Single-cell Transcriptogenomics

Researchers from the Albert Einstein College of Medicine have developed 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 SCGT. 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 SCGT can be instrumental in the direct assessment of phenotypic consequences of genomic variants.


  • A novel method of concurrent genomic and transcriptomic analysis of a single cell.
  • Direct analysis of allele-specific transcription from germline and somatic variants.
  • Extensive transcriptional exclusion of ENU-induced mutant alleles.
  • Exclusion of mutant alleles may contribute to the maintenance of genome integrity.

(More about Single-Cell Transcriptogenomics)

Li W, Calder RB, Mar JC, Vijg J. (2015) Single-cell transcriptogenomics reveals transcriptional exclusion of ENU-mutated alleles. Mutat Res Fundam Mol Mech Mutagen 772:55-62. [article]

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