scholarly journals Identification of the conserved long non-coding RNAs in myogenesis

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Anupam Bhattacharya ◽  
Simang Champramary ◽  
Tanya Tripathi ◽  
Debajit Thakur ◽  
Ilya Ioshikhes ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Muscle Development ◽  
Three Dimensional ◽  
C2c12 Cells ◽  
Mouse Muscle ◽  
Rna Molecules ◽  
Expression Of Genes ◽  
Novel Approach ◽  
Non Coding Rna ◽  
Topologically Associated Domains

Abstract Background Our understanding of genome regulation is ever-evolving with the continuous discovery of new modes of gene regulation, and transcriptomic studies of mammalian genomes have revealed the presence of a considerable population of non-coding RNA molecules among the transcripts expressed. One such non-coding RNA molecule is long non-coding RNA (lncRNA). However, the function of lncRNAs in gene regulation is not well understood; moreover, finding conserved lncRNA across species is a challenging task. Therefore, we propose a novel approach to identify conserved lncRNAs and functionally annotate these molecules. Results In this study, we exploited existing myogenic transcriptome data and identified conserved lncRNAs in mice and humans. We identified the lncRNAs expressing differentially between the early and later stages of muscle development. Differential expression of these lncRNAs was confirmed experimentally in cultured mouse muscle C2C12 cells. We utilized the three-dimensional architecture of the genome and identified topologically associated domains for these lncRNAs. Additionally, we correlated the expression of genes in domains for functional annotation of these trans-lncRNAs in myogenesis. Using this approach, we identified conserved lncRNAs in myogenesis and functionally annotated them. Conclusions With this novel approach, we identified the conserved lncRNAs in myogenesis in humans and mice and functionally annotated them. The method identified a large number of lncRNAs are involved in myogenesis. Further studies are required to investigate the reason for the conservation of the lncRNAs in human and mouse while their sequences are dissimilar. Our approach can be used to identify novel lncRNAs conserved in different species and functionally annotated them.

scholarly journals The Role of Extracellular Vesicles as Shuttles of RNA and Their Clinical Significance as Biomarkers in Hepatocellular Carcinoma

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 902
Author(s):  
Eva Costanzi ◽  
Carolina Simioni ◽  
Gabriele Varano ◽  
Cinzia Brenna ◽  
Ilaria Conti ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Extracellular Vesicles ◽  
Tumor Metastasis ◽  
Biological Processes ◽  
Rna Molecules ◽  
Expression Of Genes ◽  
Non Coding Rna ◽  
Donor Cells ◽  
Relevant Role

Extracellular vesicles (EVs) have attracted interest as mediators of intercellular communication following the discovery that EVs contain RNA molecules, including non-coding RNA (ncRNA). Growing evidence for the enrichment of peculiar RNA species in specific EV subtypes has been demonstrated. ncRNAs, transferred from donor cells to recipient cells, confer to EVs the feature to regulate the expression of genes involved in differentiation, proliferation, apoptosis, and other biological processes. These multiple actions require accuracy in the isolation of RNA content from EVs and the methodologies used play a relevant role. In liver, EVs play a crucial role in regulating cell–cell communications and several pathophysiological events in the heterogeneous liver class of cells via horizontal transfer of their cargo. This review aims to discuss the rising role of EVs and their ncRNAs content in regulating specific aspects of hepatocellular carcinoma development, including tumorigenesis, angiogenesis, and tumor metastasis. We analyze the progress in EV-ncRNAs’ potential clinical applications as important diagnostic and prognostic biomarkers for liver conditions.

