scholarly journals Highly Ordered Architecture of MicroRNA Cluster

2013 ◽  
Vol 2013 ◽  
pp. 1-4 ◽  
Author(s):  
Bing Shi ◽  
Mingxuan Zhu ◽  
Shuang Liu ◽  
Mandun Zhang
Keyword(s):  
Mirna Expression ◽  
Expression Patterns ◽  
Expression Level ◽  
Mirna Cluster ◽  
Microrna Cluster ◽  
Mirna Clusters ◽  
Mirna Expression Level ◽  
Cluster A ◽  
The Relationship

Although it is known that the placement of genes in a cluster may be critical for proper expression patterns, it remains largely unclear whether the orders of members in an miRNA cluster have biological insights. By investigating the relationship between expression and orders for miRNAs from the oncogenic miR-17-92 cluster, we observed a highly ordered architecture in this cluster. A significant correlation between miRNA expression level and its placement was revealed. More importantly, the placement of these miRNAs is associated with their dysregulation in cancer. Here, we presented the opinion that miRNA clusters are not arranged randomly but show highly ordered architectures, which may have critical roles in physiology and pathology.

scholarly journals The Serum Cell-Free microRNA Expression Profile in MCTD, SLE, SSc, and RA Patients

2020 ◽  
Vol 9 (1) ◽  
pp. 161 ◽  
Author(s):  
Barbara Stypinska ◽  
Anna Wajda ◽  
Ewa Walczuk ◽  
Marzena Olesinska ◽  
Aleksandra Lewandowska ◽  
...  
Keyword(s):  
Connective Tissue ◽  
Signaling Pathway ◽  
Expression Profile ◽  
Mirna Expression ◽  
Lupus Erythematosus ◽  
Connective Tissue Diseases ◽  
Mirna Expression Profile ◽  
Expression Level ◽  
Control Group ◽  
Mirna Expression Level

Mixed connective tissue disease (MCTD) is a rare disorder characterized by symptoms that overlap two or more Autoimmune Connective Tissue Diseases (ACTDs). The aim of this study was to determine whether miRNAs participating in the TLRs signaling pathway could serve as biomarkers differentiating MCTD or other ACTD entities from a healthy control group and between groups of patients. Although the selected miRNA expression level was not significantly different between MCTD and control, we observed that miR-126 distinguishes MCTD patients from all other ACTD groups. The expression level of miRNAs was significantly higher in the serum of systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) patients compared to controls. The miR-145 and -181a levels distinguished RA from other ACDT patients. miR-155 was specific for SLE patients. MiR-132, miR-143, and miR-29a distinguished RA and SLE patients from the systemic sclerosis (SSc) group. Additionally, some clinical parameters were significantly related to the miRNA expression profile in the SLE group. SLE and RA are characterized by a specific serum expression profile of the microRNAs associated with the Toll-like receptors (TLRs) signaling pathway. The analysis showed that their level distinguishes these groups from the control and from other ACTD patients. The present study did not reveal a good biomarker for MCTD patients.

scholarly journals A PROBABILISTIC FRAMEWORK TO IMPROVE MICRORNA TARGET PREDICTION BY INCORPORATING PROTEOMICS DATA

2009 ◽  
Vol 07 (06) ◽  
pp. 955-972 ◽  
Author(s):  
JINGJING LI ◽  
RENQIANG MIN ◽  
ANTHONY BONNER ◽  
ZHAOLEI ZHANG
Keyword(s):  
Mrna Expression ◽  
Mirna Expression ◽  
Probabilistic Model ◽  
Expression Level ◽  
Sequence Information ◽  
Protein Abundance ◽  
Underlying Assumption ◽  
Mrna Targets ◽  
Mirna Expression Level ◽  
Sequence Complementarity

Due to the difficulties in identifying microRNA (miRNA) targets experimentally in a high-throughput manner, several computational approaches have been proposed. To this date, most leading algorithms are based on sequence information alone. However, there has been limited overlap between these predictions, implying high false-positive rates, which underlines the limitation of sequence-based approaches. Considering the repressive nature of miRNAs at the mRNA translational level, here we describe a probabilistic model to make predictions by combining sequence complementarity, miRNA expression level, and protein abundance. Our underlying assumption is that, given sequence complementarity between a miRNA and its putative mRNA targets, the miRNA expression level should be high and the protein abundance of the mRNA should be low. Having identified a set of confident predictions, we then built a second probabilistic model to trace back to the mRNA expression of the confident targets to investigate the mechanisms of the miRNA-mediated post-transcriptional regulation. Our results suggest that translational repression (which has no effect on mRNA level), instead of mRNA degradation, is the dominant mechanism in miRNA regulation. This observation explained the previously observed discordant correlation between mRNA expression and protein abundance.

