scholarly journals Independent origin of MIRNA genes controlling homologous target genes by partial inverted duplication of antisense‐transcribed sequences

2019 ◽  
Vol 101 (2) ◽  
pp. 401-419 ◽  
Author(s):  
Lydia Gramzow ◽  
Dajana Lobbes ◽  
Nathan Innard ◽  
Günter Theißen
Keyword(s):  
Target Genes ◽  
Mirna Genes ◽  
Independent Origin ◽  
Inverted Duplication ◽  
Transcribed Sequences

scholarly journals Independent origin of MIRNA genes controlling homologous target genes by partial inverted duplication of antisense-transcribed sequences

2019 ◽  
Author(s):  
Lydia Gramzow ◽  
Dajana Lobbes ◽  
Sophia Walter ◽  
Nathan Innard ◽  
Günter Theißen
Keyword(s):  
Transcription Factors ◽  
Target Gene ◽  
Target Genes ◽  
Mirna Biogenesis ◽  
Mads Box ◽  
Mads Box Genes ◽  
Developmental Processes ◽  
Inverted Duplication ◽  
The Future ◽  
Transcribed Sequences

AbstractSome microRNAs (miRNAs) are key regulators of developmental processes, mainly by controlling the accumulation of transcripts encoding transcription factors that are important for morphogenesis. MADS-box genes encode a family of transcription factors which control diverse developmental processes in flowering plants. Here we study the convergent evolution of two MIRNA (MIR) gene families, named MIR444 and MIR824, targeting members of the same clade of MIKCC-group MADS-box genes. We show that these two MIR genes most likely originated independently in monocots (MIR444) and in Brassicales (eudicots, MIR824). We provide evidence that in both cases the future target gene was transcribed in antisense prior to the evolution of the MIR genes. Both MIR genes then likely originated by a partial inverted duplication of their target genes, resulting in natural antisense organization of the newly evolved MIR gene and its target gene at birth. We thus propose a new model for the origin of MIR genes, MEPIDAS (MicroRNA Evolution by Partial Inverted Duplication of Antisense-transcribed Sequences). MEPIDAS is a refinement of the inverted duplication hypothesis. According to MEPIDAS, a MIR gene evolves at a genomic locus at which the future target gene is also transcribed in the antisense direction. A partial inverted duplication at this locus causes the antisense transcript to fold into a stem-loop structure that is recognized by the miRNA biogenesis machinery to produce a miRNA that regulates the gene at this locus. Our analyses exemplify how to elucidate the origin of conserved miRNAs by comparative genomics and will guide future studies.

scholarly journals Genome-wide Small Rna Profiling Reveals Tiller Development in Tall Fescue (Festuca Arundinacea Schreb.)

2020 ◽  
Author(s):  
Tao Hu ◽  
Tao Wang ◽  
Huiying Li ◽  
Misganaw Wassie ◽  
Liang Chen
Keyword(s):  
Production Rate ◽  
Small Rna ◽  
Tall Fescue ◽  
Festuca Arundinacea ◽  
Target Genes ◽  
Cool Season ◽  
Rna Profiling ◽  
Mirna Genes ◽  
Genome Wide ◽  
A Genome