Nutritive implications of dietary microRNAs: facts, controversies, and perspectives

2019 ◽  
Vol 10 (6) ◽  
pp. 3044-3056 ◽  
Author(s):  
Jianting Li ◽  
Lin Lei ◽  
Fayin Ye ◽  
Yun Zhou ◽  
Hui Chang ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Pivotal Role ◽  
Rna Molecules ◽  
Non Coding Rna

As a group of non-coding RNA molecules, microRNAs have recently become more well-known due to their pivotal role in gene regulation.

scholarly journals Trim33 (Tif1γ) is not required for skeletal muscle development or regeneration but suppresses cholecystokinin expression

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Cassie A. Parks ◽  
Katherine Pak ◽  
Iago Pinal-Fernandez ◽  
Wilson Huang ◽  
Assia Derfoul ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Satellite Cells ◽  
Knockout Mice ◽  
Muscle Regeneration ◽  
Skeletal Muscles ◽  
Muscle Development ◽  
Conditional Knockout ◽  
C2c12 Cells ◽  
Mouse Muscle ◽  
Muscle Histology

AbstractThe expression of Trim33 (Tif1γ) increases in skeletal muscles during regeneration and decreases upon maturation. Although Trim33 is required for the normal development of other tissues, its role in skeletal muscle is unknown. The current study aimed to define the role of Trim33 in muscle development and regeneration. We generated mice with muscle-specific conditional knockout of Trim33 by combining floxed Trim33 and Cre recombinase under the Pax7 promoter. Muscle regeneration was induced by injuring mouse muscles with cardiotoxin. We studied the consequences of Trim33 knockdown on viability, body weight, skeletal muscle histology, muscle regeneration, and gene expression. We also studied the effect of Trim33 silencing in satellite cells and the C2C12 mouse muscle cell line. Although Trim33 knockdown mice weighed less than control mice, their skeletal muscles were histologically unremarkable and regenerated normally following injury. Unexpectedly, RNAseq analysis revealed dramatically increased expression of cholecystokinin (CCK) in regenerating muscle from Trim33 knockout mice, satellite cells from Trim33 knockout mice, and C2C12 cells treated with Trim33 siRNA. Trim33 knockdown had no demonstrable effect on muscle differentiation or regeneration. However, Trim33 knockdown induced CCK expression in muscle, suggesting that suppression of CCK expression requires Trim33.

scholarly journals MicroRNAs in Obesity and Related Metabolic Disorders

Cells ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 859 ◽  
Author(s):  
Jean-François Landrier ◽  
Adel Derghal ◽  
Lourdes Mounien
Keyword(s):  
Metabolic Disease ◽  
Metabolic Disorders ◽  
Molecular Mechanisms ◽  
Metabolic Diseases ◽  
Untranslated Regions ◽  
Rna Molecules ◽  
Expression Of Genes ◽  
Non Coding Rna ◽  
Micro Rnas

Metabolic disorders are characterized by the inability to properly use and/or store energy. The burdens of metabolic disease, such as obesity or diabetes, are believed to arise through a complex interplay between genetics and epigenetics predisposition, environment and nutrition. Therefore, understanding the molecular mechanisms for the onset of metabolic disease will provide new insights for prevention and treatment. There is growing concern about the dysregulation of micro-RNAs (miRNAs) in metabolic diseases. MiRNAs are short non-coding RNA molecules that post-transcriptionally repress the expression of genes by binding to untranslated regions and coding sequences of the target mRNAs. This review aims to provide recent data about the potential involvement of miRNAs in metabolic diseases, particularly obesity and type 2 diabetes.

The impact of epigenetics on cardiovascular disease

2020 ◽  
Vol 98 (1) ◽  
pp. 12-22 ◽  
Author(s):  
Dimple Prasher ◽  
Steven C. Greenway ◽  
Raja B. Singh
Keyword(s):  
Cardiac Fibrosis ◽  
Mortality And Morbidity ◽  
Rna Molecules ◽  
Expression Of Genes ◽  
Non Coding Rna ◽  
Novel Biomarkers ◽  
External Risk ◽  
And Function ◽  
The Impact

