Allele Specific Expression (ASE) analysis between Bos Taurus and Bos Indicus cows using RNA-Seq data at SNP level and gene level

Varkoohi, Sheida; Banabazi, Mohammad Hossein; Ghsemi-Siab, Mojgan

doi:10.1590/0001-3765202120191453

Cited by 6 publications

(2 citation statements)

References 23 publications

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“…As our research group [ 8 , 9 ] and others reported, ASE is widespread in bovine [ 4 , 6 , 8 , 10 , 11 ]. Previously, we described a high coverage list of single nucleotide polymorphisms (SNPs) located in transcripts with ASE (ASE SNPs) distributed in Nelore ( Bos indicus ) muscle and the candidate cis -regulatory variants potentially affecting the allelic expression.…”

Section: Introductionmentioning

confidence: 83%

Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality Traits in B. indicus Muscle

Bruscadin

Cardoso

Diniz

et al. 2022

Genes

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Traditional transcriptomics approaches have been used to identify candidate genes affecting economically important livestock traits. Regulatory variants affecting these traits, however, remain under covered. Genomic regions showing allele-specific expression (ASE) are under the effect of cis-regulatory variants, being useful for improving the accuracy of genomic selection models. Taking advantage of the better of these two methods, we investigated single nucleotide polymorphisms (SNPs) in regions showing differential ASE (DASE SNPs) between contrasting groups for beef quality traits. For these analyses, we used RNA sequencing data, imputed genotypes and genomic estimated breeding values of muscle-related traits from 190 Nelore (Bos indicus) steers. We selected 40 contrasting unrelated samples for the analysis (N = 20 animals per contrasting group) and used a beta-binomial model to identify ASE SNPs in only one group (i.e., DASE SNPs). We found 1479 DASE SNPs (FDR ≤ 0.05) associated with 55 beef-quality traits. Most DASE genes were involved with tenderness and muscle homeostasis, presenting a co-expression module enriched for the protein ubiquitination process. The results overlapped with epigenetics and phenotype-associated data, suggesting that DASE SNPs are potentially linked to cis-regulatory variants affecting simultaneously the transcription and phenotype through chromatin state modulation.

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Section: Introductionmentioning

confidence: 83%

Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality Traits in B. indicus Muscle

Bruscadin

Cardoso

Diniz

et al. 2022

Genes

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“…In diploid organisms, allele specific expression (ASE) provides strong evidence that genes may be under differential cis-regulatory control [26,27]. Using a method that has been applied to a variety of taxa [26,[28][29][30][31][32] but not mosquitoes, we describe the identification of genes showing ASE in An. gambiae which potentially confer metabolic resistance.…”

Section: Introductionmentioning

confidence: 99%

Mechanisms of transcriptional regulation inAnopheles gambiaerevealed by allele specific expression

Dyer,

Lucas,

Nagi

et al. 2023

Preprint

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Malaria control relies on insecticides targeting the mosquito vector, but this is increasingly compromised by insecticide resistance, which can be achieved by elevated expression of detoxifying enzymes that metabolize the insecticide. In diploid organisms, gene expression is regulated both incis, by regulatory sequences on the same chromosome, and bytransacting factors, affecting both alleles equally. Differing levels of transcription can be caused by mutations incis-regulatory modules (CRM), but few of these have been identified in mosquitoes. We crossed bendiocarb resistant and susceptibleAnopheles gambiaestrains to identifycis-regulated genes that might be responsible for the resistant phenotype using RNAseq, andcis-regulatory module sequences controlling gene expression in insecticide resistance relevant tissues were predicted using machine learning. We found 115 genes showing allele specific expression in hybrids of insecticide susceptible and resistant strains, suggestingcisregulation is an important mechanism of gene expression regulation inAnopheles gambiae. The genes showing allele specific expression included a higher proportion ofAnophelesspecific genes on average younger than genes those with balanced allelic expression.Author SummaryThe evolution of insecticide resistance, including resistance that is due to changes in the expression levels of certain resistance associated genes is threatening progress in malaria control. We investigated how the expression of genes in the malaria vectorAnopheles gambiaeis controlled, by implementing a method for the first time in this species. Each mosquito inherits a set of chromosomes from both parents, so has a maternal and paternal copy of most genes. When a gene is expressed, the DNA encoding that gene is transcribed into messenger RNA. This process is controlled by the cellular environment and by other DNA sequences on the same chromosome as each gene. We crossed mosquitoes from insecticide resistant and susceptible strains to equalize the cellular environment and then measured the levels of messenger RNA from both gene copies. 115 genes showed consistently different messenger RNA levels between gene copies in most crosses, suggesting these genes are regulated by factors on the same chromosome. There were relatively more Anopheles specific genes with imbalanced expression. Using machine learning we identified DNA sequences that may be responsible for controlling gene expression in mosquito tissues; several of these sequences were close to genes with imbalanced expression.

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Conservation and upgradation of indigenous Cholistani cattle breed of Pakistan: a pathway to sustainable livestock

Farooq,

Idris,

Rashid

2024

Trop Anim Health Prod

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Allele Specific Expression (ASE) analysis between Bos Taurus and Bos Indicus cows using RNA-Seq data at SNP level and gene level

Cited by 6 publications

References 23 publications

Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality Traits in B. indicus Muscle

Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality Traits in B. indicus Muscle

Mechanisms of transcriptional regulation inAnopheles gambiaerevealed by allele specific expression

Conservation and upgradation of indigenous Cholistani cattle breed of Pakistan: a pathway to sustainable livestock

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