11 Citations (Scopus)

Abstract

Dinucleotide microsatellites are dynamic DNA sequences that affect genome stability. Here, we focused on mature microsatellites, defined as pure repeats of lengths above the threshold and unlikely to mutate below it in a single mutational event. We investigated the prevalence and mutational behavior of these sequences by using human genome sequence data, human cells in culture, and purified DNA polymerases. Mature dinucleotides (≥10 units)are present within exonic sequences of >350 genes, resulting in vulnerability to cellular genetic integrity. Mature dinucleotide mutagenesis was examined experimentally using ex vivo and in vitro approaches. We observe an expansion bias for dinucleotide microsatellites up to 20 units in length in somatic human cells, in agreement withprevious computational analyses of germline biases. Using purified DNA polymerases and human cell lines deficient for mismatch repair (MMR), we show that the expansion bias is caused by functional MMR and is not due to DNA polymerase error biases. Specifically, we observe that the MutSa and MutLa complexes protect against expansion mutations. Our data support a model wherein different MMR complexes shift the balance of mutations toward deletionor expansion. Finally, we show that replication fork progression is stalled within long dinucleotides, suggesting that mutational mechanisms within long repeats may be distinct from shorter lengths, depending on the biochemistry of fork resolution. Our work combines computational and experimental approaches to explain the complex mutational behavior of dinucleotide microsatellites in humans.

Original languageEnglish (US)
Pages (from-to)451-463
Number of pages13
JournalG3: Genes, Genomes, Genetics
Volume3
Issue number3
DOIs
StatePublished - Mar 2013

Fingerprint

Microsatellite Repeats
DNA Mismatch Repair
DNA-Directed DNA Polymerase
Mutation
Genomic Instability
Human Genome
Mutagenesis
Biochemistry
Cell Culture Techniques
Cell Line
Genes

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

Cite this

Baptiste, Beverly A. ; Ananda, Guruprasad ; Strubczewski, Noelle ; Lutzkanin, Andrew ; Khoo, Su Jen ; Srikanth, Abhinaya ; Kim, Nari ; Makova, Kateryna D. ; Krasilnikova, Maria M. ; Eckert, Kristin A. / Mature microsatellites : Mechanisms underlying dinucleotide microsatellite mutational biases in human cells. In: G3: Genes, Genomes, Genetics. 2013 ; Vol. 3, No. 3. pp. 451-463.
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abstract = "Dinucleotide microsatellites are dynamic DNA sequences that affect genome stability. Here, we focused on mature microsatellites, defined as pure repeats of lengths above the threshold and unlikely to mutate below it in a single mutational event. We investigated the prevalence and mutational behavior of these sequences by using human genome sequence data, human cells in culture, and purified DNA polymerases. Mature dinucleotides (≥10 units)are present within exonic sequences of >350 genes, resulting in vulnerability to cellular genetic integrity. Mature dinucleotide mutagenesis was examined experimentally using ex vivo and in vitro approaches. We observe an expansion bias for dinucleotide microsatellites up to 20 units in length in somatic human cells, in agreement withprevious computational analyses of germline biases. Using purified DNA polymerases and human cell lines deficient for mismatch repair (MMR), we show that the expansion bias is caused by functional MMR and is not due to DNA polymerase error biases. Specifically, we observe that the MutSa and MutLa complexes protect against expansion mutations. Our data support a model wherein different MMR complexes shift the balance of mutations toward deletionor expansion. Finally, we show that replication fork progression is stalled within long dinucleotides, suggesting that mutational mechanisms within long repeats may be distinct from shorter lengths, depending on the biochemistry of fork resolution. Our work combines computational and experimental approaches to explain the complex mutational behavior of dinucleotide microsatellites in humans.",
author = "Baptiste, {Beverly A.} and Guruprasad Ananda and Noelle Strubczewski and Andrew Lutzkanin and Khoo, {Su Jen} and Abhinaya Srikanth and Nari Kim and Makova, {Kateryna D.} and Krasilnikova, {Maria M.} and Eckert, {Kristin A.}",
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Mature microsatellites : Mechanisms underlying dinucleotide microsatellite mutational biases in human cells. / Baptiste, Beverly A.; Ananda, Guruprasad; Strubczewski, Noelle; Lutzkanin, Andrew; Khoo, Su Jen; Srikanth, Abhinaya; Kim, Nari; Makova, Kateryna D.; Krasilnikova, Maria M.; Eckert, Kristin A.