Mortality and morbidity from cardiovascular diseases (CVDs) represents a huge burden to society. It is recognized that environmental factors and individual lifestyles play important roles in disease susceptibility, but the link between these external risk factors and our genetics has been unclear. However, the discovery of sequence-independent heritable DNA changes (epigenetics) have helped us to explain the link between genes and the environment. Multiple diverse epigenetic processes, including DNA methylation, histone modification, and the expression of non-coding RNA molecules affect the expression of genes that produce important changes in cellular differentiation and function, influencing the health and adaptability of the organism. CVDs such as congenital heart disease, cardiomyopathy, heart failure, cardiac fibrosis, hypertension, and atherosclerosis are now being viewed as much more complex and dynamic disorders. The role of epigenetics in these and other CVDs is currently under intense scrutiny, and we can expect important insights to emerge, including novel biomarkers and new approaches to enable precision medicine. This review summarizes the recent advances in our understanding of the role of epigenetics in CVD.

scholarly journals In silico prediction of high-resolution Hi-C interaction matrices

2018 ◽  
Author(s):  
Shilu Zhang ◽  
Deborah Chasman ◽  
Sara Knaack ◽  
Sushmita Roy
Keyword(s):  
High Resolution ◽  
Cell Lines ◽  
Regulatory Protein ◽  
Three Dimensional ◽  
Predictive Performance ◽  
Computational Prediction ◽  
Range Interaction ◽  
Novel Approach ◽  
Sequence Elements ◽  
Topologically Associated Domains

AbstractThe three-dimensional organization of the genome plays an important role in gene regulation by enabling distal sequence elements to control the expression level of genes hundreds of kilobases away. Hi-C is a powerful genome-wide technique to measure the contact count of pairs of genomic loci needed to study three-dimensional organization. Due to experimental costs high resolution Hi-C datasets are available only for a handful of cell lines. Computational prediction of Hi-C contact counts can offer a scalable and inexpensive approach to examine three-dimensional genome organization across many cellular contexts. Here we present HiC-Reg, a novel approach to predict contact counts from one-dimensional regulatory signals such as epigenetic marks and regulatory protein binding. HiC-Reg exploits the signal from the region spanning two interacting regions and from across multiple cell lines to generalize to new contexts. Using existing feature importance measures and a new matrix factorization based approach, we found CTCF and chromatin marks, especially repressive and elongation marks, as important for predictive performance. Predicted counts from HiC-Reg identify topologically associated domains as well as significant interactions that are enriched for CTCF bi-directional motifs and agree well with interactions identified from complementary long-range interaction assays. Taken together, HiC-Reg provides a powerful framework to generate high-resolution profiles of contact counts that can be used to study individual locus level interactions as well as higher-order organizational units of the genome.

scholarly journals The Role of MiR-124 in Bladder Cancer – A Review of the Literature

2021 ◽  
Vol 29 (1) ◽  
pp. 9-18
Author(s):  
Costin Petcu ◽  
Catalin Baston ◽  
Emil Angelescu ◽  
Maria Mirela Iacob ◽  
Ileana Constantinescu ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Cancer Cells ◽  
Cellular Functions ◽  
Rna Molecules ◽  
Diagnosis And Prognosis ◽  
Expression Of Genes ◽  
Non Coding Rna ◽  
Tumor Tissues ◽  
Normal Urothelium

Abstract MicroRNAs (miRNAs) are a group of non-coding RNA molecules that have an important role in modulating the expression of genes involved in regulating cellular functions. A growing number of studies suggest the abnormal expression of microRNAs in different types of cancer cells. MiRNA-124 is a microRNA that is down-regulated in many types of cancer cells, including bladder cancer. Our objective is to provide a review of the key publications that studied the effect of miR-124 on bladder cancer. This review focus on the targets and different pathways of miR-124 that were identified in various studies and differences between their expressions in normal urothelium and tumor tissues. We also include data regarding urinary methylations levels of miR-124 and their role in bladder cancer diagnosis and prognosis. Subsequently, we establish future perspectives of miR-124 research and its promising role in bladder cancer.

