Single-cell transcriptogenomics reveals transcriptional exclusion of ENU-mutated alleles

Wenge Li, R. Brent Calder, Jessica C. Mar, Jan Vijg

Research output: Contribution to journalArticlepeer-review

23 Scopus citations


Recently, great progress has been made in single cell genomics and transcriptomics. Here, we present an integrative method, termed single-cell transcriptogenomics (SCTG), in which whole exome sequencing and RNA-seq is performed concurrently on single cells. This methodology enables one to track germline and somatic variants directly from the genome to the transcriptome in individual cells. Mouse embryonic fibroblasts were treated with the powerful mutagen ethylnitrosourea (ENU) and subjected to SCTG. Interestingly, while germline variants were found to be transcribed in an allelically balanced fashion, a significantly different pattern of allelic exclusion was observed for ENU-mutant variants. These results suggest that the adverse effects of induced mutations, in contrast to germline variants, may be mitigated by allelically biased transcription. They also illustrate how SCTG can be instrumental in the direct assessment of phenotypic consequences of genomic variants.

Original languageEnglish (US)
Pages (from-to)55-62
Number of pages8
JournalMutation Research - Fundamental and Molecular Mechanisms of Mutagenesis
StatePublished - Feb 1 2015


  • Allelic exclusion
  • ENU
  • Germline mutations
  • Next generation sequencing
  • Single cell transcriptogenomics
  • Somatic mutations

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Health, Toxicology and Mutagenesis


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