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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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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Transcriptome Analysis of Single Cells
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Revealing allele-specific gene expression by single-cell transcriptomics.

Julio Aguila Benitez1, Shangli Cheng1, Qiaolin Deng1

  • 1Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.

The International Journal of Biochemistry & Cell Biology
|June 5, 2017
PubMed
Summary
This summary is machine-generated.

Full-length single-cell RNA sequencing advances the study of allele-specific expression (ASE) and haplotype phasing. This review highlights recent single-cell RNA-seq achievements in understanding ASE for autosomal and X-chromosome genes.

Keywords:
Allele-specific expressionFull-length transcriptomicsSingle-cell RNA sequencing

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Area of Science:

  • Genomics and Molecular Biology
  • Single-cell analysis
  • Transcriptomics

Background:

  • Single-cell sequencing offers high-resolution insights into biological processes, impacting various fields.
  • Investigating alternative splicing, novel exon detection, and allele-specific expression (ASE) requires full-length single-cell RNA sequencing (scRNA-seq) for comprehensive coverage and single nucleotide polymorphism (SNP) identification.

Purpose of the Study:

  • To review recent advancements in understanding allele-specific expression (ASE) using single-cell RNA sequencing.
  • To explore the application of full-length scRNA-seq in analyzing both autosomal and X-chromosome genes.
  • To summarize bioinformatic tools for identifying haplotype phase from scRNA-seq data.

Main Methods:

  • Review of existing literature and studies utilizing single-cell RNA sequencing.
  • Focus on full-length scRNA-seq methodologies for enhanced sequence coverage and SNP detection.
  • Analysis of bioinformatic approaches for haplotype phasing in single-cell contexts.

Main Results:

  • Significant progress has been made in understanding allele-specific expression (ASE) through single-cell RNA sequencing.
  • Studies have successfully applied full-length scRNA-seq to analyze ASE in autosomal and X-chromosome genes.
  • Development of effective bioinformatic tools aids in identifying haplotype phase from single-cell data.

Conclusions:

  • Full-length single-cell RNA sequencing is crucial for detailed analysis of allele-specific expression and related genomic features.
  • Recent studies demonstrate the power of scRNA-seq in advancing our knowledge of gene expression regulation at the single-cell level.
  • The availability of specialized bioinformatic tools enhances the utility of scRNA-seq for complex genomic analyses, including haplotype phasing.