Abstract Background: Tall fescue (Festuca arundinacea Schreb.) is a major cool-season forage and turfgrass species. The low tiller density and size dramatically limits its turf performance and forage yield. MicroRNAs (miRNA)-genes modules play critical roles in tiller development in plants. In this study, a genome-wide small RNA profiling was carried out in two tall fescue genotypes contrasting for tillering production (‘Ch-3’, high tiller production rate and ‘Ch-5’, low tiller production rate) andtwo types of tissue samples at different tillering development stage (Pre-tillering, grass before tillering; Tillering, grass after tillering). ‘Ch-3’, ‘Ch-5’, Pre-tillering, and Tillering samples were analyzed using high-throughput RNA sequencing.Results: A total of 222 million high-quality clean reads were generated and 208 miRNAs were discovered, including 148 known miRNAs belonging to 70 families and 60 novel ones. Furthermore, 18 miRNAs were involved in tall fescue tiller development process. Among them, 14 miRNAs displayed increased abundance in both Ch-3 and Tillering plants compared with that in Ch-5 and Pre-tillering plants and were positive with tillering, while another four miRNAs were negative with tiller development. Out ofthe three miRNAs osa-miR156a, zma-miR528a-3p and osa-miR444b.2, the rest of 15 miRNAs were newfound controllers mediating tiller development in plants. Based on our previous full-length transcriptome analysis in tall fescue, 2 8927 potential target genes were discoveredfor all identified miRNAs. Most of the 212 target genes of the 18 miRNAs were dominantly enriched into “ubiquitin-mediated proteolysis”, “phagosome”, “fatty acid biosynthesis”, “oxidative phosphorylation”, and “biosynthesis of unsaturated fatty acids” KEGG pathways.Conclusions: This is the first genome-wide miRNA profiles analysis to identifyregulators involved in tiller development in cool-season turfgrass. Tillering related 18 miRNAs and their 212 target genes provide novel information for the understanding of the molecular mechanisms of miRNA-genes mediated tiller development in cool-season turfgrass.

scholarly journals Genome-wide small RNA profiling reveals tiller development in tall fescue (Festuca arundinacea Schreb.)

2020 ◽  
Author(s):  
Tao Hu ◽  
Tao Wang ◽  
Huiying Li ◽  
Misganaw Wassie ◽  
Huawei Xu ◽  
...  
Keyword(s):  
Production Rate ◽  
Small Rna ◽  
Tall Fescue ◽  
Festuca Arundinacea ◽  
Target Genes ◽  
Cool Season ◽  
Rna Profiling ◽  
Mirna Genes ◽  
Genome Wide ◽  
A Genome

Abstract Background: Tall fescue (Festuca arundinacea Schreb.) is a major cool-season forage and turfgrass species. The low tiller density and size dramatically limits its turf performance and forage yield. MicroRNAs (miRNA)-genes modules play critical roles in tiller development in plants. In this study, a genome-wide small RNA profiling was carried out in two tall fescue genotypes contrasting for tillering production (‘Ch-3’, high tiller production rate and ‘Ch-5’, low tiller production rate) and two types of tissue samples at different tillering development stage (Pre-tillering, grass before tillering; Tillering, grass after tillering). ‘Ch-3’, ‘Ch-5’, Pre-tillering, and Tillering samples were analyzed using high-throughput RNA sequencing. Results: A total of 222 million high-quality clean reads were generated and 208 miRNAs were discovered, including 148 known miRNAs belonging to 70 families and 60 novel ones. Furthermore, 18 miRNAs were involved in tall fescue tiller development process. Among them, 14 miRNAs displayed increased abundance in both Ch-3 and Tillering plants compared with that in Ch-5 and Pre-tillering plants and were positive with tillering, while another four miRNAs were negative with tiller development. Out of the three miRNAs osa-miR156a, zma-miR528a-3p and osa-miR444b.2, the rest of 15 miRNAs were newfound and associated with tiller development in plants. Based on our previous full-length transcriptome analysis in tall fescue, 2 8927 potential target genes were discovered for all identified miRNAs. Most of the 212 target genes of the 18 miRNAs were dominantly enriched into “ubiquitin-mediated proteolysis”, “phagosome”, “fatty acid biosynthesis”, “oxidative phosphorylation”, and “biosynthesis of unsaturated fatty acids” KEGG pathways. In addition, bdi-miR167e-3p targets two kinase proteins EIF2AK4 and IRAK4, and osa-miR397a targets auxin response factor 5, which may be the significant miRNA-genes controllers in tillering development. Conclusions: This is the first genome-wide miRNA profiles analysis to identify regulators involved in tiller development in cool-season turfgrass. Tillering related 18 miRNAs and their 212 target genes provide novel information for the understanding of the molecular mechanisms of miRNA-genes mediated tiller development in cool-season turfgrass.

