Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene

Erick W. Loomis, John S. Eid, Paul Peluso, Jun Yin, Luke Hickey, David Rank, Sarah McCalmon, Randi J Hagerman, Flora Tassone, Paul J Hagerman

Research output: Contribution to journalArticle

105 Scopus citations

Abstract

The human fragile X mental retardation 1 (FMR1) gene contains a (CGG) n trinucleotide repeat in its 59 untranslated region (5′UTR). Expansions of this repeat result in a number of clinical disorders with distinct molecular pathologies, including fragile X syndrome (FXS; full mutation range, greater than 200 CGG repeats) and fragile X-associated tremor/ataxia syndrome (FXTAS; premutation range, 55-200 repeats). Study of these diseases has been limited by an inability to sequence expanded CGG repeats, particularly in the full mutation range, with existing DNA sequencing technologies. Single-molecule, real-time (SMRT) sequencing provides an approach to sequencing that is fundamentally different from other "next-generation" sequencing platforms, and is well suited for long, repetitive DNA sequences. We report the first sequence data for expanded CGG-repeat FMR1 alleles in the full mutation range that reveal the confounding effects of CGG-repeat tracts on both cloning and PCR. A unique feature of SMRT sequencing is its ability to yield real-time information on the rates of nucleoside addition by the tethered DNA polymerase; for the CGG-repeat alleles, we find a strand-specific effect of CGG-repeat DNA on the interpulse distance. This kinetic signature reveals a novel aspect of the repeat element; namely, that the particular G bias within the CGG/CCG-repeat element influences polymerase activity in a manner that extends beyond simple nearest-neighbor effects. These observations provide a baseline for future kinetic studies of repeat elements, as well as for studies of epigenetic and other chemical modifications thereof.

Original languageEnglish (US)
Pages (from-to)121-128
Number of pages8
JournalGenome Research
Volume23
Issue number1
DOIs
StatePublished - Jan 2013

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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