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Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells.
Shareef, Sarah J; Bevill, Samantha M; Raman, Ayush T; Aryee, Martin J; van Galen, Peter; Hovestadt, Volker; Bernstein, Bradley E.
Afiliación
  • Shareef SJ; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
  • Bevill SM; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Raman AT; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
  • Aryee MJ; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • van Galen P; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
  • Hovestadt V; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Bernstein BE; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Nat Biotechnol ; 39(9): 1086-1094, 2021 09.
Article en En | MEDLINE | ID: mdl-33958785
ABSTRACT
The biological roles of DNA methylation have been elucidated by profiling methods based on whole-genome or reduced-representation bisulfite sequencing, but these approaches do not efficiently survey the vast numbers of non-coding regulatory elements in mammalian genomes. Here we present an extended-representation bisulfite sequencing (XRBS) method for targeted profiling of DNA methylation. Our design strikes a balance between expanding coverage of regulatory elements and reproducibly enriching informative CpG dinucleotides in promoters, enhancers and CTCF binding sites. Barcoded DNA fragments are pooled before bisulfite conversion, allowing multiplex processing and technical consistency in low-input samples. Application of XRBS to single leukemia cells enabled us to evaluate genetic copy number variations and methylation variability across individual cells. Our analysis highlights heterochromatic H3K9me3 regions as having the highest cell-to-cell variability in their methylation, likely reflecting inherent epigenetic instability of these late-replicating regions, compounded by differences in cell cycle stages among sampled cells.
Asunto(s)

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Sulfitos / Redes Reguladoras de Genes / Análisis de la Célula Individual / Secuenciación de Nucleótidos de Alto Rendimiento Límite: Humans Idioma: En Revista: Nat Biotechnol Asunto de la revista: BIOTECNOLOGIA Año: 2021 Tipo del documento: Article País de afiliación: Estados Unidos

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Sulfitos / Redes Reguladoras de Genes / Análisis de la Célula Individual / Secuenciación de Nucleótidos de Alto Rendimiento Límite: Humans Idioma: En Revista: Nat Biotechnol Asunto de la revista: BIOTECNOLOGIA Año: 2021 Tipo del documento: Article País de afiliación: Estados Unidos
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