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Related Experiment Video

Updated: May 30, 2025

Transcriptome Profiling of In-Vivo Produced Bovine Pre-implantation Embryos Using Two-color Microarray Platform

Transcriptome Profiling of In-Vivo Produced Bovine Pre-implantation Embryos Using Two-color Microarray Platform

Published on: January 30, 2017

A comprehensive allele specific expression resource for the equine transcriptome.

Harrison D Heath¹, Sichong Peng^1,2, Tomasz Szmatola^1,3

¹Department of Population Health and Reproduction, Davis School of Veterinary Medicine, University of California, Room 4206 Vet Med3A One Shields Ave, Davis, CA, 95616, USA.

|January 30, 2025

Summary

This summary is machine-generated.

Allele-specific expression (ASE) analysis reveals regulatory variation in horse genomes. This study identified significant ASE events, particularly in liver tissue, offering insights into equine gene regulation.

Keywords:

Epigenetics FAANG Haplotype Horse RNA-sequencing

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Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

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Published on: November 11, 2014

Area of Science:

Genomics
Molecular Biology
Animal Science

Background:

Allele-specific expression (ASE) analysis offers detailed insights into cis-regulatory mechanisms governing gene expression.
Understanding ASE is crucial for deciphering gene regulation complexities.

Purpose of the Study:

To conduct a comprehensive allele-specific expression analysis in equine tissues.
To identify and characterize allele expression events in horses.
To investigate the tissue-specific patterns of allelic imbalance.

Main Methods:

Integrated analysis of Iso-seq and short-read RNA sequencing data from four Thoroughbred horses across nine tissues.
Quantification of allele expression using haplotypes derived from long-read sequencing data.
Validation of identified allele-specific variants in a larger cohort of equine liver samples.

Main Results:

Comparison of 42,900 allele expression events revealed 635 (1.48%) instances of ASE.
Liver tissue exhibited the highest proportion of ASE events.
Genetic variants associated with ASE were frequently located within histone-modified regions (64.2%).
Validation confirmed ASE in 97% of tested allele-specific variants.

Conclusions:

The study generated a valuable, publicly accessible resource for equine gene regulation research.
Results underscore the significant tissue-specific nature of allelic imbalance in the equine genome.
This work facilitates future investigations into regulatory variation within equine tissues.