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Results for “gene expression”

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bioRxiv2023

ChIP-DIP: A multiplexed method for mapping hundreds of proteins to DNA uncovers diverse regulatory elements controlling gene expression

Gene expression is controlled by the dynamic localization of thousands of distinct regulatory proteins to precise regions of DNA. Understanding this cell-type specific process has been a goal of molecular biology for decades yet remains challenging because most current DNA-protein mapping methods study one protein at a time. To overcome this, we developed ChIP-DIP (ChIP Done In Parallel), a split-pool based method that enables simultaneous, genome-wide mapping of hundreds of diverse regulatory proteins in a single experiment. We demonstrate that ChIP-DIP generates highly accurate maps for all classes of DNA-associated proteins, including histone modifications, chromatin regulators, transcription factors, and RNA Polymerases. Using these data, we explore quantitative combinations of protein localization on genomic DNA to define distinct classes of regulatory elements and their functional activity. Our data demonstrate that ChIP-DIP enables the generation of consortium level, context-specific protein localization maps within any molecular biology lab.

genomics↗

bioRxiv2021

Genomic signatures of sexual selection on pollen-expressed genes in Arabis alpina

Fertilization in angiosperms involves the germination of pollen on the stigma, followed by the extrusion of a pollen tube that elongates through the style and delivers two sperm cells to the embryo sac. Sexual selection could occur throughout this process when male gametophytes compete for fertilization. The strength of sexual selection during pollen competition should be affected by the number of genotypes deposited on the stigma. As increased self-fertilization reduces the number of mating partners, and the genetic diversity and heterozygosity of populations, it should thereby reduce the intensity of sexual selection during pollen competition. Despite the prevalence of mating system shifts, few studies have directly compared the molecular signatures of sexual selection during pollen competition in populations with different mating systems. Here we analyzed whole-genome sequences from natural populations of Arabis alpina, a species showing mating system variation across its distribution, to test whether shifts from cross- to self-fertilization result in molecular signatures consistent with sexual selection on genes involved in pollen competition. We found evidence for efficient purifying selection on genes expressed in vegetative pollen, and overall weaker selection on sperm-expressed genes. This pattern was robust when controlling for gene expression level and specificity. In agreement with the expectation that sexual selection intensifies under cross-fertilization, we found that the efficacy of purifying selection on male gametophyte-expressed genes was significantly stronger in genetically more diverse and outbred populations. Our results show that intra-sexual competition shapes the evolution of pollen-expressed genes, and that its strength fades with increasing self-fertilization rates.

evolutionary biology↗

bioRxiv2022

Inducible degradation of the Drosophila Mediator subunit Med19 reveals its role in regulating developmental but not constitutively-expressed genes

The multi-subunit Mediator complex plays a critical role in gene expression by bridging enhancer-bound transcription factors and the RNA polymerase II machinery. Although experimental case studies suggest differential roles of Mediator subunits, a comprehensive view of the specific set of genes regulated by individual subunits in a developing tissue is still missing. Here we address this fundamental question by focusing on the Med19 subunit and using the Drosophila wing imaginal disc as a developmental model. By coupling auxin- inducible degradation of endogenous Med19 in vivo with RNA-seq, we got access to the early consequences of Med19 elimination on gene expression. Differential gene expression analysis reveals that Med19 is not globally required for mRNA transcription but specifically regulates positively or negatively less than a quarter of the expressed genes. By crossing our transcriptomic data with those of Drosophila gene expression profile database, we found that Med19-dependent genes are highly enriched with spatially-regulated genes while the expression of most constitutively expressed genes is not affected upon Med19 loss. Whereas globally downregulation does not exceed upregulation, we identified a functional class of genes encoding spatially-regulated transcription factors, and more generally developmental regulators, responding unidirectionally to Med19 loss with an expression collapse. Moreover, we show in vivo that the Notch-responsive wingless and the E(spl)-C genes require Med19 for their expression. Combined with experimental evidences suggesting that Med19 could function as a direct transcriptional effector of Notch signaling, our data support a model in which Med19 plays a critical role in the transcriptional activation of developmental genes in response to cell signaling pathways. Author summaryThe Mediator is a large evolutionarily conserved multisubunit complex that plays essential functions in gene expression by relaying cues emanating from enhancer-bound transcription factors to the RNA polymerase II machinery. The transcriptional landscapes regulated by each Mediator subunit, especially in vivo in the context of developmental processes, remains poorly characterized. We therefore sought to provide a comprehensive view of the genes directly regulated by Med19, an archetypal Mediator subunit, in the context of the development of the Drosophila wing. Our work has important methodological implications as to carry out our analysis in the best experimental conditions, we generated mutant flies in which we could trigger fast degradation of the Med19 subunit on demand in the tissues of the living animal. We found that only a small part of the genes expressed in the developing wing are controlled by Med19 showing that this Mediator component exercises specific functions. Another major finding is the strong involvement of Med19 in the regulation of the expression of the genes involved in developmental processes supporting the idea that Med19 is a Mediator component dedicated to highly regulated mode of gene expression. The most unanticipated discovery of our study is the fact that Med19 does not appear to play a role in the expression of the genes that are constitutively transcribed, among which the housekeeping genes. This raises the notion that in the context of simple --non-regulated-- mode of expression, part of the Mediator functionalities, among which Med19, otherwise dedicated to highly regulated type of transcription, may become dispensable.

