Allele-specific expression and splicing provides insight into the phenotypic differences between thin- and fat-tailed sheep breeds

2022 ◽  
Author(s):  
Fei Wang ◽  
Junjie Shao ◽  
Sangang He ◽  
Yingwei Guo ◽  
Xiangyu Pan ◽  
...  
Keyword(s):  
Specific Expression ◽  
Allele Specific Expression ◽  
Phenotypic Differences ◽  
Sheep Breeds ◽  
Allele Specific ◽  
Insight Into

scholarly journals Allele-specific expression reveals the phenotypic differences between thin- and fat-tailed sheep

2020 ◽  
Author(s):  
Junjie Shao ◽  
Sangang He ◽  
Xiangyu Pan ◽  
Zhirui Yang ◽  
Hojjat Asadollahpour Nanaei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fat Deposition ◽  
Meat Production ◽  
Production Traits ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Phenotypic Differences ◽  
Sheep Breeds ◽  
Muscle Tissues ◽  
Allele Specific

Abstract Background: The thin-tailed sheep breeds from Europe and the fat-tailed sheep breeds from China exhibit distinct phenotypic differences in fat deposition and meat production traits. However, the molecular mechanisms underlying gene expression related to these phenotypic differences are not well understood. Allele-specific expression (ASE) refers to the significant imbalance of expression levels of two parental alleles. Characterization of such events in F1 hybrid offspring generated from these two groups of sheep breeds can minimize the external factors influencing gene expression and reveal the variants with a cis -regulatory effect on gene expression. The aim of the present study was to investigate the genetic factors that influence different fat-deposition and meat production traits between thin- and fat-tailed sheep.Results: Fifteen F1 hybrids were generated from crosses between Texel and Kazakh sheep as the representative phenotypes of thin- and fat-tailed breeds, respectively. Totally, 33 whole genomes from F1 individuals and their parents were sequenced with an average depth of ~17.21× coverage per sample. ASE analysis results from 70 RNA-seq samples of adipose and skeleton muscle tissues showed 128 ASE candidate genes were related to the function of fat deposition and meat production traits. A genome-wide scan of selective sweeps was also conducted between these two groups of sheep breeds in an effort to identify genomic regions related to fat deposition and meat production, respectively. We detected signatures of selection in ASE genes associated with fat deposition (e.g., PDGFD ) and meat production traits (e.g., LRCC2 ). Further analysis suggested that PDGFD and LRCC2 genes were speculated to be causative genes for fat deposition and meat production traits in sheep, respectively. Furthermore, AMPK signaling pathway was significantly enriched in ASE genes related to fatty acid biosynthesis in both adipose and skeleton muscle tissues, while PPAR signaling pathway was significantly enriched in ASE genes related to lipid metabolism in adipose tissue. Conclusions: Our finding illustrates that the expression of identified ASE genes could potentially lead to the differences in traits of fat deposition and meat production between thin- and fat-tailed sheep. Keywords: allele-specific expression, phenotypic difference, thin- and fat-tailed sheep, whole-genome sequencing, transcriptome

scholarly journals CompMap: an allele-specific expression read-counter based on competitive mapping

2021 ◽  
Author(s):  
S. Sánchez-Ramírez ◽  
A. D. Cutter
Keyword(s):  
Error Rates ◽  
Supplementary Information ◽  
Homologous Region ◽  
Regulatory Sequences ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Phenotypic Differences ◽  
Mapping Bias ◽  
Individual Snps ◽  
Allele Specific

