Allele-specific expression variation at different ploidy levels in Squalius alburnoides

AbstractGene expression variation between alleles in a diploid cell is mediated by variation in cis regulatory sequences, which usually refers to the differences in DNA sequence between two alleles near the gene of interest. Expression differences caused by cis variation has been estimated by the ratio of the expression level of the two alleles under a binomial model. However, the binomial model underestimates the variance among replicated experiments resulting in the exaggerated statistical significance of estimated cis effects and thus many false discoveries of cis-affected genes. Here we describe a beta-binomial model that estimates the cis-effect for each gene while permitting overdispersion of variance among replicates. We demonstrated with simulated null data (data without true cis-effect) that the new model fits the true distribution better, resulting in approximately 5% false positive rate under 5% significance level in all null datasets, considerably better than the 6%-40% false positive rate of the binomial model. Additional replicates increase the performance of the beta-binomial model but not of the binomial model. We also collected new allele-specific expression data from an experiment comprised of 20 replicates of a yeast hybrid (YPS128/RM11-1a). We eliminated the mapping bias problem with de novo assemblies of the two parental genomes. By applying the beta-binomial model to this dataset, we found that cis effects are ubiquitous, affecting around 70% of genes. However, most of these changes are small in magnitude. The high number of replicates enabled us a better approximation of cis landscape within species and also provides a resource for future exploration for better models.

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

Scientific Reports ◽

10.1038/s41598-021-83459-8 ◽

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.

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