Skip to main content

Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome.

Publication ,  Journal Article
Pinter, SF; Colognori, D; Beliveau, BJ; Sadreyev, RI; Payer, B; Yildirim, E; Wu, C-T; Lee, JT
Published in: Genetics
June 2015

In mammals, several classes of monoallelic genes have been identified, including those subject to X-chromosome inactivation (XCI), genomic imprinting, and random monoallelic expression (RMAE). However, the extent to which these epigenetic phenomena are influenced by underlying genetic variation is unknown. Here we perform a systematic classification of allelic imbalance in mouse hybrids derived from reciprocal crosses of divergent strains. We observe that deviation from balanced biallelic expression is common, occurring in ∼20% of the mouse transcriptome in a given tissue. Allelic imbalance attributed to genotypic variation is by far the most prevalent class and typically is tissue-specific. However, some genotype-based imbalance is maintained across tissues and is associated with greater genetic variation, especially in 5' and 3' termini of transcripts. We further identify novel random monoallelic and imprinted genes and find that genotype can modify penetrance of parental origin even in the setting of large imprinted regions. Examination of nascent transcripts in single cells from inbred parental strains reveals that genes showing genotype-based imbalance in hybrids can also exhibit monoallelic expression in isogenic backgrounds. This surprising observation may suggest a competition between alleles and/or reflect the combined impact of cis- and trans-acting variation on expression of a given gene. Our findings provide novel insights into gene regulation and may be relevant to human genetic variation and disease.

Duke Scholars

Altmetric Attention Stats
Dimensions Citation Stats

Published In

Genetics

DOI

EISSN

1943-2631

Publication Date

June 2015

Volume

200

Issue

2

Start / End Page

537 / 549

Location

United States

Related Subject Headings

  • Transcriptome
  • Organ Specificity
  • Mice
  • Genotype
  • Genomic Imprinting
  • Genetic Variation
  • Gene Expression Profiling
  • Developmental Biology
  • Crosses, Genetic
  • Cluster Analysis
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Pinter, S. F., Colognori, D., Beliveau, B. J., Sadreyev, R. I., Payer, B., Yildirim, E., … Lee, J. T. (2015). Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome. Genetics, 200(2), 537–549. https://doi.org/10.1534/genetics.115.176263
Pinter, Stefan F., David Colognori, Brian J. Beliveau, Ruslan I. Sadreyev, Bernhard Payer, Eda Yildirim, Chao-Ting Wu, and Jeannie T. Lee. “Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome.Genetics 200, no. 2 (June 2015): 537–49. https://doi.org/10.1534/genetics.115.176263.
Pinter SF, Colognori D, Beliveau BJ, Sadreyev RI, Payer B, Yildirim E, et al. Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome. Genetics. 2015 Jun;200(2):537–49.
Pinter, Stefan F., et al. “Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome.Genetics, vol. 200, no. 2, June 2015, pp. 537–49. Pubmed, doi:10.1534/genetics.115.176263.
Pinter SF, Colognori D, Beliveau BJ, Sadreyev RI, Payer B, Yildirim E, Wu C-T, Lee JT. Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome. Genetics. 2015 Jun;200(2):537–549.

Published In

Genetics

DOI

EISSN

1943-2631

Publication Date

June 2015

Volume

200

Issue

2

Start / End Page

537 / 549

Location

United States

Related Subject Headings

  • Transcriptome
  • Organ Specificity
  • Mice
  • Genotype
  • Genomic Imprinting
  • Genetic Variation
  • Gene Expression Profiling
  • Developmental Biology
  • Crosses, Genetic
  • Cluster Analysis