Dynamic, Mono allelic expression in Mammalian (PMID: 24408435)

Paper: Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science. (2014)
Organism: Mus Musculus
Cell types: from zygote to the cells of the late blastocyst
Sample number: 317
Library preparation: Smart-seq1/2
DATA: GSE45719

  1. 12-24% of genes are expressed monoallelically and independently
  2. CAST/EiJxC57BL/6J is used to detect mono allelic expression, 82% of all expressing genes contain >=1 informative SNPs
  3. Simulation of loss of transcripts by Spike-in RNAs
  4. maternal is dominant during zygote to two cell.
  5. 50SE / SNP tolerant GSNAP mapper or STAR / only unique best alignment / RPKM / PCA
  6. Allelic transcription: i)expressed allele should have >=2 allele-informative reads, ii)allele need to have at least 2% of the reads of other allele if expressed etc…
  7. Independent and stochastic allelic transcription generates abundant random mono allelic expression
  8. Monoallelic expression during preimplantation development is 54% on average
  9. Split single cell lysate to 2 equal volume and process each independently. 54%(original) -> 17%(66% loss) of genes (median) is confirmed
  10. Allelic transcription in mature cells are evaluated with liver cells, random mono allelic expression is observed on average 24% of cells
  11. Independent bursts of transcription occur from both alleles over time, but mono allelic expression is often present at any given time

Related Review (PMID: 26442639)
Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation.
Nature Reviews Genetics (2015)

Posted in Reference, Single cell and tagged .

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