scholarly journals Potential Impact of MicroRNA Gene Polymorphisms in the Pathogenesis of Diabetes and Atherosclerotic Cardiovascular Disease

2019 ◽  
Vol 9 (4) ◽  
pp. 51 ◽  
Author(s):  
Imadeldin Elfaki ◽  
Rashid Mir ◽  
Mohammad Muzaffar Mir ◽  
Faisel M AbuDuhier ◽  
Abdullatif Taha Babakr ◽  
...  
Keyword(s):  
Cardiovascular Disease ◽  
Gene Polymorphisms ◽  
Target Genes ◽  
Association Studies ◽  
Atherosclerotic Cardiovascular Disease ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Rna Molecules ◽  
Mirna Genes ◽  
Microrna Gene

MicroRNAs (miRNAs) are endogenous, small (18–23 nucleotides), non-coding RNA molecules. They regulate the posttranscriptional expression of their target genes. MiRNAs control vital physiological processes such as metabolism, development, differentiation, cell cycle and apoptosis. The control of the gene expression by miRNAs requires efficient binding between the miRNA and their target mRNAs. Genome-wide association studies (GWASs) have suggested the association of single-nucleotide polymorphisms (SNPs) with certain diseases in various populations. Gene polymorphisms of miRNA target sites have been implicated in diseases such as cancers, diabetes, cardiovascular and Parkinson’s disease. Likewise, gene polymorphisms of miRNAs have been reported to be associated with diseases. In this review, we discuss the SNPs in miRNA genes that have been associated with diabetes and atherosclerotic cardiovascular disease in different populations. We also discuss briefly the potential underlining mechanisms through which these SNPs increase the risk of developing these diseases.

scholarly journals MicroRNAs Differentially Expressed in ACTH-Secreting Pituitary Tumors

2009 ◽  
Vol 94 (1) ◽  
pp. 320-323 ◽  
Author(s):  
Fernando Colbari Amaral ◽  
Natalia Torres ◽  
Fabiano Saggioro ◽  
Luciano Neder ◽  
Hélio Rubens Machado ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Tumor Size ◽  
Target Genes ◽  
Pituitary Tumors ◽  
Mirna Expression Profile ◽  
Fragile Sites ◽  
Cushing Disease ◽  
Small Noncoding Rnas ◽  
Mirna Genes ◽  
Acth Secreting

Abstract Context: MicroRNAs (miRNAs) are small noncoding RNAs, functioning as antisense regulators of gene expression by targeting mRNA and contributing to cancer development and progression. More than 50% of miRNA genes are located in cancer-associated genomic regions or in fragile sites of the genome. Objective: The aim of the study was to analyze the differential expression of let-7a, miR-15a, miR-16, miR-21, miR-141, miR-143, miR-145, and miR-150 in corticotropinomas and normal pituitary tissue and verify whether their profile of expression correlates with tumor size or remission after treatment. Material and Methods: ACTH-secreting pituitary tumor samples were obtained during transphenoidal surgery from patients with Cushing disease and normal pituitary tissues from autopsies. The relative expression of miRNAs was measured by real-time PCR using RNU44 and RNU49 as endogenous controls. Relative quantification of miRNA expression was calculated using the 2−ΔΔCt method. Results: We found underexpression of miR-145 (2.0-fold; P = 0.04), miR-21 (2.4-fold; P = 0.004), miR-141 (2.6-fold; P = 0.02), let-7a (3.3-fold; P = 0.003), miR-150 (3.8-fold; P = 0.04), miR-15a (4.5-fold; P = 0.03), miR-16 (5.0-fold; P = 0.004), and miR-143 (6.4-fold; P = 0.004) in ACTH-secreting pituitary tumors when compared to normal pituitary tissues. There were no differences between miRNA expression and tumor size as well as miRNA expression and ratio of remission after surgery, except in patients presenting lower miR-141 expression who showed a better chance of remission. Conclusion: Our results support the possibility that altered miRNA expression profile might be involved in corticotrophic tumorigenesis. However, the lack of knowledge about miRNA target genes postpones full understanding of the biological functions of down-regulated or up-regulated miRNAs in corticotropinomas.

