scholarly journals Impact of the X chromosome and sex on regulatory variation

2015 ◽  
Author(s):  
Kimberly R Kukurba ◽  
Princy Parsana ◽  
Kevin S Smith ◽  
Zachary Zappala ◽  
David A Knowles ◽  
...  

The X chromosome, with its unique mode of inheritance, contributes to differences between the sexes at a molecular level, including sex-specific gene expression and sex-specific impact of genetic variation. We have conducted an analysis of the impact of both sex and the X chromosome on patterns of gene expression identified through transcriptome sequencing of whole blood from 922 individuals. We identified that genes on the X chromosome are more likely to have sex-specific expression compared to the autosomal genes. Furthermore, we identified a depletion of regulatory variants on the X chromosome, especially among genes under high selective constraint. In contrast, we discovered an enrichment of sex-specific regulatory variants on the X chromosome. To resolve the molecular mechanisms underlying such effects, we generated and connected sex-specific chromatin accessibility to sex-specific expression and regulatory variation. As sex-specific regulatory variants can inform sex differences in genetic disease prevalence, we have integrated our data with genome-wide association study data for multiple immune traits and to identify traits with significant sex biases. Together, our study provides genome-wide insight into how the X chromosome and sex shape human gene regulation and disease.

2018 ◽  
Author(s):  
Sarada Ketharnathan ◽  
Megan Leask ◽  
James Boocock ◽  
Amanda J. Phipps-Green ◽  
Jisha Antony ◽  
...  

ABSTRACTSeveral dozen genetic variants associate with serum urate levels, but the precise molecular mechanisms by which they affect serum urate are unknown. Here we tested for functional linkage of the maximally-associated genetic variant rs1967017 at the PDZK1 locus to elevated PDZK1 expression.We performed expression quantitative trait locus (eQTL) and likelihood analyses followed by gene expression assays. Zebrafish were used to determine the ability of rs1967017 to direct tissue-specific gene expression. Luciferase assays in HEK293 and HepG2 cells measured the effect of rs1967017 on transcription amplitude.PAINTOR analysis revealed rs1967017 as most likely to be causal and rs1967017 was an eQTL for PDZK1 in the intestine. The region harboring rs1967017 was capable of directly driving green fluorescent protein expression in the kidney, liver and intestine of zebrafish embryos, consistent with a conserved ability to confer tissue-specific expression. The urate-increasing T-allele of rs1967017 strengthens a binding site for the transcription factor HNF4A. siRNA depletion of HNF4A reduced endogenous PDZK1 expression in HepG2 cells. Luciferase assays showed that the T-allele of rs1967017 gains enhancer activity relative to the urate-decreasing C-allele, with T-allele enhancer activity abrogated by HNF4A depletion. HNF4A physically binds the rs1967017 region, suggesting direct transcriptional regulation of PDZK1 by HNF4A.With other reports our data predict that the urate-raising T-allele of rs1967017 enhances HNF4A binding to the PDZK1 promoter, thereby increasing PDZK1 expression. As PDZK1 is a scaffold protein for many ion channel transporters, increased expression can be predicted to increase activity of urate transporters and alter excretion of urate.


Microbiology ◽  
2005 ◽  
Vol 151 (2) ◽  
pp. 399-420 ◽  
Author(s):  
Leif Steil ◽  
Mónica Serrano ◽  
Adriano O. Henriques ◽  
Uwe Völker

Temporal and compartment-specific control of gene expression during sporulation in Bacillus subtilis is governed by a cascade of four RNA polymerase subunits. σ F in the prespore and σ E in the mother cell control early stages of development, and are replaced at later stages by σ G and σ K, respectively. Ultimately, a comprehensive description of the molecular mechanisms underlying spore morphogenesis requires the knowledge of all the intervening genes and their assignment to specific regulons. Here, in an extension of earlier work, DNA macroarrays have been used, and members of the four compartment-specific sporulation regulons have been identified. Genes were identified and grouped based on: i) their temporal expression profile and ii) the use of mutants for each of the four sigma factors and a bofA allele, which allows σ K activation in the absence of σ G. As a further test, artificial production of active alleles of the sigma factors in non-sporulating cells was employed. A total of 439 genes were found, including previously characterized genes whose transcription is induced during sporulation: 55 in the σ F regulon, 154 σ E-governed genes, 113 σ G-dependent genes, and 132 genes under σ K control. The results strengthen the view that the activities of σ F, σ E, σ G and σ K are largely compartmentalized, both temporally as well as spatially, and that the major vegetative sigma factor (σ A) is active throughout sporulation. The results provide a dynamic picture of the changes in the overall pattern of gene expression in the two compartments of the sporulating cell, and offer insight into the roles of the prespore and the mother cell at different times of spore morphogenesis.