scholarly journals Comprehensive analysis of the alteration of plasma miRNA expression level in mice exposed to diesel exhaust

2021 ◽  
Vol 8 (1) ◽  
pp. 1-6
Author(s):  
Ken Tachibana ◽  
Iori Kodaira ◽  
Noriko Kuroiwa ◽  
Ryo Uzuki ◽  
Yusuke Shinkai ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Diesel Exhaust ◽  
Comprehensive Analysis ◽  
Expression Level ◽  
Mirna Expression Level ◽  
Plasma Mirna

scholarly journals Identification of miRNA-eQTLs in maize mature leaf by GWAS

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Shu-Yun Chen ◽  
Mei-Hsiu Su ◽  
Karl A. Kremling ◽  
Nicholas K. Lepak ◽  
M. Cinta Romay ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Target Genes ◽  
Genome Wide Association Study ◽  
Developmental Stages ◽  
Mature Leaf ◽  
Plant Genome ◽  
Expression Level ◽  
Genome Wide ◽  
Mirna Expression Level ◽  
Next Generation Sequencing Ngs

Abstract Background MiRNAs play essential roles in plant development and response to biotic and abiotic stresses through interaction with their target genes. The expression level of miRNAs shows great variations among different plant accessions, developmental stages, and tissues. Little is known about the content within the plant genome contributing to the variations in plants. This study aims to identify miRNA expression-related quantitative trait loci (miR-QTLs) in the maize genome. Results The miRNA expression level from next generation sequencing (NGS) small RNA libraries derived from mature leaf samples of the maize panel (200 maize lines) was estimated as phenotypes, and maize Hapmap v3.2.1 was chosen as the genotype for the genome-wide association study (GWAS). A total of four significant miR-eQTLs were identified contributing to miR156k-5p, miR159a-3p, miR390a-5p and miR396e-5p, and all of them are trans-eQTLs. In addition, a strong positive coexpression of miRNA was found among five miRNA families. Investigation of the effects of these miRNAs on the expression levels and target genes provided evidence that miRNAs control the expression of their targets by suppression and enhancement. Conclusions These identified significant miR-eQTLs contribute to the diversity of miRNA expression in the maize penal at the developmental stages of mature leaves in maize, and the positive and negative regulation between miRNA and its target genes has also been uncovered.

66 Blood MicroRNAomes Revealed Signatures of Lameness Phenotypes in Feedlot Cattle

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 38-38
Author(s):  
Wentao Li ◽  
Eóin O’Hara ◽  
Hui-Zeng Sun ◽  
Karen S Schwartzkopf-Genswein ◽  
Leluo Guan
Keyword(s):  
Mirna Expression ◽  
Skin Diseases ◽  
Expression Patterns ◽  
Feedlot Cattle ◽  
Economic Losses ◽  
Physiological Status ◽  
Blood Samples ◽  
Healthy Cattle ◽  
Novel Biomarkers ◽  
The Relationship

