Dataset Information

Immune-Related Transcriptional Responses to Parasitic Infection in a Naturally Inbred Fish: Roles of Genotype and Individual Variation.

ABSTRACT: Parasites are strong drivers of evolutionary change and the genetic variation of both host and parasite populations can co-evolve as a function of parasite virulence and host resistance. The role of transcriptome variation in specific interactions between host and parasite genotypes has been less studied and can be confounded by differences in genetic variation. We employed two naturally inbred lines of a self-fertilizing fish to estimate the role of host genotype in the transcriptome response to parasite infection using RNA-seq. In addition, we targeted several differentially expressed immune-related genes to further investigate the relative role of individual variation in the immune response using RT-qPCR, taking advantage of the genomic uniformity of the self-fertilizing lines. We found significant differences in gene expression between lines in response to infection both in the transcriptome and in individual gene RT-qPCR analyses. Individual RT-qPCR analyses of gene expression identified significant variance differences between lines for six genes but only for three genes between infected and control fish. Our results indicate that although the genetic background plays an important role in the transcriptome response to parasites, it cannot fully explain individual differences within genetically homogeneous lines, which can be important for determining the response to parasites.

SUBMITTER: Pawluk RJ

PROVIDER: S-EPMC5786212 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Immune-Related Transcriptional Responses to Parasitic Infection in a Naturally Inbred Fish: Roles of Genotype and Individual Variation.

Pawluk Rebecca Jane RJ Uren Webster Tamsyn M TM Cable Joanne J Garcia de Leaniz Carlos C Consuegra Sofia S

Genome biology and evolution 20180101 1

Parasites are strong drivers of evolutionary change and the genetic variation of both host and parasite populations can co-evolve as a function of parasite virulence and host resistance. The role of transcriptome variation in specific interactions between host and parasite genotypes has been less studied and can be confounded by differences in genetic variation. We employed two naturally inbred lines of a self-fertilizing fish to estimate the role of host genotype in the transcriptome response t ...[more]

PMID: 29340582

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Project description:Phenotypic variability among inbred littermates reared in controlled environments remains poorly understood. Metastable epialleles refer to loci that intrinsically behave in this way and a few examples have been described. They display differential methylation in association with differential expression. For example, inbred mice carrying the agouti viable yellow (A (vy) ) allele show a range of coat colours associated with different DNA methylation states at the locus. The availability of next-generation sequencing, in particular whole genome sequencing of bisulphite converted DNA, allows us, for the first time, to search for metastable epialleles at base pair resolution.Using whole genome bisulphite sequencing of DNA from the livers of five mice from the A (vy) colony, we searched for sites at which DNA methylation differed among the mice. A small number of loci, 356, were detected and we call these inter-individual Differentially Methylated Regions, iiDMRs, 55 of which overlap with endogenous retroviral elements (ERVs). Whole genome resequencing of two mice from the colony identified very few differences and these did not occur at or near the iiDMRs. Further work suggested that the majority of ERV iiDMRs are metastable epialleles; the level of methylation was maintained in tissue from other germ layers and the level of mRNA from the neighbouring gene inversely correlated with methylation state. Most iiDMRs that were not overlapping ERV insertions occurred at tissue-specific DMRs and it cannot be ruled out that these are driven by changes in the ratio of cell types in the tissues analysed.Using the most thorough genome-wide profiling technologies for differentially methylated regions, we find very few intrinsically epigenetically variable regions that we term iiDMRs. The most robust of these are at retroviral elements and appear to be metastable epialleles. The non-ERV iiDMRs cannot be described as metastable epialleles at this stage but provide a novel class of variably methylated elements for further study.

Project description:Crying is the principal means by which newborn infants shape parental behavior to meet their needs. While this mechanism can be highly effective, infant crying can also be an aversive stimulus that leads to parental frustration and even abuse. Fathers have recently become more involved in direct caregiving activities in modern, developed nations, and fathers are more likely than mothers to physically abuse infants. In this study, we attempt to explain variation in the neural response to infant crying among human fathers, with the hope of identifying factors that are associated with a more or less sensitive response. We imaged brain function in 39 first-time fathers of newborn infants as they listened to both their own and a standardized unknown infant cry stimulus, as well as auditory control stimuli, and evaluated whether these neural responses were correlated with measured characteristics of fathers and infants that were hypothesized to modulate these responses. Fathers also provided subjective ratings of each cry stimulus on multiple dimensions. Fathers showed widespread activation to both own and unknown infant cries in neural systems involved in empathy and approach motivation. There was no significant difference in the neural response to the own vs. unknown infant cry, and many fathers were unable to distinguish between the two cries. Comparison of these results with previous studies in mothers revealed a high degree of similarity between first-time fathers and first-time mothers in the pattern of neural activation to newborn infant cries. Further comparisons suggested that younger infant age was associated with stronger paternal neural responses, perhaps due to hormonal or novelty effects. In our sample, older fathers found infant cries less aversive and had an attenuated response to infant crying in both the dorsal anterior cingulate cortex (dACC) and the anterior insula, suggesting that compared with younger fathers, older fathers may be better able to avoid the distress associated with empathic over-arousal in response to infant cries. A principal components analysis revealed that fathers with more negative emotional reactions to the unknown infant cry showed decreased activation in the thalamus and caudate nucleus, regions expected to promote positive parental behaviors, as well as increased activation in the hypothalamus and dorsal ACC, again suggesting that empathic over-arousal might result in negative emotional reactions to infant crying. In sum, our findings suggest that infant age, paternal age and paternal emotional reactions to infant crying all modulate the neural response of fathers to infant crying. By identifying neural correlates of variation in paternal subjective reactions to infant crying, these findings help lay the groundwork for evaluating the effectiveness of interventions designed to increase paternal sensitivity and compassion.

Dataset Information

Immune-Related Transcriptional Responses to Parasitic Infection in a Naturally Inbred Fish: Roles of Genotype and Individual Variation.

Publications

Immune-Related Transcriptional Responses to Parasitic Infection in a Naturally Inbred Fish: Roles of Genotype and Individual Variation.

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