MicroRNAs: Potentially important regulators for schistosome development and therapeutic targets against schistosomiasis

Parasitology ◽  
2012 ◽  
Vol 139 (5) ◽  
pp. 669-679 ◽  
Author(s):  
GUOFENG CHENG ◽  
YOUXIN JIN
Keyword(s):  
Gene Regulation ◽  
Complex Life Cycle ◽  
Current Status ◽  
Biological Processes ◽  
Messenger Rnas ◽  
Regulate Gene Expression ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Evolutionarily Conserved ◽  
Multicellular Organisms

SUMMARYMicroRNAs (miRNAs) are small, endogenous non-coding RNA molecules that regulate gene expression post-transcriptionally by targeting the 3′ untranslated region (3′ UTR) of messenger RNAs. Since the discovery of the first miRNA in Caenorhabditis elegans, important regulatory roles for miRNAs in many key biological processes including development, cell proliferation, cell differentiation and apoptosis of many organisms have been described. Hundreds of miRNAs have been identified in various multicellular organisms and many are evolutionarily conserved. Schistosomes are multi-cellular eukaryotes with a complex life-cycle that require genes to be expressed and regulated precisely. Recently, miRNAs have been identified in two major schistosome species, Schistosoma japonicum and S. mansoni. These miRNAs are likely to play critical roles in schistosome development and gene regulation. Here, we review recent studies on schistosome miRNAs and discuss the potential roles of miRNAs in schistosome development and gene regulation. We also summarize the current status for targeting miRNAs and the potential of this approach for therapy against schistosomiasis.

Cross-Kingdom Regulation by Dietary Plant miRNAs: An Evidence-Based Review with Recent Updates

2021 ◽  
Author(s):  
Mingxi Jia ◽  
JinTao He ◽  
weidong Bai ◽  
Qinlu Lin ◽  
Jing Deng ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Oral Administration ◽  
Critical Role ◽  
Evidence Based ◽  
Plant Mirnas ◽  
Rna Molecules ◽  
Non Coding Rna

As non-coding RNA molecules, microRNAs (miRNAs) are widely known for their critical role in gene regulation. Recent studies have shown that plant miRNAs obtained through dietary oral administration can survive...

scholarly journals Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Michela Quadrini
Keyword(s):  
Hydrogen Bonding ◽  
Secondary Structure ◽  
Nucleotide Sequence ◽  
Thermus Thermophilus ◽  
Three Dimensional ◽  
Secondary Structures ◽  
Structural Effect ◽  
Biological Processes ◽  
Structural Pattern ◽  
Rna Molecules

Abstract RNA molecules play crucial roles in various biological processes. Their three-dimensional configurations determine the functions and, in turn, influences the interaction with other molecules. RNAs and their interaction structures, the so-called RNA–RNA interactions, can be abstracted in terms of secondary structures, i.e., a list of the nucleotide bases paired by hydrogen bonding within its nucleotide sequence. Each secondary structure, in turn, can be abstracted into cores and shadows. Both are determined by collapsing nucleotides and arcs properly. We formalize all of these abstractions as arc diagrams, whose arcs determine loops. A secondary structure, represented by an arc diagram, is pseudoknot-free if its arc diagram does not present any crossing among arcs otherwise, it is said pseudoknotted. In this study, we face the problem of identifying a given structural pattern into secondary structures or the associated cores or shadow of both RNAs and RNA–RNA interactions, characterized by arbitrary pseudoknots. These abstractions are mapped into a matrix, whose elements represent the relations among loops. Therefore, we face the problem of taking advantage of matrices and submatrices. The algorithms, implemented in Python, work in polynomial time. We test our approach on a set of 16S ribosomal RNAs with inhibitors of Thermus thermophilus, and we quantify the structural effect of the inhibitors.

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