scholarly journals Human genetic variation and its effect on miRNA biogenesis, activity and function

2014 ◽  
Vol 42 (4) ◽  
pp. 1184-1189 ◽  
Author(s):  
Daniel R. Hogg ◽  
Lorna W. Harries

miRNAs are small non-coding regulators of gene expression that are estimated to regulate over 60% of all human genes. Each miRNA can target multiple mRNA targets and as such, miRNAs are responsible for some of the ‘fine tuning’ of gene expression and are implicated in regulation of all cellular processes. miRNAs bind to target genes by sequence complementarity, resulting in target degradation or translational blocking and usually a reduction in target gene expression. Like mRNA, miRNAs are transcribed from genomic DNA and are processed in several steps that are heavily reliant on correct secondary and tertiary structure. Secondary structure is determined by RNA sequence, which is in turn determined by the sequence of the genome. The human genome, however, like most eukaryotes is variable. Large numbers of SNPs (single nucleotide polymorphisms), small insertions and deletions (indels) and CNVs (copy number variants) have been described in our genome. Should this genetic variation occur in regions critical for the correct secondary structure or target binding, it may interfere with normal gene regulation and cause disease. In this review, we outline the consequences of genetic variation involving different aspects of miRNA biosynthesis, processing and regulation, with selected examples of incidences when this has potential to affect human disease.

2002 ◽  
Vol 48 (11) ◽  
pp. 1873-1882 ◽  
Author(s):  
Elaine M Weidenhammer ◽  
Brenda F Kahl ◽  
Ling Wang ◽  
Larry Wang ◽  
Melanie Duhon ◽  
...  

Abstract Background: Electronic microarrays comprise independent microelectrode test sites that can be electronically biased positive or negative, or left neutral, to move and concentrate charged molecules such as DNA and RNA to one or more test sites. We developed a protocol for multiplexed gene expression profiling of mRNA targets that uses electronic field-facilitated hybridization on electronic microarrays. Methods: A multiplexed, T7 RNA polymerase-mediated amplification method was used for expression profiling of target mRNAs from total cellular RNA; targets were detected by hybridization to sequence-specific capture oligonucleotides on electronic microarrays. Activation of individual test sites on the electronic microarray was used to target hybridization to designated subsets of sites and allow comparisons of target concentrations in different samples. We used multiplexed amplification and electronic field-facilitated hybridization to analyze expression of a model set of 10 target genes in the U937 cell line during lipopolysaccharide-mediated differentiation. Performance of multiple genetic analyses (single-nucleotide polymorphism detection, gene expression profiling, and splicing isoform detection) on a single electronic microarray was demonstrated using the ApoE and ApoER2 genes as a model system. Results: Targets were detected after a 2-min hybridization reaction. With noncomplementary capture probes, no signal was detectable. Twofold changes in target concentration were detectable throughout the (∼64-fold) range of concentrations tested. Levels of 10 targets were analyzed side by side across seven time points. By confining electronic activation to subsets of test sites, polymorphism detection, expression profiling, and splicing isoform analysis were performed on a single electronic microarray. Conclusions: Microelectronic array technology provides specific target detection and quantification with advantages over currently available methodologies for targeted gene expression profiling and combinatorial genomics testing.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. SCI-39-SCI-39
Author(s):  
Paul F. Bray