ABSTRACTSummaryChanges to regulatory sequences account for important phenotypic differences between species and populations. In heterozygote individuals, regulatory polymorphism typically manifests as allele-specific expression (ASE) of transcripts. ASE data from inter-species and inter-population hybrids, in conjunction with expression data from the parents, can be used to infer regulatory changes in cis and trans throughout the genome. Improper data handling, however, can create problems of mapping bias and excessive loss of information, which are prone to arise unintentionally from the cumbersome pipelines with multiple dependencies that are common among current methods. Here, we introduce a new, selfcontained method implemented in Python that generates allele-specific expression counts from genotype-specific map alignments. Rather than assessing individual SNPs, our approach sorts and counts reads within a given homologous region by comparing individual read-mapping statistics from each parental alignment. Reads that are aligned ambiguously to both references are resolved proportionally to the allele-specific matching read counts or statistically using a binomial distribution. Using simulations, we show CompMap has low error rates in assessing regulatory divergence.AvailabilityThe Python code with examples and installation instructions is available on the GitHub repository https://github.com/santiagosnchez/[email protected] information

scholarly journals Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
M. Joseph Tomlinson ◽  
Shawn W. Polson ◽  
Jing Qiu ◽  
Juniper A. Lake ◽  
William Lee ◽  
...  
Keyword(s):  
Broiler Chickens ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Specific Expression ◽  
Single Nucleotide ◽  
Allele Specific Expression ◽  
Detection Tool ◽  
Commercial Broiler ◽  
Significant Phenomenon ◽  
Allele Specific

AbstractDifferential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.

scholarly journals Analysis of Allele-Specific Expression in Mouse Liver by RNA-Seq: A Comparison With Cis-eQTL Identified Using Genetic Linkage

Genetics ◽  
2013 ◽  
Vol 195 (3) ◽  
pp. 1157-1166 ◽  
Author(s):  
Sandrine Lagarrigue ◽  
Lisa Martin ◽  
Farhad Hormozdiari ◽  
Pierre-François Roux ◽  
Calvin Pan ◽  
...  
Keyword(s):  
Mouse Liver ◽  
Genetic Linkage ◽  
Rna Seq ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific

scholarly journals Nucleus-specific expression in the multinuclear mushroom-forming fungusAgaricus bisporusreveals different nuclear regulatory programs

2018 ◽  
Vol 115 (17) ◽  
pp. 4429-4434 ◽  
Author(s):  
Thies Gehrmann ◽  
Jordi F. Pelkmans ◽  
Robin A. Ohm ◽  
Aurin M. Vos ◽  
Anton S. M. Sonnenberg ◽  
...  
Keyword(s):  
Agaricus Bisporus ◽  
Sequencing Data ◽  
Carbohydrate Active Enzymes ◽  
Nuclear Level ◽  
Specific Expression ◽  
Phenotypic Differences ◽  
Gene Level ◽  
Nuclear Separation ◽  
Insight Into ◽  
Specific Mrna

Many fungi are polykaryotic, containing multiple nuclei per cell. In the case of heterokaryons, there are different nuclear types within a single cell. It is unknown what the different nuclear types contribute in terms of mRNA expression levels in fungal heterokaryons. Each cell of the mushroomAgaricus bisporuscontains two to 25 nuclei of two nuclear types originating from two parental strains. Using RNA-sequencing data, we assess the differential mRNA contribution of individual nuclear types and its functional impact. We studied differential expression between genes of the two nuclear types, P1 and P2, throughout mushroom development in various tissue types. P1 and P2 produced specific mRNA profiles that changed through mushroom development. Differential regulation occurred at the gene level, rather than at the locus, chromosomal, or nuclear level. P1 dominated mRNA production throughout development, and P2 showed more differentially up-regulated genes in important functional groups. In the vegetative mycelium, P2 up-regulated almost threefold more metabolism genes and carbohydrate active enzymes (cazymes) than P1, suggesting phenotypic differences in growth. We identified widespread transcriptomic variation between the nuclear types ofA. bisporus. Our method enables studying nucleus-specific expression, which likely influences the phenotype of a fungus in a polykaryotic stage. Our findings have a wider impact to better understand gene regulation in fungi in a heterokaryotic state. This work provides insight into the transcriptomic variation introduced by genomic nuclear separation.

Sign in / Sign up

Export Citation Format

Share Document