biostudies-arrayexpressDaniel RuncieStrongylocentrotus purpuratushttps://www.ebi.ac.uk/biostudies/studies/E-GEOD-38606Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter the contribution of additive genetic variation to gene expression during development of the purple sea urchin, Strongylocentrotus purpuratus, under increased temperatures that model realistic climate change scenarios. We first measured gene expression responses in the embryos by RNA-seq to characterize molecular signatures of mild, chronic temperature stress in an unbiased manner. We found that an increase from 12 °C to 18 °C caused widespread alterations in gene expression including in genes involved in protein folding, RNA processing, and development. To understand the quantitative genetic architecture of this response, we then focused on a well-characterized gene network involved in endomesoderm and ectoderm specification. Using a breeding design with wild-caught individuals, we measured genetic and gene-environment interaction effects on 72 genes within this network. We found genetic or maternal effects in 33 of these genes, and that the genetic effects were correlated in the network. 14 network genes also responded to higher temperatures, but we found no significant genotype-environment interactions in any of the genes. This absence may be due to an effective buffering of the temperature perturbations within the network. In support of this hypothesis, perturbations to regulatory genes did not affect the expression of the genes that they regulate. Together, these results provide novel insights into the relationship between environmental change and developmental evolution and suggest that climate change may not expose large amounts of cryptic genetic variation to selection in this species. 7 RNAseq samples representing embryos grown at 2 temperatures, from 3 female parents and 2 male parentsbiostudies-arrayexpressGrowth Protocol - Adult urchins were spawned by injecting 0.5M KCl. Eggs and sperm were mixed, fertilization rates assessed, washed, and then moved to larger culture dishes for growth. Embryos were cultured at low density until they reached the mid-point of gastrulation in artificial sea water at 18C or 12C.Sample Processing - Growth chambers were set to either 12C or 18C, and water was equilibrated prior to adding the fertilized embryos.Library Construction - 6.5 − 8.5μg of DNase-treated total RNA was used as the input sample. mRNA was isolated via two rounds of poly-A selection using 100μl of Dynabeads (Invitrogen). Bar- coded SOLiD libraries were prepared using the RNA-seq protocol for the SOLiD Total RNA-Seq kit and the SOLiD Transcriptome Multiplexing Kit (Applied Biosystems). Library quality was assessed using a 2100 Bioanalyzer (Agilent). Libraries were quantitated using qPCR, and prepared for standard stand-specific SOLiD sequencing in equimolar concentrations. 50bp single-end reads were generated on 2 slides by the IGSP Genome Sequencing and Analysis Core Resource at Duke University.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesFeature Extraction - Initial filtering by Corona Reads were mapped to the S purpuratus genome with Bowtie v0.12.7. Mapping parameters were -C -n 2 -l 9 -e 100 -M 1 -t -best -trim3 15 Reads were counted in gene models using Htseq with the parameters --mode=intersection-nonempty --stranded=yes Genome_build: Spur_3.1.LinearScaffold.fa from www.SpBase.org Supplementary_files_format_and_content: SPU_counts.txt countains total counts of reads per gene model per sample, as generated by HtseqMetabolomicsUnknownTranscriptomicsGenomicsProteomicsStress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter the contribution of additive genetic variation to gene expression during development of the purple sea urchin, Strongylocentrotus purpuratus, under increased temperatures that model realistic climate change scenarios. We first measured gene expression responses in the embryos by RNA-seq to characterize molecular signatures of mild, chronic temperature stress in an unbiased manner. We found that an increase from 12 to 18 °C caused widespread alterations in gene expression including in genes involved in protein folding, RNA processing and development. To understand the quantitative genetic architecture of this response, we then focused on a well-characterized gene network involved in endomesoderm and ectoderm specification. Using a breeding design with wild-caught individuals, we measured genetic and gene-environment interaction effects on 72 genes within this network. We found genetic or maternal effects in 33 of these genes and that the genetic effects were correlated in the network. Fourteen network genes also responded to higher temperatures, but we found no significant genotype-environment interactions in any of the genes. This absence may be owing to an effective buffering of the temperature perturbations within the network. In support of this hypothesis, perturbations to regulatory genes did not affect the expression of the genes that they regulate. Together, these results provide novel insights into the relationship between environmental change and developmental evolution and suggest that climate change may not expose large amounts of cryptic genetic variation to selection in this species.RNA-seq of coding RNAStrongylocentrotus purpuratusGenetics of gene expression responses to temperature stress in a sea urchin gene network.Sayan MukherjeeGregory WrayRuncie DE, Garfield DA, Babbitt CC, Wygoda JA, Mukherjee S, Wray GACourtney BabbittJennifer WygodaDaniel RuncieDavid GarfieldfalseGenetics of gene expression responses to temperature stress in a sea urchin gene network (HTS)Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter the contribution of additive genetic variation to gene expression during development of the purple sea urchin, Strongylocentrotus purpuratus, under increased temperatures that model realistic climate change scenarios. We first measured gene expression responses in the embryos by RNA-seq to characterize molecular signatures of mild, chronic temperature stress in an unbiased manner. We found that an increase from 12 °C to 18 °C caused widespread alterations in gene expression including in genes involved in protein folding, RNA processing, and development. To understand the quantitative genetic architecture of this response, we then focused on a well-characterized gene network involved in endomesoderm and ectoderm specification. Using a breeding design with wild-caught individuals, we measured genetic and gene-environment interaction effects on 72 genes within this network. We found genetic or maternal effects in 33 of these genes, and that the genetic effects were correlated in the network. 14 network genes also responded to higher temperatures, but we found no significant genotype-environment interactions in any of the genes. This absence may be due to an effective buffering of the temperature perturbations within the network. In support of this hypothesis, perturbations to regulatory genes did not affect the expression of the genes that they regulate. Together, these results provide novel insights into the relationship between environmental change and developmental evolution and suggest that climate change may not expose large amounts of cryptic genetic variation to selection in this species. 7 RNAseq samples representing embryos grown at 2 temperatures, from 3 female parents and 2 male parents2012-11-30T00:00:00Z2023-09-04T11:52:06.409Z2022-02-02T12:24:42.072ZE-GEOD-3860622856327SRP013629EFO_000373810.1111/j.1365-294X.2012.05717.x