scholarly journals Natural transposable element insertions drive expression changes in genes underlying Drosophila immune response

2019 ◽  
Author(s):  
Anna Ullastres ◽  
Miriam Merenciano ◽  
Josefa González
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Transposable Element ◽  
Individual Variability ◽  
Gram Negative Bacteria ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific ◽  
Immune Related Genes ◽  
First Time

ABSTRACTVariation in gene expression underlies inter-individual variability in immune response. However, the mutations responsible for gene expression changes remain largely unknown. In this work, we searched for transposable element insertions present at high population frequencies and located nearby immune-related genes in Drosophila melanogaster. We identified 12 insertions associated with allele-specific expression changes in immune-related genes. We showed that transgenically induced expression changes in most of these genes are associated with differences in survival to infection with the gram-negative bacteria Pseudomonas entomophila. We provide experimental evidence suggesting a causal role for five insertions in the allele-specific expression changes observed. Furthermore, for two insertions we found a significant association with increased tolerance to bacterial infection. Our results showed for the first time that polymorphic transposable element insertions from different families drive expression changes in genes that are relevant for inter-individual differences in immune response.

scholarly journals Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Anna Ullastres ◽  
Miriam Merenciano ◽  
Josefa González
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Transposable Elements ◽  
Transposable Element ◽  
Natural Populations ◽  
Regulatory Elements ◽  
Genomic Context ◽  
Specific Expression ◽  
Survival Capacity ◽  
Immune Related Genes

Abstract Background Variation in gene expression underlies interindividual variability in relevant traits including immune response. However, the genetic variation responsible for these gene expression changes remains largely unknown. Among the non-coding variants that could be relevant, transposable element insertions are promising candidates as they have been shown to be a rich and diverse source of cis-regulatory elements. Results In this work, we use a population genetics approach to identify transposable element insertions likely to increase the tolerance of Drosophila melanogaster to bacterial infection by affecting the expression of immune-related genes. We identify 12 insertions associated with allele-specific expression changes in immune-related genes. We experimentally validate three of these insertions including one likely to be acting as a silencer, one as an enhancer, and one with a dual role as enhancer and promoter. The direction in the change of gene expression associated with the presence of several of these insertions is consistent with an increased survival to infection. Indeed, for one of the insertions, we show that this is the case by analyzing both natural populations and CRISPR/Cas9 mutants in which the insertion is deleted from its native genomic context. Conclusions We show that transposable elements contribute to gene expression variation in response to infection in D. melanogaster and that this variation is likely to affect their survival capacity. Because the role of transposable elements as regulatory elements is not restricted to Drosophila, transposable elements are likely to play a role in immune response in other organisms as well.

scholarly journals Hypoxic Response-Dependent Genetic Regulation Revealed By Allele-Specific Expression in Reticulocytes of Chuvash Polycythemia

Blood ◽  
2017 ◽  
Vol 130 (Suppl_1) ◽  
pp. 926-926
Author(s):  
Xu Zhang ◽  
Jihyun Song ◽  
Binal N. Shah ◽  
Galina Miasnikova ◽  
Adelina Sergueeva ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Dna Damage ◽  
Wild Type ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Hypoxic Response ◽  
Cis Acting ◽  
Exonic Snps ◽  
Allele Specific