Identification and characterization of microRNAs and their target genes from Nile tilapia (Oreochromis niloticus)

2016 ◽  
Vol 71 (7-8) ◽  
pp. 215-223 ◽  
Author(s):  
Yong Huang ◽  
Xiu Ying Ma ◽  
You Bing Yang ◽  
Hong Tao Ren ◽  
Xi Hong Sun ◽  
...  
Keyword(s):  
Stress Responses ◽  
Nile Tilapia ◽  
Target Genes ◽  
Expressed Sequence Tag ◽  
Mrna Levels ◽  
Stem Loop ◽  
Mirna Genes ◽  
Nile Tilapia Oreochromis Niloticus ◽  
Survey Sequence

Abstract MicroRNAs (miRNAs) are a class of small single-stranded, endogenous 21–22 nt non-coding RNAs that regulate their target mRNA levels by causing either inactivation or degradation of the mRNAs. In recent years, miRNA genes have been identified from mammals, insects, worms, plants, and viruses. In this research, bioinformatics approaches were used to predict potential miRNAs and their targets in Nile tilapia from the expressed sequence tag (EST) and genomic survey sequence (GSS) database, respectively, based on the conservation of miRNAs in many animal species. A total of 19 potential miRNAs were detected following a range of strict filtering criteria. To test the validity of the bioinformatics method, seven predicted Nile tilapia miRNA genes were selected for further biological validation, and their mature miRNA transcripts were successfully detected by stem–loop RT-PCR experiments. Using these potential miRNAs, we found 56 potential targets in this species. Most of the target mRNAs appear to be involved in development, metabolism, signal transduction, transcription regulation and stress responses. Overall, our findings will provide an important foundation for further research on miRNAs function in the Nile tilapia.

scholarly journals Computational Identification of Novel Family Members of MicroRNA Genes in Arabidopsis thaliana and Oryza sativa

2005 ◽  
Vol 37 (2) ◽  
pp. 75-87 ◽  
Author(s):  
Yang Li ◽  
Wei Li ◽  
You-Xin Jin
Keyword(s):  
Arabidopsis Thaliana ◽  
Oryza Sativa ◽  
Target Genes ◽  
Expression Profiles ◽  
Biological Effects ◽  
Family Members ◽  
Gene Expression Profiles ◽  
Homology Search ◽  
Mirna Regulation ◽  
Mirna Genes

Abstract MicroRNAs (miRNAs) are a class of endogenous small RNAs that play important regulatory roles in both animals and plants. miRNA genes have been intensively studied in animals, but not in plants. In this study, we adopted a homology search approach to identify homologs of previously validated plant miRNAs in Arabidopsis thaliana and Oryza sativa. We identified 20 potential miRNA genes in Arabidopsis and 40 in O. sativa, providing a relatively complete enumeration of family members for these miRNAs in plants. In addition, a greater number of Arabidopsis miRNAs (MIR168, MIR159 and MIR172) were found to be conserved in rice. With the novel homologs, most of the miRNAs have closely related fellow miRNAs and the number of paralogs varies in the different miRNA families. Moreover, a probable functional segment highly conserved on the elongated stem of pre-miRNA fold-backs of MIR319 and MIR159 family was identified. These results support a model of variegated miRNA regulation in plants, in which miRNAs with different functional elements on their pre-miRNA fold-backs can differ in their function or regulation, and closely related miRNAs can be diverse in their specificity or competence to downregulate target genes. It appears that the sophisticated regulation of miRNAs can achieve complex biological effects through qualitative and quantitative modulation of gene expression profiles in plants.

scholarly journals Hsa-miR-222 Is Involved in Differentiation of Endometrial Stromal Cells in Vitro

Endocrinology ◽  
2009 ◽  
Vol 150 (10) ◽  
pp. 4734-4743 ◽  
Author(s):  
Kun Qian ◽  
Linli Hu ◽  
Hong Chen ◽  
Haixia Li ◽  
Na Liu ◽  
...  
Keyword(s):  
Stromal Cells ◽  
Target Genes ◽  
Embryo Implantation ◽  
Endometrial Stromal Cells ◽  
Protein Levels ◽  
Mirna Genes ◽  
False Discovery ◽  
Decidual Cells ◽  
Expression Variance

Abstract Decidualization is a critical step during embryo implantation and characterized by the differentiation of endometrial stromal cells (ESCs) into decidual cells. Because miRNAs are important determinants of cellular fate specification, in this study, the miRNA expression in ESCs during in vitro decidualization was profiled by using a microarray. Significance analysis of microarrays revealed that 49 miRNA genes were differently (>2-fold) expressed between the noninduced ESCs and induced ESCs with a false discovery rate of 0. The expression variance of hsa-miR-222, 221, 143, 101, 30d, 30c, 181b, 27b, 29b, 507, and 23a was validated by using quantitative PCR (P < 0.05). Based on microRNA (miRNA) and mRNA expression variance and predicted target genes of miRNAs, a bioinformatic model of miRNAs controlling ESCs differentiation was formulated. Finally, we proved that down-regulation of has-miR-222 could decrease the number of cells in S phase during ESCs differentiation (P < 0.05). Antisense oligonucleotides of has-miR-222 could increase reporter gene expression by targeting the 3′ untranslated regions of CDKN1C/p57kip2 mRNAs as well as increase CDKN1C/p57kip2 protein levels (P < 0.05). In conclusion, our results suggest that a subset of miRNAs play a key role in gene reprogramming during ESCs decidualization and that hsa-miR-222 participates in ESC differentiation by regulating ESCs terminally withdrawing from the cell cycle.

Involvement of methylation of group of miRNA genes in regulation of expression of RAR-beta2 and NKIRAS1 target genes in lung cancer

2012 ◽  
Vol 46 (5) ◽  
pp. 693-704 ◽  
Author(s):  
D. S. Khodyrev ◽  
I. V. Pronina ◽  
S. V. Rykov ◽  
E. V. Beresneva ◽  
M. V. Freedman ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Target Genes ◽  
Regulation Of Expression ◽  
Mirna Genes

Role of rs10406069 in miR-5196 in hyperdiploid childhood acute lymphoblastic leukemia

Epigenomics ◽  
2020 ◽  
Vol 12 (22) ◽  
pp. 1949-1955
Author(s):  
Angela Gutierrez-Camino ◽  
Chantal Richer ◽  
Pascal St-Onge ◽  
Elixabet Lopez-Lopez ◽  
Ana Carbone Bañeres ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
Target Genes ◽  
Lymphoblastic Leukemia ◽  
Childhood Acute Lymphoblastic Leukemia ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Mirna Genes ◽  
Relevant Role ◽  
The Impact

Aim: To determine the role of single nucleotide polymorphisms (SNPs) in noncoding RNAs in childhood acute lymphoblastic leukemia (ALL) subtypes. Materials & methods: We screened all SNPs in 130 pre-miRNA genes to assess their role in the susceptibility of the most common subtypes of ALL: hyperdiploid and ETV6-RUNX1. Results: In two independent cohorts, we found a significant association between rs10406069 in miR-5196 and the risk of developing hyperdiploid ALL. This observation could be explained by the impact of the SNP on miR-5196 expression and in turn, in its target genes. Indeed, rs10406069 was associated with expression changes in SMC1A, a gene involved in sister chromatin cohesion. Conclusion: rs10406069 in miR-5196 may have a relevant role in hyperdiploid ALL risk.

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