In: G3: Genes, Genomes, Genetics, Vol. 3, No. 3, 03.2013, p. 451-463.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Mature microsatellites

T2 - Mechanisms underlying dinucleotide microsatellite mutational biases in human cells

AU - Baptiste, Beverly A.

AU - Ananda, Guruprasad

AU - Strubczewski, Noelle

AU - Lutzkanin, Andrew

AU - Khoo, Su Jen

AU - Srikanth, Abhinaya

AU - Kim, Nari

AU - Makova, Kateryna D.

AU - Krasilnikova, Maria M.

AU - Eckert, Kristin A.

PY - 2013/3

Y1 - 2013/3

N2 - Dinucleotide microsatellites are dynamic DNA sequences that affect genome stability. Here, we focused on mature microsatellites, defined as pure repeats of lengths above the threshold and unlikely to mutate below it in a single mutational event. We investigated the prevalence and mutational behavior of these sequences by using human genome sequence data, human cells in culture, and purified DNA polymerases. Mature dinucleotides (≥10 units)are present within exonic sequences of >350 genes, resulting in vulnerability to cellular genetic integrity. Mature dinucleotide mutagenesis was examined experimentally using ex vivo and in vitro approaches. We observe an expansion bias for dinucleotide microsatellites up to 20 units in length in somatic human cells, in agreement withprevious computational analyses of germline biases. Using purified DNA polymerases and human cell lines deficient for mismatch repair (MMR), we show that the expansion bias is caused by functional MMR and is not due to DNA polymerase error biases. Specifically, we observe that the MutSa and MutLa complexes protect against expansion mutations. Our data support a model wherein different MMR complexes shift the balance of mutations toward deletionor expansion. Finally, we show that replication fork progression is stalled within long dinucleotides, suggesting that mutational mechanisms within long repeats may be distinct from shorter lengths, depending on the biochemistry of fork resolution. Our work combines computational and experimental approaches to explain the complex mutational behavior of dinucleotide microsatellites in humans.

AB - Dinucleotide microsatellites are dynamic DNA sequences that affect genome stability. Here, we focused on mature microsatellites, defined as pure repeats of lengths above the threshold and unlikely to mutate below it in a single mutational event. We investigated the prevalence and mutational behavior of these sequences by using human genome sequence data, human cells in culture, and purified DNA polymerases. Mature dinucleotides (≥10 units)are present within exonic sequences of >350 genes, resulting in vulnerability to cellular genetic integrity. Mature dinucleotide mutagenesis was examined experimentally using ex vivo and in vitro approaches. We observe an expansion bias for dinucleotide microsatellites up to 20 units in length in somatic human cells, in agreement withprevious computational analyses of germline biases. Using purified DNA polymerases and human cell lines deficient for mismatch repair (MMR), we show that the expansion bias is caused by functional MMR and is not due to DNA polymerase error biases. Specifically, we observe that the MutSa and MutLa complexes protect against expansion mutations. Our data support a model wherein different MMR complexes shift the balance of mutations toward deletionor expansion. Finally, we show that replication fork progression is stalled within long dinucleotides, suggesting that mutational mechanisms within long repeats may be distinct from shorter lengths, depending on the biochemistry of fork resolution. Our work combines computational and experimental approaches to explain the complex mutational behavior of dinucleotide microsatellites in humans.

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JO - G3: Genes, Genomes, Genetics

JF - G3: Genes, Genomes, Genetics

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