu repeats were eliminated because unique primers could not be designed. Various classes of microsatellites are associated with different classes of Alu repeats. Very abundant and poly(A)-rich microsatellite classes (ATA, AATA) are frequently associated with an evolutionarily older subclass of Alu repeats, AluSx, whereas most of GATA and CA microsatellites are associated with a recent Alu subfamily, AluY. Our observations support all three possible mechanisms for the association of Alu repeats to microsatellites. Primers designed using a set of sequences from a particular microsatellite class showed higher homology with more sequences of that class than probes designed for other classes. We developed an efficient method of prescreening GGAA and ATA microsatellite clones for Alu repeats with probes designed in this study. We also showed that Alu probes labeled in a single reaction (multiplex labeling) could be used efficiently for prescreening of GGAA clones. Sequencing of these prescreened GGAA microsatellites revealed only 5% Alu repeats. Prescreening with primers designed for ATA microsatellite class resulted in the reduction of the loss of markers from approximately 50% to 10%. The new Alu probes that were designed have also proved to be useful in Alu-Alu fingerprinting.

Animals

Chromosomes, Artificial, Yeast

Humans

Repetitive Sequences, Nucleic Acid

Chromosome Mapping

Mice

Genome, Human

Microsatellite Repeats - genetics

Details

Title: Subtitle: Characterization of Alu repeats that are associated with trinucleotide and tetranucleotide repeat microsatellites
Creators: Chandri N Yandava - Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA. Yandava@rascal.med.harvard.edu
Julie M Gastier
Jacqueline C Pulido
Tom Brody
Val Sheffield
Jeffrey Murray
Kenneth Buetow
Geoffrey M Duyk
Resource Type: Journal article
Publication Details: Genome research, Vol.7(7), pp.716-724
DOI: 10.1101/gr.7.7.716
PMID: 9253600
NLM abbreviation: Genome Res
ISSN: 1088-9051
eISSN: 1549-5469
Publisher: United States
Grant note: 1 P50 H00835-01 / PHS HHS
Language: English
Date published: 07/1997
Academic Unit: Anatomy and Cell Biology; Stead Family Department of Pediatrics; Epidemiology; Iowa Neuroscience Institute; Medical Genetics and Genomics; Pediatric Dentistry; Craniofacial Anomalies Research Center; Dental Research; Ophthalmology and Visual Sciences
Record Identifier: 9984025303802771

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