Abstract Lameness is a significant health issue in Canadian feedlots resulting in substantial economic losses. However, the high frequency of misdiagnosis of lameness using traditional methods leads to ineffective treatment, suggesting a new diagnostic method is needed. Growing evidence indicates that microRNAs (miRNAs) can be used as biomarkers for identifying the animals’ physiological status and the diagnosis of certain diseases, but this approach has not been utilized in beef cattle. The objective of this study was to compare blood miRNA profiles between lame and healthy cattle to investigate the relationship between miRNA expression patterns and specific lameness phenotypes. Blood samples were collected from 156 feedlot cattle at 0, 1, 2 and 3 weeks after being diagnosed with either digital dermatitis (DD; n=62), toe tip necrosis syndrome (TTNS; n = 40), or footrot (FR; n = 40) and healthy controls (HC; n = 12) for miRNA libraries construction and sequencing. A total of 314 expressed miRNAs were identified in 89 blood samples collected at week 0 across all groups, with TTN having the largest number of expressed miRNAs (291, P < 0.01) compared to all other groups (HC=276, DD=281, FR=278). Although miRNA profiles did not differ among the lameness types, type-specific miRNAs were identified; 6 in DD, 10 in TTN, 5 in FR and 7 in HC cattle. In addition, 3, 6 and 7 DE miRNAs were detected in DD, TTNS and FR when compared with HC cattle. Most of the DE and group-specific miRNAs are related to inflammation and skin diseases. The DE miRNAs were different between week 0 and all other weeks, indicating miRNA profiles may differ over time and with disease progression and recovery. These findings provide an initial understanding of the relationship between the cattle blood miRNAome and lameness and suggest that miRNA expression holds promise in the discovery of novel biomarkers for identifying lameness.

scholarly journals The Role of miRNAs, miRNA Clusters, and isomiRs in Development of Cancer Stem Cell Populations in Colorectal Cancer

2021 ◽  
Vol 22 (3) ◽  
pp. 1424
Author(s):  
Victoria A. Stark ◽  
Caroline O. B. Facey ◽  
Vignesh Viswanathan ◽  
Bruce M. Boman
Keyword(s):  
Colorectal Cancer ◽  
Mirna Expression ◽  
Target Genes ◽  
Critical Role ◽  
Mirna Cluster ◽  
Mrna Levels ◽  
Developmental Defects ◽  
Altered Expression ◽  
Mirna Clusters ◽  
Stem Cell Populations

MicroRNAs (miRNAs or miRs) have a critical role in regulating stem cells (SCs) during development and altered expression can cause developmental defects and/or disease. Indeed, aberrant miRNA expression leads to wide-spread transcriptional dysregulation which has been linked to many cancers. Mounting evidence also indicates a role for miRNAs in the development of the cancer SC (CSC) phenotype. Our goal herein is to provide a review of: (i) current research on miRNAs and their targets in colorectal cancer (CRC), and (ii) miRNAs that are differentially expressed in colon CSCs. MicroRNAs can work in clusters or alone when targeting different SC genes to influence CSC phenotype. Accordingly, we discuss the specific miRNA cluster classifications and isomiRs that are predicted to target the ALDH1, CD166, BMI1, LRIG1, and LGR5 SC genes. miR-23b and miR-92A are of particular interest because our previously reported studies on miRNA expression in isolated normal versus malignant human colonic SCs showed that miR-23b and miR-92a are regulators of the LGR5 and LRIG1 SC genes, respectively. We also identify additional miRNAs whose expression inversely correlated with mRNA levels of their target genes and associated with CRC patient survival. Altogether, our deliberation on miRNAs, their clusters, and isomiRs in regulation of SC genes could provide insight into how dysregulation of miRNAs leads to the emergence of different CSC populations and SC overpopulation in CRC.

The Predominant microRNAs in β-cell Clusters for Insulin Regulation and Diabetic Control

2020 ◽  
Vol 21 (7) ◽  
pp. 722-734
Author(s):  
Adele Soltani ◽  
Arefeh Jafarian ◽  
Abdolamir Allameh
Keyword(s):  
Mirna Expression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Diabetic Control ◽  
In Vitro Proliferation ◽  
Cell Functions ◽  
Mirna Expression Profiles ◽  
Multiple Processes ◽  
The Impact

micro (mi)-RNAs are vital regulators of multiple processes including insulin signaling pathways and glucose metabolism. Pancreatic β-cells function is dependent on some miRNAs and their target mRNA, which together form a complex regulative network. Several miRNAs are known to be directly involved in β-cells functions such as insulin expression and secretion. These small RNAs may also play significant roles in the fate of β-cells such as proliferation, differentiation, survival and apoptosis. Among the miRNAs, miR-7, miR-9, miR-375, miR-130 and miR-124 are of particular interest due to being highly expressed in these cells. Under diabetic conditions, although no specific miRNA profile has been noticed, the expression of some miRNAs and their target mRNAs are altered by posttranscriptional mechanisms, exerting diverse signs in the pathobiology of various diabetic complications. The aim of this review article is to discuss miRNAs involved in the process of stem cells differentiation into β-cells, resulting in enhanced β-cell functions with respect to diabetic disorders. This paper will also look into the impact of miRNA expression patterns on in vitro proliferation and differentiation of β-cells. The efficacy of the computational genomics and biochemical analysis to link the changes in miRNA expression profiles of stem cell-derived β-cells to therapeutically relevant outputs will be discussed as well.

T-cell Activation Induces Dynamic Changes in miRNA Expression Patterns in CD4 and CD8 T-cell Subsets

MicroRNA ◽  
2015 ◽  
Vol 4 (2) ◽  
pp. 117-122 ◽  
Author(s):  
Nato Teteloshvili ◽  
Katarzyna Smigielska-Czepiel ◽  
Bart-Jan Kroesen ◽  
Elisabeth Brouwer ◽  
Joost Kluiver ◽  
...  
Keyword(s):  
T Cell ◽  
T Cell Activation ◽  
Mirna Expression ◽  
Cell Activation ◽  
Expression Patterns ◽  
Cd8 T Cell ◽  
T Cell Subsets ◽  
Dynamic Changes

scholarly journals Role of miRNAs in Normal Endometrium and in Endometrial Disorders: Comprehensive Review

2021 ◽  
Vol 10 (16) ◽  
pp. 3457
Author(s):  
Kamila Kolanska ◽  
Sofiane Bendifallah ◽  
Geoffroy Canlorbe ◽  
Arsène Mekinian ◽  
Cyril Touboul ◽  
...  
Keyword(s):  
Endometrial Cancer ◽  
Mirna Expression ◽  
Expression Patterns ◽  
Mirna Regulation ◽  
Rigorous Analysis ◽  
Sexual Hormones ◽  
Physiological Mechanisms ◽  
Normal Endometrium ◽  
Gynecological Disorders

The molecular responses to hormonal stimuli in the endometrium are modulated at the transcriptional and post-transcriptional stages. Any imbalance in cellular and molecular endometrial homeostasis may lead to gynecological disorders. MicroRNAs (miRNAs) are involved in a wide variety of physiological mechanisms and their expression patterns in the endometrium are currently attracting a lot of interest. miRNA regulation could be hormone dependent. Conversely, miRNAs could regulate the action of sexual hormones. Modifications to miRNA expression in pathological situations could either be a cause or a result of the existing pathology. The complexity of miRNA actions and the diversity of signaling pathways controlled by numerous miRNAs require rigorous analysis and findings need to be interpreted with caution. Alteration of miRNA expression in women with endometriosis has been reported. Thus, a potential diagnostic test supported by a specific miRNA signature could contribute to early diagnosis and a change in the therapeutic paradigm. Similarly, specific miRNA profile signatures are expected for RIF and endometrial cancer, with direct implications for associated therapies for RIF and adjuvant therapies for endometrial cancer. Advances in targeted therapies based on the regulation of miRNA expression are under evaluation.

scholarly journals Genome-Wide Identification and Genetic Variations of the Starch Synthase Gene Family in Rice

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1154
Author(s):  
Hongjia Zhang ◽  
Seong-Gyu Jang ◽  
San Mar Lar ◽  
Ah-Rim Lee ◽  
Fang-Yuan Cao ◽  
...  
Keyword(s):  
Gene Family ◽  
Catalytic Domain ◽  
Amylose Content ◽  
Expression Patterns ◽  
Starch Synthase ◽  
Eating Quality ◽  
Segmental Duplications ◽  
Genome Wide ◽  
The Relationship

Starch is a major ingredient in rice, and the amylose content of starch significantly impacts rice quality. OsSS (starch synthase) is a gene family related to the synthesis of amylose and amylopectin, and 10 members have been reported. In the present study, a synteny analysis of a novel family member belonging to the OsSSIV subfamily that contained a starch synthase catalytic domain showed that three segmental duplications and multiple duplications were identified in rice and other species. Expression data showed that the OsSS gene family is involved in diverse expression patterns. The prediction of miRNA targets suggested that OsSS are possibly widely regulated by miRNA functions, with miR156s targeted to OsSSII-3, especially. Haplotype analysis exhibited the relationship between amylose content and diverse genotypes. These results give new insight and a theoretical basis for the improved amylose content and eating quality of rice.

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