Abstract Homozygosity for the VHLR200W mutation in Chuvash polycythemia (CP) leads to decreased degradation of the α subunits of hypoxia inducible factor (HIF)-1 and HIF-2 by the hypomorphic variant of VHL, the principal negative regulator of HIFs. The constitutively activated HIFs directly regulate the transcription of a suite of hypoxic responsible genes, including the principal regulators of erythropoiesis, vessel development, and glycolytic metabolism, which further trigger a downstream cascade of gene expression. Besides these transcriptional factors, cis acting elements play an important role in the hypoxic gene regulatory network. To assess the extent of cis regulatory variation in hypoxic gene expression, we compared allele-specific expression (ASE) in purified reticulocytes between VHLR200W homozygote individuals and age- and gender-matched wild type control individuals living at the same altitude of ~200 meters from the Chuvash population. Cell fractions of reticulocytes were purified from 17 VHLR200W homozygotes and 13 wild type individuals. Total RNA was extracted, depleted of ribosomal RNA and hemoglobin transcripts, and reverse transcribed. Strand-specific libraries were constructed for 125 bp paired-end sequencing to 30-45 million read pairs per sample using Illumina HiSeq 2500 platform. The samples were collected and processed in three batches across two years, with VHL genotype randomized in each batch. The sequencing data were mapped to human reference genome and analyzed for differential expression and differential ASE between VHLR200W homozygotes and wild type individuals. At 5% false discovery rate (FDR, i.e., <5 false positives in 100 detected genes), 1,267 genes were differentially expressed with more than 1.2-fold change in CP patients, 703 elevated and 564 decreased. Genes up-regulated in CP were enriched (fold enrichment >5, FDR <0.05) in REACTOME pathways of epigenetic remodeling (Packaging of telomere ends, DNA methylation, HDACs deacetylate histones, PRC2 methylates histones and DNA, Deposition of new CENPA-containing nucleosomes at the centromere, HATs acetylate histones) and oxidative stress induced senescence (DNA damage/telomere stress induced senescence, Senescence-associated secretory phenotype, Oxidative stress induced senescence). Genes decreased in CP were enriched in REACTOME pathways of cell cycle (E2F-enabled inhibition of pre-replication complex formation, Nuclear pore complex disassembly, SUMOylation of DNA replication proteins) and DNA damage repair (Activation of ATR in response to replication stress, SUMOylation of DNA damage response and repair proteins). ASE was analyzed between CP and wild type individuals to assess hypoxic response-dependent genetic effects on gene expression. For the 1,267 genes differentially expressed in the CP, we selected genes containing exonic SNPs with heterozygous alleles for ASE analysis. With a null hypothesis of no cis acting regulation on the gene expression, both alleles are expected to be expressed at the same level, whereas allelic imbalance indicates linked cis regulation. At a given bi-allelic SNP, individuals with ≥2 read counts covering each of the reference and alternative alleles and with ≥20 total counts were included in the analysis. Exonic SNPs with at least one individual in each of the CP and wild type group were further selected to test for differential ASE between the CP and wild type groups, using a generalized linear model. A total of 147 genes passed the filtering and were analyzed, among which 32 were detected to have significant CP-dependent ASE at 5% FDR. Some of these genes may have important roles in hypoxic responses in CP reticulocytes, for example NEIL3, encoding a DNA glycosylase that initiates the first step in base excision repair by cleaving bases damaged by reactive oxygen species, and STOM, encoding an integral membrane protein that localizes to the cell membrane of red blood cells, loss of which is associated with hereditary stomatocytosis. Our study reveals plethora of gene expression changes in CP reticulocytes compared to wild type controls, among which 22% could be regulated by hypoxic response-specific cis genetic variations. These observations indicate the prominence of cis elements in hypoxic response, for which substantial inter-individual differences exist even among a relatively isolated population. Disclosures Gordeuk: Emmaus Life Sciences: Consultancy.

scholarly journals RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and Cis-Regulation Analysis by Allele-Specific Expression in Livestock Species

2021 ◽  
Vol 12 ◽  
Author(s):  
Frédéric Jehl ◽  
Fabien Degalez ◽  
Maria Bernard ◽  
Frédéric Lecerf ◽  
Laetitia Lagoutte ◽  
...  
Keyword(s):  
Gene Expression ◽  
Call Rate ◽  
Rna Seq ◽  
Snp Detection ◽  
Specific Expression ◽  
Genotype Calling ◽  
Allele Specific Expression ◽  
Livestock Species ◽  
Allele Specific ◽  
The Impact

In addition to their common usages to study gene expression, RNA-seq data accumulated over the last 10 years are a yet-unexploited resource of SNPs in numerous individuals from different populations. SNP detection by RNA-seq is particularly interesting for livestock species since whole genome sequencing is expensive and exome sequencing tools are unavailable. These SNPs detected in expressed regions can be used to characterize variants affecting protein functions, and to study cis-regulated genes by analyzing allele-specific expression (ASE) in the tissue of interest. However, gene expression can be highly variable, and filters for SNP detection using the popular GATK toolkit are not yet standardized, making SNP detection and genotype calling by RNA-seq a challenging endeavor. We compared SNP calling results using GATK suggested filters, on two chicken populations for which both RNA-seq and DNA-seq data were available for the same samples of the same tissue. We showed, in expressed regions, a RNA-seq precision of 91% (SNPs detected by RNA-seq and shared by DNA-seq) and we characterized the remaining 9% of SNPs. We then studied the genotype (GT) obtained by RNA-seq and the impact of two factors (GT call-rate and read number per GT) on the concordance of GT with DNA-seq; we proposed thresholds for them leading to a 95% concordance. Applying these thresholds to 767 multi-tissue RNA-seq of 382 birds of 11 chicken populations, we found 9.5 M SNPs in total, of which ∼550,000 SNPs per tissue and population with a reliable GT (call rate ≥ 50%) and among them, ∼340,000 with a MAF ≥ 10%. We showed that such RNA-seq data from one tissue can be used to (i) detect SNPs with a strong predicted impact on proteins, despite their scarcity in each population (16,307 SIFT deleterious missenses and 590 stop-gained), (ii) study, on a large scale, cis-regulations of gene expression, with ∼81% of protein-coding and 68% of long non-coding genes (TPM ≥ 1) that can be analyzed for ASE, and with ∼29% of them that were cis-regulated, and (iii) analyze population genetic using such SNPs located in expressed regions. This work shows that RNA-seq data can be used with good confidence to detect SNPs and associated GT within various populations and used them for different analyses as GTEx studies.

scholarly journals A Bayesian mixture model for the analysis of allelic expression in single cells

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Kwangbom Choi ◽  
Narayanan Raghupathy ◽  
Gary A. Churchill
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Mixture Model ◽  
Time Course ◽  
Single Cells ◽  
Expression Patterns ◽  
Allelic Expression ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific

AbstractAllele-specific expression (ASE) at single-cell resolution is a critical tool for understanding the stochastic and dynamic features of gene expression. However, low read coverage and high biological variability present challenges for analyzing ASE. We demonstrate that discarding multi-mapping reads leads to higher variability in estimates of allelic proportions, an increased frequency of sampling zeros, and can lead to spurious findings of dynamic and monoallelic gene expression. Here, we report a method for ASE analysis from single-cell RNA-Seq data that accurately classifies allelic expression states and improves estimation of allelic proportions by pooling information across cells. We further demonstrate that combining information across cells using a hierarchical mixture model reduces sampling variability without sacrificing cell-to-cell heterogeneity. We applied our approach to re-evaluate the statistical independence of allelic bursting and track changes in the allele-specific expression patterns of cells sampled over a developmental time course.

scholarly journals The Transcriptional Aftermath in Two Independently Formed Hybrids of the Opportunistic Pathogen Candida orthopsilosis

mSphere ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Hrant Hovhannisyan ◽  
Ester Saus ◽  
Ewa Ksiezopolska ◽  
Toni Gabaldón
Keyword(s):  
Gene Expression ◽  
Loss Of Heterozygosity ◽  
Opportunistic Pathogen ◽  
Specific Gene ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Content Type ◽  
Additional Layer ◽  
Allele Specific ◽  
Candida Orthopsilosis

ABSTRACT Interspecific hybridization can drive evolutionary adaptation to novel environments. The Saccharomycotina clade of budding yeasts includes many hybrid lineages, and hybridization has been proposed as a source for new pathogenic species. Candida orthopsilosis is an emerging opportunistic pathogen for which most clinical isolates are hybrids, each derived from one of at least four independent crosses between the same two parental lineages. To gain insight into the transcriptomic aftermath of hybridization in these pathogens, we analyzed allele-specific gene expression in two independently formed hybrid strains and in a homozygous strain representative of one parental lineage. Our results show that the effect of hybridization on overall gene expression is rather limited, affecting ∼4% of the genes studied. However, we identified a larger effect in terms of imbalanced allelic expression, affecting ∼9.5% of the heterozygous genes in the hybrids. This effect was larger in the hybrid with more extensive loss of heterozygosity, which may indicate a tendency to avoid loss of heterozygosity in these genes. Consistently, the number of shared genes with allele-specific expression in the two independently formed hybrids was higher than random expectation, suggesting selective retention. Some of the imbalanced genes have functions related to pathogenicity, including zinc transport and superoxide dismutase activities. While it remains unclear whether the observed imbalanced genes play a role in virulence, our results suggest that differences in allele-specific expression may add an additional layer of phenotypic plasticity to traits related to virulence in C. orthopsilosis hybrids. IMPORTANCE How new pathogens emerge is an important question that remains largely unanswered. Some emerging yeast pathogens are hybrids originated through the crossing of two different species, but how hybridization contributes to higher virulence is unclear. Here, we show that hybrids selectively retain gene regulation plasticity inherited from the two parents and that this plasticity affects genes involved in virulence.

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 Cis-regulatory changes in locomotor genes are associated with the evolution of burrowing behavior

2021 ◽  
Author(s):  
Caroline K. Hu ◽  
Ryan A. York ◽  
Hillery C. Metz ◽  
Nicole L. Bedford ◽  
Hunter B. Fraser ◽  
...  
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Sister Species ◽  
Behavioral Context ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Regulatory Changes ◽  
Allele Specific ◽  
Burrowing Behavior ◽  
Regulated Gene Expression

SummaryHow evolution modifies complex, innate behaviors is largely unknown. Divergence in many morphological traits has been linked, at least in part, to cis-regulatory changes in gene expression, a pattern also observed in some behaviors of recently diverged populations. Given this, we compared the gene expression in the brains of two interfertile sister species of Peromyscus mice, including allele-specific expression (ASE) of their F1 hybrids, that show large and heritable differences in burrowing behavior. Because cis-regulation may contribute to constitutive as well as activity-dependent gene expression, we also captured a molecular signature of burrowing circuit divergence by quantifying gene expression in mice shortly after burrowing. We found that several thousand genes were differentially expressed between the two sister species regardless of behavioral context, with several thousand more showing behavior-dependent differences. Allele-specific expression in F1 hybrids showed a similar pattern, suggesting that much of the differential expression is driven by cis-regulatory divergence. Genes related to locomotor coordination showed the strongest signals of lineage-specific selection on burrowing-induced cis-regulatory changes. By comparing these candidate genes to independent quantitative trait locus (QTL) mapping data, we found that the closest QTL markers to these candidate genes are associated with variation in burrow shape, demonstrating an enrichment for candidate locomotor genes near segregating causal loci. Together, our results provide insight into how cis-regulated gene expression can depend on behavioral context as well as how this dynamic regulatory divergence between species can be integrated with forward genetics to enrich our understanding of the genetic basis of behavioral evolution.

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