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Cell Specific Gene Expression01:58

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Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
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Updated: Jan 27, 2026

Using an Automated Cell Counter to Simplify Gene Expression Studies: siRNA Knockdown of IL-4 Dependent Gene Expression in Namalwa Cells
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Human genes escaping X-inactivation revealed by single cell expression data.

Kerem Wainer Katsir1, Michal Linial2

  • 1Department of Biological Chemistry, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190400, Jerusalem, Israel.

BMC Genomics
|March 16, 2019
PubMed
Summary

Female mammals silence one X-chromosome to balance gene expression. This study used single-cell RNA sequencing to identify genes that escape this inactivation, revealing new insights into sex-linked traits.

Keywords:
Allele specific expressionAllelic biasEscapeesRNA-SeqSingle cellX-inactivation

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Area of Science:

  • Genetics
  • Molecular Biology
  • Epigenetics

Background:

  • Mammalian females possess two X-chromosomes, necessitating a mechanism to balance gene dosage with males who have one.
  • X-chromosome inactivation (XCI) silences most genes on one X-chromosome in female somatic cells.
  • A subset of X-chromosome genes escape XCI, contributing to sex-specific phenotypic variation.

Purpose of the Study:

  • To identify genes that escape X-chromosome inactivation in human somatic cells using single-cell resolution.
  • To characterize novel escapee genes, including long noncoding RNAs (lncRNAs).
  • To validate findings by comparing with existing datasets and utilizing clonal cell lines.

Main Methods:

  • Single-cell RNA sequencing (scRNA-Seq) was employed to analyze gene expression.
  • Allelic-specific expression (ASE) analysis was performed on heterozygous sites to distinguish expression from active versus inactive X-chromosomes.
  • Fibroblast and lymphoblast cell lines, including clonal populations with sequenced parental genomes, were studied.

Main Results:

  • 24 candidate escapee genes were identified in fibroblasts and 49 in lymphoblasts.
  • 66% of the unified set of identified escapees were previously reported.
  • 11 novel long noncoding RNA (lncRNA) escapees were discovered, representing 20% of the candidates.

Conclusions:

  • Single-cell resolution is crucial for robustly studying X-chromosome inactivation and escape.
  • Clonal cell lines with genomic phasing enhance the confidence in identifying escapee genes.
  • This study expands the catalog of human X-chromosome escapees, including lncRNAs, improving our understanding of sex-linked gene expression.