developmental biology↗

bioRxiv2018

Epigenetic signatures associated with imprinted paternally-expressed genes in the Arabidopsis endosperm

BackgroundImprinted genes are epigenetically modified during gametogenesis and maintain the established epigenetic signatures after fertilization, causing parental-specific gene expression.\n\nResultsIn this study, we show that imprinted paternally-expressed genes (PEGs) in the Arabidopsis endosperm are marked by an epigenetic signature of Polycomb Repressive Complex2 (PRC2)-mediated H3K27me3 together with heterochromatic H3K9me2 and CHG methylation, which specifically mark the silenced maternal alleles of PEGs. The co-occurrence of H3K27me3 and H3K9me2 on defined loci in the endosperm drastically differs from the strict separation of both pathways in vegetative tissues, revealing tissue-specific employment of repressive epigenetic pathways in plants. Based on the presence of this epigenetic signature on maternal alleles we were able to predict known PEGs at high accuracy and identified several new PEGs that we confirmed using INTACT-based transcriptomes generated in this study.\n\nConclusionsThe presence of the three repressive epigenetic marks, H3K27me3, H3K9me2, and CHG methylation on the maternal alleles in the endosperm serves as a specific epigenetic signature that allows to predict genes with parental-specific gene expression. Our study reveals that there are substantially more PEGs than previously identified, indicating that paternal-specific gene expression is of higher functional relevance than currently estimated. The combined activity of PRC2-mediated H3K27me3 together with the heterochromatic H3K9me3 has also been reported to silence the maternal Xist locus in mammalian preimplantation embryos, suggesting convergent employment of both pathways during the evolution of genomic imprinting.

genetics↗

bioRxiv2021

Comprehensive Analysis of Ubiquitously Expressed Genes in Human, From a Data-Driven Perspective

Comprehensive characterization of spatial and temporal gene expression patterns in humans is critical for uncovering regulatory codes of the human genome and understanding molecular mechanisms of human diseases. The ubiquitously expressed genes (UEGs) refer to those genes expressed across a majority, if not all, phenotypic and physiological conditions of an organism. It is known that many human genes are broadly expressed across tissues. However, most previous UEG studies have only focused on providing a list of UEGs without capturing their global expression patterns, thus limiting the potential use of UEG information. In this article, we propose a novel data-driven framework to leverage the extensive collection of [~]40,000 human transcriptomes to derive a list of UEGs and their corresponding global expression patterns, which offers a valuable resource to further validate and characterize human UEGs. Our results suggest that about half (12,234; 49.01%) of the human genes are expressed in at least 80% of human transcriptomes and the median size of the human transcriptome is 16,342 (65.44%). This suggests that the average difference in gene content between human transcriptomes is only 16.43%. Through gene clustering, we identified a set of UEGs, named LoVarUEGs, that have stable expression across human transcriptomes and can be used as internal reference genes for expression measurement. To further demonstrate the usefulness of this resource, we evaluated the uniqueness of repression for 16 previously predicted disallowed genes in islets beta cells and found that seven of these genes showed relatively more varied expression patterns, suggesting that the repression of these genes may not be unique to islets beta cells. We have made our resource publicly available at https://github.com/macroant/HumanUEGs.

genomics↗

bioRxiv2023

Gene expression is the main driver of purifying selection in large penguin populations

Purifying selection is the most pervasive type of selection, as it constantly removes deleterious mutations arising in populations, directly scaling with population size. Highly expressed genes appear to accumulate fewer deleterious mutations between divergent species lineages (known as E-R anticorrelation), pointing towards gene expression as an additional driver of purifying selection. However, estimates of the effect of gene expression on segregating deleterious variants in natural populations are scarce, as is an understanding of the relative contribution of population size and gene expression to purifying selection. Here, we analyse genomic and transcriptomic data from two natural populations of closely related sister species with different demographic histories, the Emperor penguin (Aptenodytes forsteri) and the King penguin (A. patagonicus), and show that purifying selection at the population-level depends on gene expression rate, resulting in very high selection coefficients at highly expressed genes. Leveraging realistic forward simulations, we estimate that the top 10% of the most highly expressed genes in a genome experience a selection pressure corresponding to an average selection coefficient of -0.1, which decreases to a selection coefficient of -0.01 for the top 50%. Gene expression rate can be regarded as a fundamental parameter of protein evolution in natural populations, maintaining selection effective even at small population size. We suggest it could be used as a proxy for gene selection coefficients, which are notoriously difficult to derive in non-model species under real-world conditions.

evolutionary biology↗

bioRxiv2026

A functional annotation based integration of different similarity measures for gene expressions

Genes with similar expression profiles often exhibit similar functional properties. An "integrated similarity score" (ISS) is developed by combining different expression similarity measures through weights, obtained using biological information, for improving gene similarity. The expression similarity measures are converted to the common framework of positive predictive value using functional annotation. A fitness function, called "fitness function using functional annotation of genes" (FFFAG), is also developed by minimizing the difference between functional similarity value and the ISS. The FFFAG is used to determine the weight combination of different similarity measures in ISS. In addition, an existing similarity measure, called TMJ (integrated similarity measure by multiplying Triangle and Jaccard similarity), is also modified to incorporate biological knowledge involving functional annotation. The results demonstrate that ISS is superior to individual similarity measure to find similar gene pairs. Further, the ISS predicts the functional categories of 40 unclassified yeast genes at p-value cutoff of 10-10 from 12 clusters. The associated code is accessible at http://www.isical.ac.in/[~]shubhra/ISS.html.

bioinformatics↗

bioRxiv2026

Spatial transcriptomic analysis of progressing oral epithelial dysplasia reveals unique differentially expressed genes and microenvironmental changes.

Oral squamous cell carcinoma (OSCC) often arises from oral epithelial dysplasia (OED); however, the gene expression changes during OED progression and its microenvironment are not fully understood. This study used spatial transcriptomics to identify differentially expressed genes and microenvironmental alterations associated with OEDs malignant transformation of OED. A ten-year retrospective analysis of paired OSCC and prior OED samples was conducted at the University of Toronto Oral Pathology Laboratory. A total of 24 paired progressing OED cases and 23 matched non-progressing OED cases were examined using spatial transcriptomics in PanCK+ (dysplastic epithelium or OSCC) and PanCK- (stroma) regions. The analysis included differential gene expression, pathway analysis and spatial deconvolution. Three genes (STOM, KIF26A, and CDKN2A) showed increased expression in the epithelial component of progressing OED compared with non-progressing OED, whereas 41 genes were differentially expressed in OSCC versus the precursor samples. Ubiquitination-related pathways were enriched during OED progression. Functional validation identified TNFRSF12A (Fn14) as a potential regulator of OED progression to OSCC. The OSCC microenvironment displayed increased numbers of fibroblasts, neutrophils, monocytes, and mast cells compared with that of the precursor samples. Our findings suggest that spatial profiling of OED can help identify unique gene signatures and microenvironmental changes that occur before the malignant transformation.

cancer biology↗

bioRxiv2023

Growth-dependent gene expression variation influences the strength of codon usage biases

The most highly expressed genes in microbial genomes tend to use a limited set of synonymous codons, often referred to as "preferred codons." The existence of preferred codons is commonly attributed to selection pressures on various aspects of protein translation including accuracy and/or speed. However, gene expression is condition-dependent and even within single-celled organisms transcript and protein abundances can vary depending on a variety of environmental and other factors. Here, we show that growth rate-dependent expression variation is an important constraint that significantly influences the evolution of gene sequences. Using large-scale transcriptomic and proteomic data sets in Escherichia coli and Saccharomyces cerevisiae, we confirm that codon usage biases are strongly associated with gene expression but highlight that this relationship is most pronounced when gene expression measurements are taken during rapid growth conditions. Specifically, genes whose relative expression increases during periods of rapid growth have stronger codon usage biases than comparably expressed genes whose expression decreases during rapid growth conditions. These findings highlight that gene expression measured in any particular condition tells only part of the story regarding the forces shaping the evolution of microbial gene sequences. More generally, our results imply that microbial physiology during rapid growth is critical for explaining long-term translational constraints.

evolutionary biology↗

bioRxiv2025

Tissue-specificity of gene expression in the Ciona embryo is subtly bimodal

Expressed genes potentially fall into two distinct categories: tissue-specific genes expressed in a subset of cell types that carry out the distinctive functions of those cells; and housekeeping genes that are broadly expressed across all cell types and carry out the basic functions of life. It is unclear, however, whether these are actually two distinct classes or whether they represent an intuitive but false dichotomy imposed upon gene expression patterns that vary widely and continuously in how specific they are to particular tissues. We address this question using a high-coverage, whole-embryo single cell RNAseq atlas of the model invertebrate chordate Ciona robusta. There is a major complication in that quantitative measures of tissue-specificity such as the Tau and Gini metrics show a strong negative correlation with expression level. We show here that this correlation is the result of sampling error and not a fundamental biological relationship. Raw Tau scores are bimodal, but this is largely an artifact of Taus sigmoidal relationship with expression level for uniformly expressed genes. Simulations and statistical analyses indicate that the Tau metric is badly confounded by expression level for ubiquitously and/or weakly expressed genes but is relatively accurate for genes that have statistical evidence of differential expression. The distribution of tissue-specificity scores for these differentially expressed genes is broad and flat, spanning from near-binary to near-uniform. While only subtly bimodal, ubiquitously expressed and tissue-specific genes are clearly distinguishable, especially at higher expression levels. We explore the use of pseudocounts to shrink the high tissue-specificity scores of weakly expressed genes and find that they are effective at separating tissue-specific from ubiquitously expressed genes but distort rankings of tissue-specificity. Gene ontology code analysis indicates that the most tissue-specific genes are strongly enriched for predicted roles as transcriptional regulators and tissue-specific effector molecules, whereas the most ubiquitously expressed genes are enriched for predicted housekeeping functions. We conclude that the tissue-specific vs housekeeping dichotomy is meaningful in the Ciona embryo despite the broad range of Tau scores for tissue-specific genes. These findings provide a framework for formally assessing the tissue-specificity of gene expression across a broad range of taxa and developmental stages.

genomics↗

bioRxiv2019

Differential gene expression and gene variants drive color and pattern development in divergent color morphs of a mimetic poison frog

A common goal in evolutionary biology is to discern the mechanisms that produce the astounding diversity of morphologies seen across the tree of life. Aposematic species, those with a conspicuous phenotype coupled with some form of defense, are excellent models to understand the link between vivid color pattern variations, the natural selection shaping it, and the underlying genetic mechanisms underpinning this variation. Mimicry systems in which multiple species share the same conspicuous phenotype can provide an even better model for understanding the mechanisms of color production in aposematic species, especially if comimics have divergent evolutionary histories. Here we investigate the genetic mechanisms by which vivid color and pattern are produced in a Mullerian mimicry complex of poison frogs. We did this by first assembling a high-quality de novo genome assembly for the mimic poison frog Ranitomeya imitator. This assembled genome is 6.8 Gbp in size, with a contig N50 of 300 Kbp and 93% of expected tetrapod genes. We then leveraged this genome to conduct gene expression analyses throughout development of four color morphs of R. imitator and two color morphs from both R. fantastica and R. variabilis which R. imitator mimics. We identified a large number of pigmentation and patterning genes that are differentially expressed throughout development, many of them related to melanocyte development, melanin synthesis, iridophore development, and guanine synthesis. In addition, we identify the pteridine synthesis pathway (including genes such as qdpr and xdh) as a key driver of the variation in color between morphs of these species. Finally, we hypothesize that genes in the keratin family are important for producing different structural colors within these frogs.

evolutionary biology↗

bioRxiv2020

A modular chromosomally integrated toolkit for ectopic gene expression in Vibrio cholerae

The ability to express genes ectopically in bacteria is essential for diverse academic and industrial applications. Two major considerations when utilizing regulated promoter systems for ectopic gene expression are (1) the ability to titrate gene expression by addition of an exogenous inducer and (2) the leakiness of the promoter element in the absence of the inducer. Here, we describe a modular chromosomally integrated platform for ectopic gene expression in Vibrio cholerae. We compare the broadly used promoter elements Ptac and PBAD to versions that have an additional theophylline-responsive riboswitch (Ptac-riboswitch and PBAD-riboswitch). These constructs all exhibited unimodal titratable induction of gene expression, however, max induction varied with Ptac > PBAD > PBAD-riboswitch > Ptac-riboswitch. We also developed a sensitive reporter system to quantify promoter leakiness and show that leakiness for Ptac > Ptac-riboswitch > PBAD; while the newly developed PBAD-riboswitch exhibited no detectable leakiness. We demonstrate the utility of the tightly inducible PBAD-riboswitch construct using the dynamic activity of type IV competence pili in V. cholerae as a model system. The modular chromosomally integrated toolkit for ectopic gene expression described here should be valuable for the genetic study of Vibrio cholerae and could be adapted for use in other species.

microbiology↗

bioRxiv2019

All of gene expression (AOE): integrated index for public gene expression databases

Gene expression data have been archived as microarray and RNA-seq datasets in two public databases, Gene Expression Omnibus (GEO) and ArrayExpress (AE). In 2018, the DNA DataBank of Japan started a similar repository called the Genomic Expression Archive (GEA). These databases are useful resources for the functional interpretation of genes, but have been separately maintained and may lack RNA-seq data, while the original sequence data are available in the Sequence Read Archive (SRA). We constructed an index for those gene expression data repositories, called All Of gene Expression (AOE), to integrate publicly available gene expression data. The web interface of AOE can graphically query data in addition to the application programming interface. By collecting gene expression data from RNA-seq in the SRA, AOE also includes data not included in GEO and AE. AOE is accessible as a search tool from the GEA website and is freely available at https://aoe.dbcls.jp/.

bioinformatics↗

bioRxiv2024

Identification and functional categorization of the most stably and most variably expressed genes and retained introns in Arabidopsis thaliana seedlings

We used a large, uniform, RNA-seq dataset to investigate the stability of gene expression and intron retention in Arabidopsis thaliana seedlings. Functional classification of the most stably and most variably expressed genes was determined by GO enrichment analyses. Many variably expressed genes encoded proteins involved in photosynthesis and chloroplast structure, likely reflecting their sensitivity to changeable light intensities, and in stress responses, which allow plants to cope with environmental challenges. As revealed by GO enrichment analysis, the most stably expressed genes were involved in protein, lipid and vesicle trafficking, suggesting that fluctuations in expression of these genes are suboptimal for normal seedling development. GO analyses of genes containing either usually retained or usually spliced introns revealed no consistent enrichments for any specific functional categories. However, highly retained introns were often located in the first or last position, which may contain 5 and 3 UTRs necessary for transcriptional regulation and mRNA transport and stability. Conversely, usually spliced introns were more frequently located in internal portions of pre-mRNAs, indicating that reliable splicing in coding regions is needed to prevent the formation of premature stop codons. The large RNA-seq dataset we generated can be useful for investigating additional aspects of gene expression and pre-mRNA splicing in Arabidopsis seedlings and sets a precedent for future large scale transcriptome analyses.

plant biology↗

bioRxiv2021

In Silico Analysis and Characterization of Differentially Expressed Genes to Distinguish Glioma Stem Cells from Normal Neural Stem Cells

Glioblastoma multiforme (GBM) is a heterogeneous, invasive primary brain tumor that develops chemoresistance post therapy. Theories regarding the aetiology of GBM focus on transformation of normal neural stem cells (NSCs) to a cancerous phenotype or tumorigenesis driven via glioma stem cells (GSCs). Comparative RNA-Seq analysis of GSCs and NSCs can provide a better understanding of the origin of GBM. Thus, in the current study, we performed various bioinformatics analyses on transcriptional profiles of a total 40 RNA-seq samples including 20 NSC and 20 GSC, that were obtained from the NCBI-SRA (SRP200400). First, differential gene expression (DGE) analysis using DESeq2 revealed 348 significantly differentially expressed genes between GSCs and NSCs (padj. value <0.05, log2fold change [≥] 3.0 (for GSCs) and [≤] -3.0 (for NSCs)) with 192 upregulated and 156 downregulated genes in GSCs in comparison to NSCs. Subsequently, exploratory data analysis using principal component analysis (PCA) based on key significant genes depicted the clear separation between both the groups. Further, Hierarchical clustering confirmed the distinct clusters of GSC and NSC samples. Eventually, the biological enrichment analysis of the significant genes showed their enrichment in tumorigenesis pathways such as Wnt-signalling, VEGF-signalling and TGF-{beta}-signalling pathways. Conclusively, our study depicted significant differences in the gene expression patterns between NSCs and GSCs. Besides, we also identified novel genes and genes previously unassociated with gliomagenesis that may prove to be valuable in establishing diagnostic, prognostic biomarkers and therapeutic targets for GBM.

cancer biology↗

bioRxiv2023

Sex-specific differences in DNA methylation and gene expression in late-gestation mouse placentas

BackgroundThe placenta is vital for fetal development and its contributions to various developmental issues, such as pregnancy complications, fetal growth restriction, and maternal exposure, have been extensively studied in mice. The placenta forms mainly from fetal tissue and therefore has the same biological sex as the fetus it supports. Extensive research has delved into the placentas involvement in pregnancy complications and future offspring development, with a notable emphasis on exploring sex-specific disparities. However, despite these investigations, sex-based disparities in epigenetic (e.g., DNA methylation) and transcriptomic features of the late-gestation mouse placenta remain largely unknown. MethodsWe collected male and female mouse placentas at late gestation (E18.5, n = 3/sex) and performed next-generation sequencing to identify genome-wide sex differences in transcription and DNA methylation. ResultsOur comparison between male and female revealed 358 differentially expressed genes (DEGs) on autosomes, which were associated with signaling pathways involved in transmembrane transport and the responses to viruses and external stimuli. X chromosome DEGs (n = 39) were associated with different pathways, including those regulating chromatin modification and small GTPase-mediated signal transduction. Differentially methylated regions (DMRs) were more common on the X chromosomes (n = 3756) than on autosomes (n = 1705). Interestingly, while most X chromosome DMRs had higher DNA methylation levels in female placentas and tended to be included in CpG dinucleotide-rich regions, 73% of autosomal DMRs had higher methylation levels in male placentas and were distant from CpG-rich regions. Several DEGs were correlated with DMRs. A subset of the DMRs present in late-stage placentas were already established in mid-gestation (E10.5) placentas (n = 348 DMRs on X chromosome and 19 DMRs on autosomes), while others were acquired later in placental development. ConclusionOur study provides comprehensive lists of DEGs and DMRs between male and female that collectively cause profound differences in the DNA methylation and gene expression profiles of late-gestation mouse placentas. Our results demonstrate the importance of incorporating sex-specific analyses into epigenetic and transcription studies to enhance the accuracy and comprehensiveness of their conclusions and help address the significant knowledge gap regarding how sex differences influence placental function. HighlightsO_LIIn the mouse placenta, sex-specific gene expression and DNA methylation profiles, enriched in various metabolic and developmental pathways, are observed for both X-linked and autosomal genes from mid-gestation onward. C_LIO_LIRegions with different DNA methylation are commonly found in CpG-rich areas on the X chromosomes and in CpG-poor regions on autosomes. C_LIO_LIA subset of the DMRs observed in late-stage placentas were already established in mid-gestation placentas, whereas others were acquired during the later stages of placental development. C_LIO_LISeveral DNA methylation sex differences could be correlated with sex differences in gene expression. C_LIO_LIThe results highlight the importance of including sex-based analyses in epigenetic and transcriptional studies of the mouse placenta. C_LI Plain English summaryThe placenta is a crucial organ for a healthy pregnancy and proper fetal development, and its functions are often studied in mice. The placenta stems from the developing embryo, and therefore shares its sex. Male fetuses have higher risks of pregnancy complications and neurodevelopmental disorders, and these risks are linked to placenta functions. However, how the placentas sex influences the proteins it contains--and therefore, how it helps the fetus develop--remains largely unknown. We used cutting-edge techniques to systematically examine late-pregnancy mouse placentas, cataloging the genes being expressed (i.e., sections of DNA used to make proteins) and the patterns of a specific DNA mark (called methylation) that controls gene expression. We identified several genes with important placental functions, such as protecting the fetus from viruses and responding to environmental changes, whose expression levels were sex-specific. We also observed differences in DNA methylation between male and female placentas. Most DNA methylation differences were on the X-chromosomes associated with sex, and the majority had higher methylation levels in female placentas. Conversely, on other chromosomes, most differences present an increased level of DNA methylation in male placentas. As methylation affects gene expression, we found links between the changes. Additionally, we found that some sex differences in the placenta were already present earlier in pregnancy. Our findings provide important insights into the molecular differences between male and female mouse placentas during late pregnancy. Including sex-specific analyses in placenta studies will improve our understanding of how the placenta ensures the healthy development of male and female fetuses.

