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opencc-zeroDec 2016View details →

Data from: Gene expression differs in codominant prairie grasses under drought

Grasslands of the Central US are expected to experience severe droughts and other climate extremes in the future, yet we know little about how these grasses will respond in terms of gene expression. We compared gene expression in Andropogon gerardii and Sorghastrum nutans, two closely related co-dominant C4 grasses responsible for the majority of ecosystem function, using RNA-seq. We compared Trinity assemblies within each species to determine annotated functions of transcripts responding to drought. Subsequently, we compared homologous annotated gene-groups across the two species using cross-species meta-level analysis and functional clustering based on key terms. The majority of variation was found between species, as opposed to between drought and watered treatments. However, there is evidence for differential responses; Andropogon allocated gene expression differently compared to Sorghastrum, suggesting Andropogon focuses on stress alleviation (such as oxygen radical scavenging) rather than prevention. In contrast, Sorghastrum may employ a drought avoidance strategy by modulating osmotic response, especially with hormonal regulation. We found Sorghastrum tended to be more sensitive within 10 key gene-groups related to stress, abscisic acid, and trichomes, suggesting gene expression may mechanistically parallel sensitivity at the physiological level. Our findings corroborate phenotypic and physiological differences in the field, and may help explain the phenotypic mechanisms of these two species in the tallgrass prairie community under future drought scenarios.

opencc-by-4.0Sep 2020View details →

Source code for models of floral initiation in pea and gene expression data extracted from published sources

The dataset contains the source code for computational models of a gene network controlling transition to flowering in pea (Pisum sativum). The models were based on ordinary differential equations (ODE) or neural networks. It also includes data on the expression dynamics of genes involved in the network, which was used for model fitting. The expression data was extracted from the following papers:  Hecht, V., Laurie, R. E., Schoor, K. Vander, Ridge, S., Knowles, C. L., Liew, L. C., Sussmilch, F. C., et al. (2011). The Pea GIGAS Gene Is a FLOWERING LOCUS T Homolog Necessary for Graft-Transmissible Specification of Flowering but Not for Responsiveness to Photoperiod. 23, 147–161. doi:10.1105/tpc.110.081042 Sussmilch, F. C., Berbel, A., Hecht, V., Schoor, K. Vander, Ferrándiz, C., Madueño, F., et al. (2015). Pea VEGETATIVE2 Is an FD Homolog That Is Essential for Flowering and Compound In fl orescence Development. 27, 1046–1060. doi:10.1105/tpc.115.136150 The source code of the DEEP software used for parameter optimization in the model fitting can be found in the Gitlab repository (https://gitlab.com/mackoel/deepmethod/-/tree/master). The files are the supplement to the following manuscript, submitted to Frontiers in Genetics: "Dynamical Modeling of the Core Gene Network Controlling Transition to Flowering in Pisum sativum" by Polina Pavlinova, Maria G. Samsonova, and Vitaly V. Gursky. All possible questions can be sent to: Polina Pavlinova (polina.pavlina1004@gmail.com), Vitaly Gursky (gursky@math.ioffe.ru).

opencc-by-4.0Oct 2020View details →

Human tissue gene expression TPM values for the advanced forensic biology course

Gene expression per tissue This dataset comes from the <a href="https://www.gtexportal.org/home/">Genotype-Tissue Expression (GTEx)</a> database that gathers gene expression data from various human tissues. Specifically, the GTEx Analysis v7 version was used. The file is called "<a href="https://zenodo.org/api/files/9f872792-6c96-4226-b659-ce0807da66e8/GTEx_Analysis_2016-01-15_v7_RNASeQCv1.1.8_gene_median_tpm.tsv">GTEx_Analysis_2016-01-15_v7_RNASeQCv1.1.8_gene_tpm.tsv</a>"  and contains tabulated-separated values of median TPM gene expression by tissue (TPM: transcript per million).   Genes with a favored sucutaneous-adipose expression profile This file contains 195 genes that have a statistically (p < 0.01) favored expression profile in subcutaneous adipose tissue compared to other tissues.   https://zenodo.org/api/files/7342bbfa-0e4d-49e7-b916-5eff5b638c33/genes_with_a_subcutaneous_adipose_favored_expression.tsv

opencc-zeroOct 2020View details →

Data from: Ocean acidification induces subtle shifts in gene expression and DNA methylation in mantle tissue of the Eastern oyster (Crassostrea virginica)

Early evidence suggests that DNA methylation can mediate phenotypic responses of marine calcifying species to ocean acidification (OA). Few studies, however, have explicitly studied DNA methylation in calcifying tissues through time. Here, we examined the phenotypic and molecular responses in the extrapallial fluid and mantle (fluid and tissue at the calcification site) in adult eastern oyster (Crassostrea virginica) exposed to experimental OA over 80 days. Oysters were reared under three experimental pCO2 treatments ('control', 580 μatm; 'moderate OA', 1000 μatm; 'high OA', 2800 μatm) and sampled at 6 time points (24 hours - 80 days). We found that high OA initially induced an increase in the pH of the extrapallial fluid (pHEPF) relative to the external seawater that peaked at day 9, but then diminished over time. Calcification rates were significantly lower in the high OA treatment compared to the other treatments. To explore how oysters regulate their extrapallial fluid, gene expression and DNA methylation were examined in the mantle-edge tissue of oysters from days 9 and 80 in the control and high OA treatments. Mantle tissue mounted a significant global molecular response (both in the transcriptome and methylome) to OA that shifted through time. Although we did not find individual genes that were significantly differentially expressed under OA, the pHEPF was significantly correlated with the eigengene expression of several co-expressed gene clusters. A small number of OA-induced differentially methylated loci were discovered, which corresponded with a weak association between OA-induced changes in genome-wide gene body DNA methylation and gene expression. Gene body methylation, however, was not significantly correlated with the eigengene expression of pHEPF-correlated gene clusters. These results suggest that OA induces a subtle response in a large number of genes in C. virginica, but also indicate that plasticity at the molecular level may be limited. Our study highlights the need to reassess our understanding of tissue-specific molecular responses in marine calcifiers, as well as the role of DNA methylation and gene expression in mediating physiological and biomineralization responses to OA.

opencc-zeroOct 2020View details →

Gene expression remodelling and immune response during adaptive divergence in an African cichlid fish

Variation in gene expression contributes to ecological speciation by facilitating population persistence in novel environments. Likewise, immune response can be a relevant factor in speciation driven by adaptation to different environments. Previous studies examining gene expression differences between recently diverged ecotypes often relied on only one pair of populations, targeted the expression of only a subset of genes, or used wild caught-individuals. Here, we investigated the contribution of habitat-specific parasites and symbionts and the underlying immunological capabilities of ecotype hosts to adaptive divergence in lake-river population pairs of the cichlid fish Astatotilapia burtoni. To shed light on the role of phenotypic plasticity in adaptive divergence, we compared parasite and microbiota communities, immune response, and gene expression patterns of fish from natural habitats and a lake-like pond setup. In all investigated population pairs, lake fish were more heavily parasitized than river fish, both in terms of parasite taxa composition and infection abundance. Innate immune response in the wild was higher in lake than in river populations and elevated in a river population exposed to lake parasites in the pond setup. Environmental differences between lake and river habitat and their distinct parasite communities shaped differential gene expression, involving genes functioning in osmoregulation and immune response. Most changes in gene expression between lake and river samples in the wild and in the pond setup were based on a plastic response. Finally, gene expression and bacterial communities of wild-caught individuals and individuals acclimated to lake-like pond conditions showed shifts underlying adaptive phenotypic plasticity.

opencc-by-4.0Jul 2020View details →

ChIP-seq of plasma cell-free nucleosomes identifies cell-of-origin gene expression programs

Genomic DNA is packed by histone proteins that carry a multitude of post-translational modifications  that reflect cellular transcriptional state. Cell-free DNA (cfDNA) is derived from fragmented chromatin in dying cells, and as such it retains the histones markings present in the cells of origin. Here, we pioneer chromatin immunoprecipitation followed by sequencing of cell-free nucleosomes (cfChIP-seq) carrying active chromatin marks. Our results show that cfChIP-seq provides multidimensional epigenetic information that recapitulates the epigenetic and transcriptional landscape in the cells of origin. We applied cfChIP-seq to 268 samples including samples from patients with heart and liver pathologies, and 135 samples from 56 metastatic CRC patients. We show that cfChIP-seq can detect pathology-related transcriptional changes at the site of the disease, beyond the information on tissue of origin. In CRC patients we detect clinically-relevant, and patient-specific information, including transcriptionally active HER2 amplifications. cfChIP-seq provides genome-wide information and requires low sequencing depth. Altogether, we establish cell-free chromatin immunoprecipitation as an exciting modality with potential for diagnosis and interrogation of physiological and pathological processes using a simple blood test.

opencc-by-4.0Dec 2020View details →

Supplementary Materials for "The Effects of Chromosome Doubling on Morphology, Salinity Tolerance, Essential Oil Composition, and Gene Expression of Biosynthesis Pathway in Peppermint (Mentha piperita L.)"

Shandong Province Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; zhaozjfrances@163.com (Z.Z.); yanli_wei@163.com (Y.W.); menshenlai@163.com (K.Y.); sdkinghills@sina.com (B.L.); liling33802400@163.com (L.L.); yanght@sdas.org (H.Y)

opencc-by-4.0Dec 2020View details →

Haberlea darkness 2018 gene expression

The desiccation-tolerant plant Haberlea rhodopensis can withstand months of darkness without any visible senescence. Here, we investigated the molecular mechanisms of this adaptation to prolonged (30 d) darkness and subsequent return to light. H. rhodopensis plants remained green and viable throughout the dark treatment. Transcriptomic analysis revealed that darkness regulated several transcription factor (TF) genes. Stress- and autophagy-related TFs such as ERF8, HSFA2b, RD26, TGA1, and WRKY33 were up-regulated, while chloroplast- and flowering-related TFs such as ATH1, COL2, COL4, RL1, and PTAC7 were repressed. PHYTOCHROME INTERACTING FACTOR4, a negative regulator of photomorphogenesis and promoter of senes-cence, also was down-regulated. In response to darkness, most of the photosynthesis- and photorespiratory-related genes were strongly down-regulated, while genes related to autophagy were up-regulated. This occurred concomitant with the induction of SUCROSE NON-FERMENTING1-RELATED PROTEIN KINASES (SnRK1) signaling pathway genes, which regulate responses to stress-induced starvation and autophagy. Most of the genes associated with chlorophyll catabolism, which are induced by darkness in dark-senescing species, were either unregulated (PHEOPHORBIDE A OXYGENASE, PAO; RED CHLOROPHYLL CATABOLITE REDUCTASE, RCCR) or repressed (STAY GREEN-LIKE, PHEOPHYTINASE, and NON-YELLOW COLORING1). Metabolite profiling revealed increases in the levels of many amino acids in darkness, suggesting increased protein degrada-tion. In darkness, levels of the chloroplastic lipids digalactosyldiacylglycerol, monogalactosyldiacylglycerol, phosphatidylglyc-erol, and sulfoquinovosyldiacylglycerol decreased, while those of storage triacylglycerols increased, suggesting degradation of chloroplast membrane lipids and their conversion to triacylglycerols for use as energy and carbon sources. Collectively, these data show a coordinated response to darkness, including repression of photosynthetic, photorespiratory, flowering, and chloro-phyll catabolic genes, induction of autophagy and SnRK1 pathways, and metabolic reconfigurations that enable survival under prolonged darkness.

opencc-by-4.0Jan 2021View details →

AhR Gene Expression in Immune cell subtypes

Benjamin J. Schmiedel, Divya Singh, Ariel Madrigal, Alan G. Valdovino-Gonzalez, Brandie M. White, Jose Zapardiel-Gonzalo, Brendan Ha, Gokmen Altay, Jason A. Greenbaum, Graham McVicker, Grégory Seumois, Anjana Rao, Mitchell Kronenberg, Bjoern Peters, Pandurangan Vijayanand, Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression, Cell, Volume 175, Issue 6, 2018, Pages 1701-1715.e16, ISSN 0092-8674, https://doi.org/10.1016/j.cell.2018.10.022. (http://www.sciencedirect.com/science/article/pii/S009286741831331X) Abstract: Summary While many genetic variants have been associated with risk for human diseases, how these variants affect gene expression in various cell types remains largely unknown. To address this gap, the DICE (database of immune cell expression, expression quantitative trait loci [eQTLs], and epigenomics) project was established. Considering all human immune cell types and conditions studied, we identified cis-eQTLs for a total of 12,254 unique genes, which represent 61% of all protein-coding genes expressed in these cell types. Strikingly, a large fraction (41%) of these genes showed a strong cis-association with genotype only in a single cell type. We also found that biological sex is associated with major differences in immune cell gene expression in a highly cell-specific manner. These datasets will help reveal the effects of disease risk-associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis (https://dice-database.org). Keywords: DICE; immunology; GWAS; genetic variants; human immune cells; gene expression; eGenes; eQTLs; sex https://dice-database.org/genes/ahr#boxplot

opencc-zeroJan 2021View details →

Wing plasticity and associated gene expression varies across the pea aphid biotype complex

Developmental phenotypic plasticity is a widespread phenomenon that allows organisms to produce different adult phenotypes in response to different environments. Investigating the molecular mechanisms underlying plasticity has the potential to reveal the precise changes that lead to the evolution of plasticity as a phenotype. Here, we study wing plasticity in multiple host-plant adapted populations of pea aphids as a model for understanding adaptation to different environments within a single species. We describe the wing plasticity response of different 'biotypes' to a crowded environment and find differences within as well as among biotypes. We then use transcriptome profiling to compare a highly plastic pea aphid genotype to one that shows no plasticity and find that the latter exhibits no gene expression differences between environments. We conclude that the loss of plasticity has been accompanied by a loss of differential gene expression and therefore that genetic assimilation has occurred. Our gene expression results generalize previous studies that have shown a correlation between plasticity in morphology and gene expression.

opencc-zeroDec 2015View details →

Data from: Context-dependent expression of the foraging gene in field colonies of ants: the interacting roles of age, environment and task

Task allocation among social insect workers is an ideal framework for studying the molecular mechanisms underlying behavioural plasticity because workers of similar genotype adopt different behavioural phenotypes. Elegant laboratory studies have pioneered this effort, but field studies involving the genetic regulation of task allocation are rare. Here, we investigate the expression of the foraging gene in harvester ant workers from five age- and task-related groups in a natural population, and we experimentally test how exposure to light affects foraging expression in brood workers and foragers. Results from our field study show that the regulation of the foraging gene in harvester ants occurs at two time scales: levels of foraging mRNA are associated with ontogenetic changes over weeks in worker age, location and task, and there are significant daily oscillations in foraging expression in foragers. The temporal dissection of foraging expression reveals that gene expression changes in foragers occur across a scale of hours and the level of expression is predicted by activity rhythms: foragers have high levels of foraging mRNA during daylight hours when they are most active outside the nests. In the experimental study, we find complex interactions in foraging expression between task behaviour and light exposure. Oscillations occur in foragers following experimental exposure to 13 L : 11 D (LD) conditions, but not in brood workers under similar conditions. No significant differences were seen in foraging expression over time in either task in 24 h dark (DD) conditions. Interestingly, the expression of foraging in both undisturbed field and experimentally treated foragers is also significantly correlated with the expression of the circadian clock gene, cycle. Our results provide evidence that the regulation of this gene is context-dependent and associated with both ontogenetic and daily behavioural plasticity in field colonies of harvester ants. Our results underscore the importance of assaying temporal patterns in behavioural gene expression and suggest that gene regulation is an integral mechanism associated with behavioural plasticity in harvester ants.

Data for: Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems

Advancements in the field of synthetic biology have been possible due to the development of genetic tools that are able to regulate gene expression. However, the current toolbox of gene regulatory tools for eukaryotic systems have been outpaced by those developed for simple, single-celled systems. Here, we engineered a set of gene regulatory tools by combining self-cleaving ribozymes with various upstream competing sequences that were designed to disrupt ribozyme self-cleavage. As a proof-of-concept, we were able to modulate GFP expression in mammalian cells, and then showed the feasibility of these tools in Drosophila embryos. For each system, the fold-reduction of gene expression was influenced by the location of the self-cleaving ribozyme/upstream competing sequence (i.e. 5′ vs. 3′ untranslated region) and the competing sequence used. Together, this work provides a set of genetic tools that can be used to tune gene expression across various eukaryotic systems.

Data from: Electroacupuncture mimics exercise-induced changes in skeletal muscle gene expression in women with polycystic ovary syndrome

Context: Autonomic nervous system activation mediates the increase in whole-body glucose uptake in response to electroacupuncture but the mechanisms are largely unknown. Objective: To identify the molecular mechanisms underlying electroacupuncture-induced glucose uptake in skeletal muscle in insulin-resistant overweight/obese women with and without polycystic ovary syndrome (PCOS). Design/Participants: In a case-control study, skeletal muscle biopsies were collected from 15 women with PCOS and 14 controls before and after electroacupuncture. Gene expression and methylation was analyzed using Illumina BeadChips arrays. Results: A single bout of electroacupuncture restores metabolic and transcriptional alterations and induces epigenetic changes in skeletal muscle. Transcriptomic analysis revealed 180 unique genes (q < 0.05) whose expression was changed by electroacupuncture, with 95% of the changes towards a healthier phenotype. We identified DNA methylation changes at 304 unique sites (q < 0.20), and these changes correlated with altered expression of 101 genes (p < 0.05). Among the 50 most upregulated genes in response to electroacupuncture, 38% were also upregulated in response to exercise. We identified a subset of genes that were selectively altered by electroacupuncture in women with PCOS. For example, MSX1 and SRNX1 were decreased in muscle tissue of women with PCOS and were increased by electroacupuncture and exercise. siRNA-mediated silencing of these two genes in cultured myotubes decreased glycogen synthesis, supporting a role for these genes in glucose homeostasis. Conclusion: Our findings provide evidence that electroacupuncture normalizes gene expression in skeletal muscle in a manner similar to acute exercise. Electroacupuncture might therefore be a useful way of assisting those who have difficulties performing exercise.

opencc-zeroDec 2017View details →

Data from: Gene expression shifts in yellow-bellied marmots prior to natal dispersal

The causes and consequences of vertebrate natal dispersal have been studied extensively, yet little is known about the molecular mechanisms involved. We used RNA-seq to quantify transcriptomic gene expression in blood of wild yellow-bellied marmots (Marmota flaviventer) prior to dispersing from or remaining philopatric to their natal colony. We tested three predictions. First, we hypothesized dispersers and residents will differentially express genes and gene networks since dispersal is physiologically demanding. Second, we expected differentially expressed genes to be involved in metabolism, circadian processes, and immune function. Finally, in dispersing individuals, we predicted differentially expressed genes would change as a function of sampling date relative to dispersal date. We detected 150 differentially expressed genes, including genes that have critical roles in lipid metabolism and antigen defense. Gene network analysis revealed a module of 126 co-expressed genes associated with dispersal that was enriched for extra-cellular immune function. Of the dispersal-associated genes, 22 altered expression as a function of days until dispersal, suggesting that dispersal-associated genes do not initiate transcription on the same time scale. Our results provide novel insights into the fundamental molecular changes required for dispersal and suggest evolutionary conservation of functional pathways during this behavioral process.

opencc-zeroDec 2017View details →

Data from: Seasonally sympatric but allochronic: differential expression of hypothalamic genes in a songbird during gonadal development

Allochrony, the mismatch of reproductive schedules, is one mechanism that can mediate sympatric speciation and diversification. In songbirds, the transition into breeding condition and gonadal growth is regulated by the hypothalamic-pituitary-gonadal (HPG) axis at multiple levels. We investigated whether the difference in reproductive timing between two, seasonally sympatric subspecies of dark-eyed juncos (Junco hyemalis) was related to gene expression along the HPG axis. During the sympatric pre-breeding stage, we measured hypothalamic and testicular mRNA expression of candidate genes via qPCR in captive male juncos. For hypothalamic mRNA, we found our earlier breeding subspecies had increased expression of gonadotropin-releasing hormone (GnRH) and decreased expression of androgen receptor, estrogen receptor alpha, and mineralocorticoid receptor (MR). Subspecies did not differ in expression of hypothalamic gonadotropin-inhibitory hormone (GnIH) and glucocorticoid receptor (GR). While our earlier breeding subspecies had higher mRNA expression of testicular GR, subspecies did not differ in testicular luteinizing hormone receptor, follicle-stimulating hormone receptor, or MR mRNA expression levels. Our findings indicate increased GnRH production and decreased hypothalamic sensitivity to sex steroid negative feedback as factors promoting differences in the timing of gonadal recrudescence between recently diverged populations. Differential gene expression along the HPG axis may facilitate species diversification under seasonal sympatry.

opencc-zeroDec 2017View details →

Data from: Transcriptome profiles of sunflower reveal the potential role of microsatellites in gene expression divergence

The mechanisms by which natural populations generate adaptive genetic variation are not well understood. Some studies propose that microsatellites can function as drivers of adaptive variation. Here we tested a potentially adaptive role for transcribed microsatellites with natural populations of the common sunflower (Helianthus annuus L.) by assessing the enrichment of microsatellites in genes that show expression divergence across latitudes. Seeds collected from six populations at two distinct latitudes in Kansas and Oklahoma were planted and grown in a common garden. Morphological measurements from the common garden demonstrated that phenotypic variation among populations is largely explained by underlying genetic variation. An RNA–Seq experiment was conducted with 96 of the individuals grown in the common garden and differentially expressed (DE) transcripts between the two latitudes were identified. A total number of 825 DE transcripts were identified. DE transcripts and non-differentially expressed (NDE) transcripts were then scanned for microsatellites. The abundance of different motif lengths and types in both groups were estimated. Our results indicate that DE transcripts are significantly enriched with mononucleotide repeats and significantly depauperate in trinucleotide repeats. Further, the standardized mononucleotide repeat motif A and dinucleotide repeat motif AG were significantly enriched within DE transcripts while motif types, C, AT, ACC, and AAC in DE transcripts are significantly differentiated in microsatellite tract length between the two latitudes. The tract length differentiation at specific microsatellite motif types across latitudes and their enrichment within DE transcripts indicate a potential functional role for transcribed microsatellites in gene expression divergence in sunflower.

opencc-zeroSep 2019View details →

Data from: Sperm competitive advantage of a rare mitochondrial haplogroup linked to differential expression of mitochondrial oxidative phosphorylation genes

Maternal inheritance of mitochondria creates a sex-specific selective sieve through which mitochondrial mutations harmful to males but not females accumulate and contribute to sexual differences in longevity and disease susceptibility. Because eggs and sperm are under disruptive selection, sperm are predicted to be particularly vulnerable to the genetic load generated by maternal inheritance, yet evidence for mitochondrial involvement in male fertility is limited and controversial. Here, we exploit the coexistence of two divergent mitochondrial haplogroups (A and B2) in a Neotropical arachnid to investigate the role of mitochondria in sperm competition. DNA profiling demonstrated that B2-carrying males sired more than three times as many offspring in sperm competition experiments than A males, and this B2 competitive advantage cannot be explained by female mitochondrial haplogroup or male nuclear genetic background. RNA-Seq of testicular tissues implicates differential expression of mitochondrial oxidative phosphorylation (OXPHOS) genes in the B2 competitive advantage, including a 22-fold upregulation of atp8 in B2 males. Previous comparative genomic analyses have revealed functionally significant amino acid substitutions in differentially expressed genes, indicating that the mitochondrial haplogroups differ not only in expression but also in DNA sequence and protein functioning. However, mitochondrial haplogroup had no effect on sperm number or sperm viability, and, when females were mated to a single male, neither male haplogroup, female haplogroup nor the interaction between male/female haplogroup significantly affected female reproductive success. Our findings therefore suggest that mitochondrial effects on male reproduction may often go undetected in noncompetitive contexts and may prove more important in nature than is currently appreciated.

opencc-by-4.0Jun 2021View details →

The Influence of Lactobacillus Acidophilus on MUC1, GAL-3, IL-1β and IL-17 Gene Expression in BALB/c Mice Stomach

Gene expression of MUC-1, GAL-3, IL-1 and IL-17 after treatment with low, moderate and high doses of Lactobacillus acidophilus ATCC 4356   in mice

Distal and proximal hypoxia response elements cooperate to regulate organ-specific erythropoietin gene expression

While it is well-established that distal hypoxia response elements (HREs) regulate hypoxia-inducible factor (HIF) target genes such as erythropoietin (Epo), an interplay between multiple distal and proximal (promoter) HREs has not been described so far. Hepatic Epo expression is regulated by a HRE located downstream of the EPO gene, but this 3' HRE is dispensable for renal EPO gene expression. We previously identified a 5' HRE and could show that both HREs direct exogenous reporter gene expression. Here, we show that whereas in hepatic cells the 3' but not the 5' HRE is required, in neuronal cells both the 5' and 3' HREs contribute to endogenous Epo induction. Moreover, two novel putative HREs were identified in the EPO promoter. In hepatoma cells HIF interacted mainly with the distal 3' HRE, but in neuronal cells HIF most strongly bound the promoter, to a lesser extent the 3' HRE, and not at all the 5' HRE. Interestingly, mutation of either of the two distal HREs abrogated HIF binding to the 3' and promoter HREs. These results suggest that a canonical functional HRE can recruit multiple, not necessarily HIF, transcription factors to mediate HIF binding to different distant HREs in an organ-specific manner.

Data from: Changes in gene expression during female reproductive development in a colour polymorphic insect

Pleiotropy (multiple phenotypic effects of single genes) and epistasis (gene interaction) have key roles in the development of complex phenotypes, especially in polymorphic taxa. The development of discrete and heritable phenotypic polymorphisms often emerges from major-effect genes that interact with other loci and have pleiotropic effects on multiple traits. We quantified gene expression changes during ontogenetic colour development in a polymorphic insect (damselfly: Ischnura elegans), with three heritable female morphs, one being a male mimic. This female colour polymorphism is maintained by male mating harassment and sexual conflict. Using transcriptome sequencing and de novo assembly, we demonstrate that all three morphs downregulate gene expression during early colour development. The morphs become increasingly differentiated during sexual maturation and when developing adult colouration. These different ontogenetic trajectories arise because the male-mimic shows accelerated (heterochronic) development, compared to the other female morphs. Many loci with regulatory functions in reproductive development are differentially regulated in the male-mimic, including upstream and downstream regulators of ecdysone signalling and transcription factors potentially influencing sexual differentiation. Our results suggest that long-term sexual conflict does not only maintain this polymorphism, but has also modulated the evolution of gene expression profiles during colour development of these sympatric female morphs.