2020 ◽  
Author(s):  
Stevie A. Bain ◽  
Hollie Marshall ◽  
Laura Ross

AbstractSexual dimorphism is exhibited in many species across the tree of life with many phenotypic differences mediated by differential expression and alternative splicing of genes present in both sexes. However, the mechanisms that regulate these sex-specific expression and splicing patterns remain poorly understood. The mealybug, Planococcus citri, displays extreme sexual dimorphism and exhibits an unusual instance of sex-specific genomic imprinting, Paternal Genome Elimination (PGE), in which the paternal chromosomes in males are highly condensed and eliminated from the sperm. P. citri also has no sex chromosomes and as such both sexual dimorphism and PGE are predicted to be under epigenetic control. We recently showed that P. citri females display a highly unusual DNA methylation profile for an insect species, with the presence of promoter methylation associated with lower levels of gene expression. In this study we therefore decided to explore genome-wide differences in DNA methylation between male and female P. citri using whole genome bisulfite sequencing. We have identified extreme differences in genome-wide levels and patterns between the sexes. Males display overall higher levels of DNA methylation which manifests as more uniform low-levels across the genome. Whereas females display more targeted high levels of methylation. We suggest these unique sex-specific differences are due to chromosomal differences caused by PGE and may be linked to possible ploidy compensation. Using RNA-Seq we identified extensive sex-specific gene expression and alternative splicing. We found cis-acting DNA methylation is not directly associated with differentially expressed or differentially spliced genes, indicating a broader role for chromosome-wide trans-acting DNA methylation in this species.


Science ◽  
2020 ◽  
Vol 369 (6509) ◽  
pp. eaba3066 ◽  
Author(s):  
Meritxell Oliva ◽  
Manuel Muñoz-Aguirre ◽  
Sarah Kim-Hellmuth ◽  
Valentin Wucher ◽  
Ariel D. H. Gewirtz ◽  
...  

Many complex human phenotypes exhibit sex-differentiated characteristics. However, the molecular mechanisms underlying these differences remain largely unknown. We generated a catalog of sex differences in gene expression and in the genetic regulation of gene expression across 44 human tissue sources surveyed by the Genotype-Tissue Expression project (GTEx, v8 release). We demonstrate that sex influences gene expression levels and cellular composition of tissue samples across the human body. A total of 37% of all genes exhibit sex-biased expression in at least one tissue. We identify cis expression quantitative trait loci (eQTLs) with sex-differentiated effects and characterize their cellular origin. By integrating sex-biased eQTLs with genome-wide association study data, we identify 58 gene-trait associations that are driven by genetic regulation of gene expression in a single sex. These findings provide an extensive characterization of sex differences in the human transcriptome and its genetic regulation.


2018 ◽  
Author(s):  
Tal Cohen ◽  
Chen Mordechai ◽  
Alal Eran ◽  
Dan Mishmar

Expression quantitative trait loci (eQTLs) are instrumental in genome-wide identification of regulatory elements, yet were overlooked in the mitochondrial DNA (mtDNA). By analyzing 5079 RNA-seq samples from 23 tissues we identified association of ancient mtDNA SNPs (haplogroups T2, L2, J2 and V) and recurrent SNPs (mtDNA positions 263, 750, 1438 and 10398) with tissue-dependent mtDNA gene-expression. Since the recurrent SNPs independently occurred in different mtDNA genetic backgrounds, they constitute the best candidates to be causal eQTLs. Secondly, the discovery of mtDNA eQTLs in both coding and non-coding mtDNA regions, propose the identification of novel mtDNA regulatory elements. Third, we identified association between low m1A 947 MT-RNR2 (16S) rRNA modification levels and altered mtDNA gene-expression in twelve tissues. Such association disappeared in skin which was exposed to sun, as compared to sun-unexposed skin from the same individuals, thus supporting the impact of UV on mtDNA gene expression. Taken together, our findings reveal that both mtDNA SNPs and mt-rRNA modification affect mtDNA gene expression in a tissue-dependent manner.


Circulation ◽  
2007 ◽  
Vol 116 (suppl_16) ◽  
Author(s):  
Kelvin Lee ◽  
Tuomo Polvikoski ◽  
Daniel Birchall ◽  
Mauro Santibanez-Koref ◽  
Alexander D Mendelow ◽  
...  

