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Direct transposition of native DNA for sensitive multimodal single-molecule sequencing.
Nanda, Arjun S; Wu, Ke; Irkliyenko, Iryna; Woo, Brian; Ostrowski, Megan S; Clugston, Andrew S; Sayles, Leanne C; Xu, Lingru; Satpathy, Ansuman T; Nguyen, Hao G; Alejandro Sweet-Cordero, E; Goodarzi, Hani; Kasinathan, Sivakanthan; Ramani, Vijay.
Afiliación
  • Nanda AS; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
  • Wu K; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
  • Irkliyenko I; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
  • Woo B; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
  • Ostrowski MS; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
  • Clugston AS; Helen-Diller Cancer Center, San Francisco, CA, USA.
  • Sayles LC; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
  • Xu L; Helen-Diller Cancer Center, San Francisco, CA, USA.
  • Satpathy AT; Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
  • Nguyen HG; Helen-Diller Cancer Center, San Francisco, CA, USA.
  • Alejandro Sweet-Cordero E; Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
  • Goodarzi H; Helen-Diller Cancer Center, San Francisco, CA, USA.
  • Kasinathan S; Department of Pathology, Stanford University, Stanford, CA, USA.
  • Ramani V; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
Nat Genet ; 56(6): 1300-1309, 2024 Jun.
Article en En | MEDLINE | ID: mdl-38724748
ABSTRACT
Concurrent readout of sequence and base modifications from long unamplified DNA templates by Pacific Biosciences of California (PacBio) single-molecule sequencing requires large amounts of input material. Here we adapt Tn5 transposition to introduce hairpin oligonucleotides and fragment (tagment) limiting quantities of DNA for generating PacBio-compatible circular molecules. We developed two methods that implement tagmentation and use 90-99% less input than current protocols (1) single-molecule real-time sequencing by tagmentation (SMRT-Tag), which allows detection of genetic variation and CpG methylation; and (2) single-molecule adenine-methylated oligonucleosome sequencing assay by tagmentation (SAMOSA-Tag), which uses exogenous adenine methylation to add a third channel for probing chromatin accessibility. SMRT-Tag of 40 ng or more human DNA (approximately 7,000 cell equivalents) yielded data comparable to gold standard whole-genome and bisulfite sequencing. SAMOSA-Tag of 30,000-50,000 nuclei resolved single-fiber chromatin structure, CTCF binding and DNA methylation in patient-derived prostate cancer xenografts and uncovered metastasis-associated global epigenome disorganization. Tagmentation thus promises to enable sensitive, scalable and multimodal single-molecule genomics for diverse basic and clinical applications.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Neoplasias de la Próstata / Metilación de ADN Límite: Animals / Humans / Male Idioma: En Revista: Nat Genet Asunto de la revista: GENETICA MEDICA Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Neoplasias de la Próstata / Metilación de ADN Límite: Animals / Humans / Male Idioma: En Revista: Nat Genet Asunto de la revista: GENETICA MEDICA Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos