Contribution of trans regulatory eQTL to cryptic genetic variation in C-elegans

Autor: Arjen E. van’t Hof, Rachel Brenchley, L. Basten Snoek, Rita J. M. Volkers, Mark G. Sterken, Andrew R. Cossins, Joost A. G. Riksen, Roel P. J. Bevers, Jan E. Kammenga
Jazyk: angličtina
Rok vydání: 2017
Předmět:
0301 basic medicine
Transcription
Genetic
Regulatory Sequences
Nucleic Acid
Heat stress
law.invention
0302 clinical medicine
Transcription (biology)
law
Gene expression
Systems and Synthetic Biology
EQTL
Genetics
Systeem en Synthetische Biologie
0303 health sciences
Cryptic genetic variation
PE&RC
Phenotype
Recombinant DNA
DNA microarray
Biotechnology
Research Article
medicine.medical_specialty
lcsh:QH426-470
lcsh:Biotechnology
Quantitative Trait Loci
Genomics
Biology
eQTL
Trans-band
03 medical and health sciences
lcsh:TP248.13-248.65
Molecular genetics
Genetic variation
medicine
Animals
Caenorhabditis elegans
Laboratorium voor Nematologie
Gene
VLAG
030304 developmental biology
eQTL hotspot
Genetic Variation
lcsh:Genetics
030104 developmental biology
Gene Expression Regulation
Expression quantitative trait loci
EQTL hotspot
Genetical genomics
Gene polymorphism
EPS
Laboratory of Nematology
030217 neurology & neurosurgery
Heat-Shock Response
Zdroj: BMC GENOMICS
BMC Genomics
BMC Genomics 18 (2017)
BMC Genomics, 18(1). BioMed Central
BMC Genomics, 18
BMC Genomics, Vol 18, Iss 1, Pp 1-15 (2017)
ISSN: 1471-2164
Popis: BackgroundCryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene expression regulation underlying CGV is scarce. Here we investigated the transcriptional architecture of CGV in response to rapid temperature changes in the nematode Caenorhabditis elegans. We analyzed regulatory variation in gene expression (and mapped eQTL) across the course of a heat stress and recovery response in a recombinant inbred population.ResultsWe measured gene expression over three temperature treatments: i) control, ii) heat stress, and iii) recovery from heat stress. Compared to control, exposure to heat stress affected the transcription of 3305 genes, whereas 942 were affected in recovering animals. These affected genes were mainly involved in metabolism and reproduction. The gene expression pattern in recovering animals resembled both the control and the heat-stress treatment. We mapped eQTL using the genetic variation of the recombinant inbred population and detected 2626 genes with an eQTL in the heat-stress treatment, 1797 in the control, and 1880 in the recovery. The cis-eQTL were highly shared across treatments. A considerable fraction of the trans-eQTL (40-57%) mapped to 19 treatment specific trans-bands. In contrast to cis-eQTL, trans-eQTL were highly environment specific and thus cryptic. Approximately 67% of the trans-eQTL were only induced in a single treatment, with heat-stress showing the most unique trans-eQTL.ConclusionsThese results illustrate the highly dynamic pattern of CGV across three different environmental conditions that can be evoked by a stress response over a relatively short time-span (2 hours) and that CGV is mainly determined by response related trans regulatory eQTL.
Databáze: OpenAIRE
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