The molecular mechanisms leading to plaque rupture are poorly understood. Genome-wide gene expression studies may reveal novel causal molecular pathways. METHODS: Snap-frozen human atherosclerotic plaques removed at carotid endarterectomy were designated as stable or ruptured using stringent clinical, radiological and histopathological criteria. Accurate gene expression profiling of macrophages in 5 ruptured and 6 stable plaques was conducted by employing Laser Micro-Dissection to specifically isolate this cell type from the plaques. High quality RNA was amplified and hybridised to the genome-wide Affymetrix U133plus2 microarray. RESULTS: Exploratory clustering by Principal Components Analysis showed the data to cluster into 2 distinct groups- stable and ruptured. We identified 889 statistically significant differentially expressed genes between the two groups (Fig.1 ). Genes involved in lipid processing, signalling, apoptosis, immune response and extracellular matrix were found to play a role in plaque rupture. Pathway analysis identified the Adipocytokine Signalling Pathway to be the most significantly represented cell signalling pathway (p<0.0006). The microarray findings were technically validated by real-time qPCR (Pearson Correlation R=0.94) and biologically cross-validated on a larger number of samples successfully (n=25). Immunocytochemical staining confirmed the differential Leptin expression in macrophages of ruptured and stable plaques. CONCLUSION: The involvement of Leptin and the Adipocytokine Signalling Pathway in macrophages in plaque rupture has been implicated here for the first time and may be a potential therapeutic target. Figure 1. Heatmap of 889 statistically significant differentially expressed genes (red for high expression, green for low expression) with the top 20 most highly expressed genes in ruptured and stable groups listed.


2017 ◽  
Author(s):  
Yuchao Jiang ◽  
Nancy R Zhang ◽  
Mingyao Li

AbstractAllele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing (scRNA-seq) allows the comparison of expression distribution between the two alleles of a diploid organism and thus the characterization of allele-specific bursting. We propose SCALE to analyze genome-wide allele-specific bursting, with adjustment of technical variability. SCALE detects genes exhibiting allelic differences in bursting parameters, and genes whose alleles burst non-independently. We apply SCALE to mouse blastocyst and human fibroblast cells and find that, globally, cis control in gene expression overwhelmingly manifests as differences in burst frequency.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 245-245
Author(s):  
Jung-Mi Lee ◽  
Bryan Goddard ◽  
Ashwini S. Hinge ◽  
Bruce J. Aronow ◽  
Nathan Salomonis ◽  
...  

Abstract Obesity is a complex pathological state defined by the excessive accumulation of adipose tissue and an array of hormonal, immunological and metabolic dysregulations. As such, obesity is a systemic stress that directly affects numerous organs and tissues. Notably, obesity and its sequelae modulate the immune system and the hematopoietic activity in the bone marrow (BM). Not surprisingly, obesity is also a well-established risk factor for leukemia associated with increased incidence and poor prognosis. However, despite their clinical relevance, mechanisms by which obesity affects the hematopoietic system remain elusive. Particularly, the impact of obesity on the hematopoietic stem cell (HSC) compartment has not been described. Using genetic and dietary mouse models of obesity, we conducted a "HSC-centered study" to determine how obesity affects HSCs and how these cells develop specific compensatory mechanisms to respond to this environment. Although HSCs in an obese environment displayed limited phenotypic and functional perturbations at steady state, they showed an aberrant response to hematopoietic stresses. In serial competitive transplantation assays, obesity-primed HSCs (defined as Lin- Sca-1+ c-Kit+ CD48- CD150+) showed a higher level of engraftment than controls in primary recipient mice (control, 20.8% +/-6.2 vs obese, 45.5% +/-14.6, p=0.022) but a dramatically reduced level of engraftment in secondary recipient mice (control: 25.8% +/-14.0 vs obese: 5.4% +/-3.9, p=0.033). Interestingly, BM analysis of secondary recipients showed reduced chimerism in all hematopoietic compartments but not in the HSC compartment. Altogether these results uncovered a biphasic behavior of the obesity-primed HSCs, characterized by an excessive differentiation response followed by a functional decline in which HSCs self-renew but fail to produce downstream progenitors. To unveil the molecular mechanisms involved in this aberrant activity, we performed a genome-wide gene expression analysis on HSCs isolated from normal and obese mice. Although the phenotype observed upon serial transplantation partially mimics HSC aging, obesity-primed HSCs did not share the molecular signature of old HSCs. Furthermore, down-regulation of interferon response-related genes (e.g Irak4, Irf7, Ifi27) and stress response-related genes (e.g. Stip1, Cgrrf1) showed that, unlike what has been described for committed progenitors, HSCs do not elicit a dramatic response to the inflammatory environment associated with obesity. In contrast obesity leads to the activation of specific molecular programs in HSCs. Firstly, obesity-primed HSCs showed up-regulation of multiples genes involved in the phosphatidylinositol signaling pathway (e.g. Pi4ka, Pi4k2b, Pi3kap1, Pi3kip1). Phosphoflow cytometry analysis indicated that this gene expression pattern was associated with the constitutive activation of the protein kinase AKT. While AKT activation is linked to functional HSC exhaustion, obesity-primed HSCs appeared refractory to this signal, suggesting the existence of compensatory mechanisms that protect the integrity of the HSCs in an obese environment. In parallel, we found that the aberrant activity of the obesity-primed HSCs was correlated with an elevated expression of Gfi1, a transcription factor critical for HSC quiescence and differentiation. Interestingly, the 2-fold increase in Gfi1 expression (p<10-5) observed in obesity-primed HSCs was maintained after serial transplantations in normal recipient mice indicating that the obese environment was able to promote the selection of a stable molecular program in the HSC compartment. Consistent with this idea, single-cell genome-wide analyses suggested a significant clonal shift within the obesity-primed HSC compartment. Finally, consistent with epidemiological data, we found that disruption of HSC homeostasis by obesity promotes the development of spontaneous hematopoietic pathologies resembling to myeloproliferative diseases. Altogether, our results establish the long lasting impact of obesity on the HSC compartment and uncover potential molecular mechanisms linking obesity to hematological diseases. Notably our results support the intriguing possibility that obesity, by directly acting on the HSC compartment, contributes to the development of a clonal hematopoiesis and favors the emergence of aberrant HSC clones. Disclosures No relevant conflicts of interest to declare.


Genetics ◽  
2021 ◽  
Author(s):  
Thomas D Brekke ◽  
Emily C Moore ◽  
Shane C Campbell-Staton ◽  
Colin M Callahan ◽  
Zachary A Cheviron ◽  
...  

AbstractEmbryonic development in mammals is highly sensitive to changes in gene expression within the placenta. The placenta is also highly enriched for genes showing parent-of-origin or imprinted expression, which is predicted to evolve rapidly in response to parental conflict. However, little is known about the evolution of placental gene expression, or if divergence of placental gene expression plays an important role in mammalian speciation. We used crosses between two species of dwarf hamsters (Phodopus sungorus and Phodopus campbelli) to examine the genetic and regulatory underpinnings of severe placental overgrowth in their hybrids. Using quantitative genetic mapping and mitochondrial substitution lines, we show that overgrowth of hybrid placentas was primarily caused by genetic differences on the maternally inherited P. sungorus X chromosome. Mitochondrial interactions did not contribute to abnormal hybrid placental development, and there was only weak correspondence between placental disruption and embryonic growth. Genome-wide analyses of placental transcriptomes from the parental species and first- and second-generation hybrids revealed a central group of co-expressed X-linked and autosomal genes that were highly enriched for maternally biased expression. Expression of this gene network was strongly correlated with placental size and showed widespread misexpression dependent on epistatic interactions with X-linked hybrid incompatibilities. Collectively, our results indicate that the X chromosome is likely to play a prominent role in the evolution of placental gene expression and the accumulation of hybrid developmental barriers between mammalian species.


Catalysts ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 62
Author(s):  
Won-Yong Jeon ◽  
Seyoung Mun ◽  
Wei Beng Ng ◽  
Keunsoo Kang ◽  
Kyudong Han ◽  
...  

Enzymatic biofuel cells (EBFCs) have excellent potential as components in bioelectronic devices, especially as active biointerfaces to regulate stem cell behavior for regenerative medicine applications. However, it remains unclear to what extent EBFC-generated electrical stimulation can regulate the functional behavior of human adipose-derived mesenchymal stem cells (hAD-MSCs) at the morphological and gene expression levels. Herein, we investigated the effect of EBFC-generated electrical stimulation on hAD-MSC cell morphology and gene expression using next-generation RNA sequencing. We tested three different electrical currents, 127 ± 9, 248 ± 15, and 598 ± 75 nA/cm2, in mesenchymal stem cells. We performed transcriptome profiling to analyze the impact of EBFC-derived electrical current on gene expression using next generation sequencing (NGS). We also observed changes in cytoskeleton arrangement and analyzed gene expression that depends on the electrical stimulation. The electrical stimulation of EBFC changes cell morphology through cytoskeleton re-arrangement. In particular, the results of whole transcriptome NGS showed that specific gene clusters were up- or down-regulated depending on the magnitude of applied electrical current of EBFC. In conclusion, this study demonstrates that EBFC-generated electrical stimulation can influence the morphological and gene expression properties of stem cells; such capabilities can be useful for regenerative medicine applications such as bioelectronic devices.


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