scholarly journals Between‐population differences in constitutive and infection‐induced gene expression in threespine stickleback

2021 ◽  
Author(s):  
Lauren E. Fuess ◽  
Jesse N. Weber ◽  
Stijn den Haan ◽  
Natalie C. Steinel ◽  
Kum Chuan Shim ◽  
...  
Keyword(s):  
Gene Expression ◽  
Threespine Stickleback ◽  
Population Differences

scholarly journals Early Life Disruption of the Microbiota Affects Organ Development and Cytokine Gene Expression in Threespine Stickleback

2020 ◽  
Author(s):  
Lucas J Kirschman ◽  
Anastasia Khadjinova ◽  
Kelly Ireland ◽  
Kathryn C Milligan-Myhre
Keyword(s):  
Gene Expression ◽  
Early Life ◽  
Genetic Background ◽  
Gasterosteus Aculeatus ◽  
Threespine Stickleback ◽  
Microbial Colonization ◽  
Cytokine Gene Expression ◽  
Immune Gene ◽  
Cytokine Gene

Synopsis The microbiota that inhabits vertebrates exerts strong effects on host physiology and can be crucial to the development of a normal phenotype. This includes development of the immune system, somatic growth and maintenance, and morphogenesis. However, the genetic background of the host can also affect these life history traits. To this end, we investigated the effects of the microbiota on growth, development, and immune gene expression on two populations of threespine stickleback (Gasterosteus aculeatus), one anadromous and one freshwater. We tested the hypotheses that microbial colonization and the genetic background of the host would affect survival, cytokine gene expression, growth, and development. We raised in vitro crosses of stickleback larvae with and without conventional microbiota. We then exposed all these treatments to Vibrio anguillarum, a potential fish pathogen, in a full factorial design. We found stickleback raised without conventional microbiota had smaller swim bladders relative to those raised with conventional microbiota. Stickleback raised with conventional microbiota exhibited small increases in cytokine gene expression. We found no differences in growth or survival regardless of treatment. These results are consistent with other investigations that show microbiota disruption, in early life, can alter host organ and tissue development and immune responses

Gene expression plasticity evolves in response to colonization of freshwater lakes in threespine stickleback

2014 ◽  
Vol 23 (13) ◽  
pp. 3226-3240 ◽  
Author(s):  
Matthew R. J. Morris ◽  
Romain Richard ◽  
Erica H. Leder ◽  
Rowan D. H. Barrett ◽  
Nadia Aubin-Horth ◽  
...  
Keyword(s):  
Gene Expression ◽  
Threespine Stickleback ◽  
Freshwater Lakes

scholarly journals Regulatory Architecture of Gene Expression Variation in the Threespine Stickleback Gasterosteus aculeatus

2016 ◽  
Vol 7 (1) ◽  
pp. 165-178 ◽  
Author(s):  
Victoria L. Pritchard ◽  
Heidi M. Viitaniemi ◽  
R. J. Scott McCairns ◽  
Juha Merilä ◽  
Mikko Nikinmaa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gasterosteus Aculeatus ◽  
Threespine Stickleback ◽  
Gene Expression Variation ◽  
Expression Variation ◽  
Regulatory Architecture

scholarly journals Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension

2014 ◽  
Vol 5 ◽  
Author(s):  
Gang Wang ◽  
Ence Yang ◽  
Kerri J. Smith ◽  
Yong Zeng ◽  
Guoli Ji ◽  
...  
Keyword(s):  
Gene Expression ◽  
Threespine Stickleback ◽  
Salt Sensitive Hypertension

scholarly journals Regulatory architecture of gene expression variation in the threespine stickleback, Gasterosteus aculeatus

2016 ◽  
Author(s):  
Victoria L. Pritchard ◽  
Heidi M. Viitaniemi ◽  
R.J. Scott McCairns ◽  
Juha Merilä ◽  
Mikko Nikinmaa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulatory Networks ◽  
Gasterosteus Aculeatus ◽  
Genotyping By Sequencing ◽  
Interval Mapping ◽  
Threespine Stickleback ◽  
Adaptive Divergence ◽  
Gene Expression Variation ◽  
Expression Variation ◽  
Regulatory Architecture

Much adaptive evolutionary change is underlain by mutational variation in regions of the genome that regulate gene expression rather than in the coding regions of the genes themselves. An understanding of the role of gene expression variation in facilitating local adaptation will be aided by an understanding of underlying regulatory networks. Here, we characterize the genetic architecture of gene expression variation in the threespine stickleback (Gasterosteus aculeatus), an important model in the study of adaptive evolution. We collected transcriptomic and genomic data from 60 half-sib families using an expression microarray and genotyping-by-sequencing, and located QTL underlying the variation in gene expression (eQTL) in liver tissue using an interval mapping approach. We identified eQTL for several thousand expression traits. Expression was influenced by polymorphism in both cis and trans regulatory regions. Trans eQTL clustered into hotspots. We did not identify master transcriptional regulators in hotspot locations: rather, the presence of hotspots may be driven by complex interactions between multiple transcription factors. One observed hotspot co-located with a QTL recently found to underlie salinity tolerance in the threespine stickleback. However, most other observed hotspots did not co-locate with regions of the genome known to be involved in adaptive divergence between marine and freshwater habitats.

scholarly journals Exploring the Genetic Basis of Human Population Differences in DNA Methylation and their Causal Impact on Immune Gene Regulation

2018 ◽  
Author(s):  
Lucas T. Husquin ◽  
Maxime Rotival ◽  
Maud Fagny ◽  
Hélène Quach ◽  
Nora Zidane ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Gene Regulation ◽  
Complex Traits ◽  
Active Role ◽  
System Level ◽  
Immune Gene ◽  
Population Differences ◽  
Mediation Effects ◽  
Causal Impact

AbstractDNA methylation is influenced by both environmental and genetic factors and is increasingly thought to affect variation in complex traits and diseases. Yet, the extent of ancestry-related differences in DNA methylation, its genetic determinants, and their respective causal impact on immune gene regulation remain elusive. We report extensive population differences in DNA methylation between individuals of African and European descent — detected in primary monocytes that were used as a model of a major innate immunity cell type. Most of these differences (~70%) were driven by DNA sequence variants nearby CpG sites (meQTLs), which account for ~60% of the variance in DNA methylation. We also identify several master regulators of DNA methylation variation in trans, including a regulatory hub nearby the transcription factor-encoding CTCF gene, which contributes markedly to ancestry-related differences in DNA methylation. Furthermore, we establish that variation in DNA methylation is associated with varying gene expression levels following mostly, but not exclusively, a canonical model of negative associations, particularly in enhancer regions. Specifically, we find that DNA methylation highly correlates with transcriptional activity of 811 and 230 genes, at the basal state and upon immune stimulation, respectively. Finally, using a Bayesian approach, we estimate causal mediation effects of DNA methylation on gene expression in ~20% of the studied cases, indicating that DNA methylation can play an active role in immune gene regulation. Using a system-level approach, our study reveals substantial ancestry-related differences in DNA methylation and provides evidence for their causal impact on immune gene regulation.

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