Abstract Abstract SCI-39 Alterations in gene expression are at the heart of both megakaryocytopoiesis and interindividual variation in platelet reactivity. Over the past decade there has been an increasing awareness of the important role played by microRNAs (miRNAs) in these diverse cell biologic and physiologic processes. MiRNAs are noncoding RNAs that target complementary sequences in mRNAs, leading to mRNA degradation or inhibition of translation. More than 1000 miRNAs have been identified, which are estimated to regulate 30%-90% of all coding genes. Expression of miRNAs is cell and developmental stage specific. MiRNAs regulate hematopoietic lineage commitment, as well as B lymphopoiesis, granulopoiesis, erythropoiesis and monocytopoiesis. Recent data also demonstrate a clear role for miRNAs in megakaryocytopoiesis (Meg-poiesis). The molecular genetic basis for the transition from one stage of Meg-poiesis to another requires fine-tuning of the various control elements, and miRNAs act as “rheostats” in this process. MiRNA-150 has a strong effect on Meg-erythroid progenitor cells, inducing commitment to the Meg lineage at the expense of erythropoiesis. MiRNA-150 directly down-regulates MYB, a transcription factor important in thrombopoiesis. Over-expressed miRNA-146a knocks down CXCR4 (receptor for SDF-1), reducing Meg proliferation and maturation. MiR-146a gene expression is negatively regulated by the promyelocytic zinc finger protein, PLZF. Thus, miRNAs act as intermediaries of transcription factors that control Meg-poiesis. An increasing number of genetic diseases are being described due to mutations in miRNA genes or their mRNA targets. Deletion of miR-145 and miR-146a on 5q is sufficient to cause the 5q- phenotype; miR-125b-2 up-regulates Meg-poiesis and may be involved in megakaryoblastic leukemia. Platelets appear to be a particularly rich source of miRNAs, many of which are expressed at very high levels. Notably, platelets contain Dicer, TRBP2 and Ago2, and are capable of synthesizing miRNAs from pre-miRNAs. MiRNAs regulate Bcl-xL and Bak, raising the possibility that platelet miRNAs affect platelet lifespan. Because miRNAs are very stable, they also represent a potential biomarker, and we have found sets of miRNAs that appear to classify platelet reactivity to epinephrine. Using bioinformatic approaches, we have identified miRNA-mRNA pairs differentially expressed in platelets with differing phenotypes. This approach permits functional characterization of novel platelet mRNAs, and elucidation of a potential genetic mechanism for adjusting megakaryocyte/platelet mRNA expression. Thus, information extracted from these RNA networks continue to provide insights into systems biology of higher organisms. Disclosures: No relevant conflicts of interest to declare.


2018 ◽  
Author(s):  
Heather E. Wheeler ◽  
Sally Ploch ◽  
Alvaro N. Barbeira ◽  
Rodrigo Bonazzola ◽  
Angela Andaleon ◽  
...  

AbstractRegulation of gene expression is an important mechanism through which genetic variation can affect complex traits. A substantial portion of gene expression variation can be explained by both local (cis) and distal (trans) genetic variation. Much progress has been made in uncovering cis-acting expression quantitative trait loci (cis-eQTL), but trans-eQTL have been more difficult to identify and replicate. Here we take advantage of our ability to predict the cis component of gene expression coupled with gene mapping methods such as PrediXcan to identify high confidence candidate trans-acting genes and their targets. That is, we correlate the cis component of gene expression with observed expression of genes in different chromosomes. Leveraging the shared cis-acting regulation across tissues, we combine the evidence of association across all available GTEx tissues and find 2356 trans-acting/target gene pairs with high mappability scores. Reassuringly, trans-acting genes are enriched in transcription and nucleic acid binding pathways and target genes are enriched in known transcription factor binding sites. Interestingly, trans-acting genes are more significantly associated with selected complex traits and diseases than target or background genes, consistent with percolating trans effects. Our scripts and summary statistics are publicly available for future studies of trans-acting gene regulation.


PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3682 ◽  
Author(s):  
Xue Chen ◽  
Wei Zhao ◽  
Ye Yuan ◽  
Yan Bai ◽  
Yong Sun ◽  
...  

Considering complicated microRNA (miRNA) biogenesis and action mechanisms, it was thought so high energy-consuming for a cell to afford simultaneous over-expression of many miRNAs. Thus it prompts that an alternative miRNA regulation pattern on protein-encoding genes must exist, which has characteristics of energy-saving and precise protein output. In this study, expression tendency of proteins encoded by miRNAs’ target genes was evaluated in human organ scale, followed by quantitative assessment of miRNA synergism. Expression tendency analysis suggests that universally expressed proteins (UEPs) tend to physically interact in clusters and participate in fundamental biological activities whereas disorderly expressed proteins (DEPs) are inclined to relatively independently execute organ-specific functions. Consistent with this, miRNAs that mainly target UEP-encoding mRNAs, such as miR-21, tend to collaboratively or even synergistically act with other miRNAs in fine-tuning protein output. Synergistic gene regulation may maximize miRNAs’ efficiency with less dependence on miRNAs’ abundance and overcome the deficiency that targeting plenty of genes by single miRNA makes miRNA-mediated regulation high-throughput but insufficient due to target gene dilution effect. Furthermore, our in vitro experiment verified that merely 25 nM transfection of miR-21 be sufficient to influence the overall state of various human cells. Thus miR-21 was identified as a hub in synergistic miRNA–miRNA interaction network. Our findings suggest that synergistic miRNA–miRNA interaction is an important endogenous miRNA regulation mode, which ensures adequate potency of miRNAs at low abundance, especially those implicated in fundamental biological regulation.


2019 ◽  
Vol 119 (05) ◽  
pp. 716-725 ◽  
Author(s):  
Xianguo Kong ◽  
Lin Ma ◽  
Edward Chen ◽  
Chad Shaw ◽  
Leonard Edelstein

AbstractMegakaryopoiesis produces specialized haematopoietic stem cells in the bone marrow that give rise to megakaryocytes which ultimately produce platelets. Defects in megakaryopoiesis can result in altered platelet counts and physiology, leading to dysfunctional haemostasis and thrombosis. Additionally, dysregulated megakaryopoiesis is also associated with myeloid pathologies. Transcription factors play critical roles in cell differentiation by regulating the temporal and spatial patterns of gene expression which ultimately decide cell fate. Several transcription factors have been described as regulating megakaryopoiesis including myocyte enhancer factor 2C (MEF2C); however, the genes regulated by MEF2C that influence megakaryopoiesis have not been reported. Using chromatin immunoprecipitation-sequencing and Gene Ontology data we identified five candidate genes that are bound by MEF2C and regulate megakaryopoiesis: MOV10, AGO3, HDAC1, RBBP5 and WASF2. To study expression of these genes, we silenced MEF2C gene expression in the Meg01 megakaryocytic cell line and in induced pluripotent stem cells by CRISPR/Cas9 editing. We also knocked down MEF2C expression in cord blood-derived haematopoietic stem cells by siRNA. We found that absent or reduced MEF2C expression resulted in defects in megakaryocytic differentiation and reduced levels of the candidate target genes. Luciferase assays confirmed that genomic sequences within the target genes are regulated by MEF2C levels. Finally, we demonstrate that small deletions linked to a platelet count-associated single nucleotide polymorphism alter transcriptional activity, suggesting a mechanism by which genetic variation in MEF2C alters platelet production. These data help elucidate the mechanism behind MEF2C regulation of megakaryopoiesis and genetic variation driving platelet production.


2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Zihua Hu ◽  
Andrew E. Bruno

MicroRNAs (miRNAs) regulate gene expression posttranscriptionally. Although previous efforts have demonstrated the functional importance of target sites on miRNAs, little is known about the influence of the rest of 3′ untranslated regions (3′UTRs) of target genes on microRNA function. We conducted a genome-wide study and found that the entire 3′UTR sequences could also play important roles on miRNA function in addition to miRNA target sites. This was evidenced by the fact that human single nucleotide polymorphisms (SNPs) on both seed target region and the rest of 3′UTRs of miRNA target genes were under significantly stronger negative selection, when compared to non-miRNA target genes. We also discovered that the flanking nucleotides on both sides of miRNA target sites were subject to moderate strong selection. A local sequence region of ~67 nucleotides with symmetric structure is herein defined. Additionally, from gene expression analysis, we found that SNPs and miRNA target sites on target sequences may interactively affect gene expression.


2016 ◽  
Author(s):  
Daniel C. Jeffares ◽  
Clemency Jolly ◽  
Mimoza Hoti ◽  
Doug Speed ◽  
Liam Shaw ◽  
...  

AbstractLarge structural variations (SVs) in the genome are harder to identify than smaller genetic variants but may substantially contribute to phenotypic diversity and evolution. Here we analyze the effects of SVs on gene expression, quantitative traits, and intrinsic reproductive isolation in the yeast Schizosaccharomyces pombe. We establish a high-quality curated catalog of SVs in the genomes of a worldwide library of S. pombe strains, including duplications, deletions, inversions and translocations. We show that copy number variants (CNVs) frequently segregate within closely related clonal populations, are weakly linked to single nucleotide polymorphisms (SNPs), and show other genetic signals consistent with rapid turnover. These transient CNVs produce stoichiometric effects on gene expression both within and outside the duplicated regions. CNVs make substantial contributions to quantitative traits such as cell shape, cell growth under diverse conditions, sugar utilization in winemaking, whereas rearrangements are strongly associated with reproductive isolation. Collectively, these findings have broad implications for evolution and for our understanding of quantitative traits including complex human diseases.


Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 2045-2045 ◽  
Author(s):  
Carlos Fernández de Larrea ◽  
Tania Díaz ◽  
María Teresa Cibeira ◽  
Natalia Tovar ◽  
Alfons Navarro ◽  
...  

Abstract Introduction: Multiple myeloma (MM) remains an incurable disease for most patients. Thus, sequential therapy when relapse or progression after first line is almost always needed. Immunomodulatory agents derived from thalidomide such as lenalidomide, has several antitumoral effects including anti-proliferative and immune-modulation by binding the intracellular protein cereblon. Lenalidomide has been approved for the treatment of relapsed or refractory MM in Europe and USA. The possibility of using biological predictors of response with this regimen could be promising. A group of genetic normal variations in DNA, mainly single nucleotide polymorphisms (SNPs), have been described in association with response to treatment in MM. A distinctive group of polymorphisms is constituted by SNPs in microRNAs (miRNA) processing machinery in miRNA precursor molecules and in miRNA binding sites, known as miRSNPs, that we have associated with response to autologous transplantation and bortezomib. The aim of this study was to ascertain the outcome of patients with relapsed myeloma treated with lenalidomide in a tertiary hospital as to investigate the prognostic impact of 9 miRSNPs located either in MM related miRNAs target genes or in miRNA biogenesis pathway proteins Methods: One hundred and three patients (54M/49F; median age 65 years, range 30 to 86) with relapsed MM after at least one treatment regimen were treated from November 2003 to January 2014 with lenalidomide plus dexamethasone. Median follow-up for alive patients was 3 years. Patients had received a median number of 2 treatment lines (range 1 – 6), but with no lenalidomide-based regimens. Genomic DNA was isolated from bone marrow slides using a commercial kit (Qiagen). The genes and SNPs evaluated in genomic DNA by allelic discrimination (TaqMan assays) were KRT81 (rs3660), FAM179b (rs1053667), MIR146A (rs2910164), MIR196A2 (rs11614913), MIR149 (rs2292832) and MIR423 (rs6505162) for miRNA target genes, and RAN (rs14035), TRBP (rs784567) and XPO5 (rs11077) for miRNA biogenesis pathway. These genes were selected based on their potential impact on prognosis in solid tumors in previous reports. Results: Overall response (OR) was achieved in 55.4% of the patients (complete remission 6.8%, partial response 40.8% and minor response 7.8%), while 16 (15.5%) and 26 (25.2%) showed no response (NR) or progressive disease (PD), respectively. 4 patients (3.9%) died before response could be evaluated. The median progression-free survival (PFS) after lenalidomide therapy was 8.1 months (95% CI 7.3 to 8.9), with a median overall survival (OS) of 2.3 years (95% CI 1.5 to 3.2). OS was significantly shorter in those patients not reaching at least MR (1 vs. 3.7 years; p<0.0001). Six patients did not progress during the first 5 years of treatment: two have died for unrelated causes; two progressed biologically but no requiring further treatments and the remaining two are in continued response while on therapy. Only 8 responding patients (7.8%) in whom therapy with lenalidomide was discontinued received re-treatment with lenalidomide at progression. OS was significantly longer in patients with SNP in FAM179b (p=0.041) (Figure 1) and MIR196A2 (p=0.01) (Figure 2), with a trend for MIR149 (p=0.117). In the two first SNPs, there were also a significant impact in PFS after lenalidomide regimen (p=0.024 and p=0.018). Interestingly, these miRSNPs have not shown the same impact as previously reported when autologous transplantation or bortezomib are used, where XPO5 is the crucial gene. Other factors associated with longer OS included lenalidomide at first relapse vs. subsequent lines (p=0.002), IgG isotype (p=0.044), normal serum LDH (p=0.032) and a trend for creatinine lower than 2 mg/dL (p=0.08) at diagnosis. In a multivariate analysis for OS, only the use of lenalidomide at first relapse (HR 2, 95% IC 1.04-3.9; p=0.039) and SNP in MIR196A2 (HR 1.86, 95% IC 1.03-3.4; p=0.04) remained at significant level. Conclusions: Lenalidomide plus dexamethasone is a very active regimen when used in daily clinical practice, particularly at the time of first relapse. A small subgroup of patients can remain disease-free for more than 5 years. Some SNPs in miRNA target genes (FAM179b and, particularly, MIR196A) could be useful as potential predictors of response. Figure 1 Figure 1. Disclosures Fernández de Larrea: Celgene: Consultancy, Honoraria. Cibeira:Celgene: Consultancy, Honoraria. Rosiñol:Janssen: Honoraria; Celgene: Honoraria. Jiménez:Janssen: Honoraria. Bladé:Janssen: Grant support Other, Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene: Grant support, Grant support Other, Honoraria, Membership on an entity's Board of Directors or advisory committees.


2021 ◽  
Vol 7 (25) ◽  
pp. eabf9808
Author(s):  
Marten A. Hoeksema ◽  
Zeyang Shen ◽  
Inge R. Holtman ◽  
An Zheng ◽  
Nathan J. Spann ◽  
...  

Mechanisms by which noncoding genetic variation influences gene expression remain only partially understood but are considered to be major determinants of phenotypic diversity and disease risk. Here, we evaluated effects of >50 million single-nucleotide polymorphisms and short insertions/deletions provided by five inbred strains of mice on the responses of macrophages to interleukin-4 (IL-4), a cytokine that plays pleiotropic roles in immunity and tissue homeostasis. Of >600 genes induced >2-fold by IL-4 across the five strains, only 26 genes reached this threshold in all strains. By applying deep learning and motif mutation analyses to epigenetic data for macrophages from each strain, we identified the dominant combinations of lineage-determining and signal-dependent transcription factors driving IL-4 enhancer activation. These studies further revealed mechanisms by which noncoding genetic variation influences absolute levels of enhancer activity and their dynamic responses to IL-4, thereby contributing to strain-differential patterns of gene expression and phenotypic diversity.


2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Vajiheh Safavi-Rizi ◽  
Marco Herde ◽  
Christine Stöhr

AbstractDue to climate change, economically important crop plants will encounter flooding periods causing hypoxic stress more frequently. This may lead to reduced yields and endanger food security. As roots are the first organ to be affected by hypoxia, the ability to sense and respond to hypoxic stress is crucial. At the molecular level, therefore, fine-tuning the regulation of gene expression in the root is essential for hypoxia tolerance. Using an RNA-Seq approach, we investigated transcriptome modulation in tomato roots of the cultivar ‘Moneymaker’, in response to short- (6 h) and long-term (48 h) hypoxia. Hypoxia duration appeared to have a significant impact on gene expression such that the roots of five weeks old tomato plants showed a distinct time-dependent transcriptome response. We observed expression changes in 267 and 1421 genes under short- and long-term hypoxia, respectively. Among these, 243 genes experienced changed expression at both time points. We identified tomato genes with a potential role in aerenchyma formation which facilitates oxygen transport and may act as an escape mechanism enabling hypoxia tolerance. Moreover, we identified differentially regulated genes related to carbon and amino acid metabolism and redox homeostasis. Of particular interest were the differentially regulated transcription factors, which act as master regulators of downstream target genes involved in responses to short and/or long-term hypoxia. Our data suggest a temporal metabolic and anatomic adjustment to hypoxia in tomato root which requires further investigation. We propose that the regulated genes identified in this study are good candidates for further studies regarding hypoxia tolerance in tomato or other crops.


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