developmental biology↗

bioRxiv2021

Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow (Salix spp.)

Many studies have highlighted the complex and diverse basis for heterosis in inbred crops. Despite the lack of a consensus model, it is vital that we turn our attention to understanding heterosis in undomesticated, heterozygous, and polyploid species, such as willow (Salix spp.). Shrub willow is a dedicated energy crop bred to be fast-growing and high yielding on marginal land without competing with food crops. A trend in willow breeding is the consistent pattern of heterosis in triploids produced from crosses between diploid and tetraploid species. Here, we test whether differentially expressed genes are associated with heterosis in triploid families derived from diploid S. purpurea, diploid S. viminalis, and tetraploid S. miyabeana parents. Three biological replicates of shoot tips from all family progeny and parents were collected after 12 weeks in the greenhouse and RNA extracted for RNA-Seq analysis. This study provides evidence that nonadditive patterns of gene expression are correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow. Expression-level dominance was most correlated with heterosis for biomass yield traits and was highly enriched for processes involved in starch and sucrose metabolism. In addition, there was a global dosage effect of parent alleles in triploid hybrids, with expression proportional to copy number variation. Importantly, differentially expressed genes between family parents were most predictive of heterosis for both field and greenhouse collected traits. Altogether, these data will be used to progress models of heterosis to complement the growing genomic resources available for the improvement of heterozygous perennial bioenergy crops.

plant biology↗

bioRxiv2023

A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture

Promoters regulate both the amplitude and pattern of gene expression--key factors needed for optimization of many synthetic biology applications. Previous work in Arabidopsis found that promoters that contain a TATA-box element tend to be expressed only under specific conditions or in particular tissues, while promoters which lack any known promoter elements, thus designated as Coreless, tend to be expressed more ubiquitously. To test whether this trend represents a conserved promoter design rule, we identified stably expressed genes across multiple angiosperm species using publicly available RNA-seq data. Comparisons between core promoter architectures and gene expression stability revealed differences in core promoter usage in monocots and eudicots. Furthermore, when tracing the evolution of a given promoter across species, we found that core promoter type was not a strong predictor of expression stability. Our analysis suggests that core promoter types are correlative rather than causative in promoter expression patterns and highlights the challenges in finding or building constitutive promoters that will work across diverse plant species.

plant biology↗