scholarly journals Non-Coding RNA Sequencing of Equine Endometrium During Maternal Recognition of Pregnancy

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 821
Author(s):  
Kristin M. Klohonatz ◽  
Stephen J. Coleman ◽  
Ashley D. Cameron ◽  
Ann M. Hess ◽  
Kailee J. Reed ◽  
...  
Keyword(s):  
Small Rna ◽  
Prostaglandin F2α ◽  
Luteal Regression ◽  
Production Studies ◽  
Non Coding Rna ◽  
Unknown Structure ◽  
Non Coding Rnas ◽  
Maternal Recognition Of Pregnancy ◽  
And Function ◽  
Small Rna Library

Maternal recognition of pregnancy (MRP) in the mare is not well defined. In a non-pregnant mare, prostaglandin F2α (PGF) is released on day 14 post-ovulation (PO) to cause luteal regression, resulting in loss of progesterone production. Equine MRP occurs prior to day 14 to halt PGF production. Studies have failed to identify a gene candidate for MRP, so attention has turned to small, non-coding RNAs. The objective of this study was to evaluate small RNA (<200 nucleotides) content in endometrium during MRP. Mares were used in a cross-over design with each having a pregnant and non-mated cycle. Each mare was randomly assigned to collection day 11 or 13 PO (n = 3/day) and endometrial biopsies were obtained. Total RNA was isolated and sequencing libraries were prepared using a small RNA library preparation kit and sequenced on a HiSeq 2000. EquCab3 was used as the reference genome and DESeq2 was used for statistical analysis. On day 11, 419 ncRNAs, representing miRNA, snRNA, snoRNA, scaRNA, and vaultRNA, were different between pregnancy statuses, but none on day 13. Equine endometrial ncRNAs with unknown structure and function were also identified. This study is the first to describe ncRNA transcriptome in equine endometrium. Identifying targets of these ncRNAs could lead to determining MRP.

Form and function of eukaryotic unstable non-coding RNAs

2012 ◽  
Vol 40 (4) ◽  
pp. 836-841 ◽  
Author(s):  
Jonathan Houseley
Keyword(s):  
Unknown Function ◽  
Budding Yeast ◽  
Rna Degradation ◽  
Present Review ◽  
Form And Function ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Higher Eukaryotes ◽  
And Function

Unstable non-coding RNAs are produced from thousands of loci in all studied eukaryotes (and also prokaryotes), but remain of largely unknown function. The present review summarizes the mechanisms of eukaryotic non-coding RNA degradation and highlights recent findings regarding function. The focus is primarily on budding yeast where the bulk of this research has been performed, but includes results from higher eukaryotes where available.

scholarly journals Emerging role of a novel small non-coding regulatory RNA: tRNA-derived small RNA

ExRNA ◽  
2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Fangfang Jin ◽  
Zhigang Guo
Keyword(s):  
Small Rna ◽  
Current Knowledge ◽  
Future Research ◽  
Regulatory Rna ◽  
Biological Functions ◽  
Research Directions ◽  
Non Coding Rna ◽  
Future Research Directions ◽  
Non Coding Rnas

Abstract The discovery of small non-coding RNAs, such as miRNA and piRNA, has dramatically changed our understanding of the role RNA plays in organisms. Recent studies show that a novel small non-coding RNA generated from cleavage of tRNA or pre-tRNA, called tRNA-derived small RNA (tsRNA), serves as a new regulator of gene expression. tsRNA has been determined participate in regulating some specific physiological and pathological processes. Although knowledge regarding the biological roles of miRNA and piRNA is expanding, whether tsRNAs play similar roles remains poorly understood. Here, we review the current knowledge regarding the mechanisms of action and biological functions of tsRNAs in intracellular, extracellular and intergenerational inheritance, and highlight the potential application of tsRNAs in human diseases, and present the current problems and future research directions.

scholarly journals Human Long Noncoding RNA Interactome: Detection, Characterization and Function

2020 ◽  
Vol 21 (3) ◽  
pp. 1027 ◽  
Author(s):  
Kazimierczyk ◽  
Kasprowicz ◽  
Kasprzyk ◽  
Wrzesinski
Keyword(s):  
Noncoding Rna ◽  
Potential Role ◽  
Integrated Analysis ◽  
Biological Functions ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
And Function ◽  
New Generation ◽  
Cellular Components ◽  
Proteins And Peptides

The application of a new generation of sequencing techniques has revealed that most of the genome has already been transcribed. However, only a small part of the genome codes proteins. The rest of the genome "dark matter” belongs to divergent groups of non-coding RNA (ncRNA), that is not translated into proteins. There are two groups of ncRNAs, which include small and long non-coding RNAs (sncRNA and lncRNA respectively). Over the last decade, there has been an increased interest in lncRNAs and their interaction with cellular components. In this review, we presented the newest information about the human lncRNA interactome. The term lncRNA interactome refers to cellular biomolecules, such as nucleic acids, proteins, and peptides that interact with lncRNA. The lncRNA interactome was characterized in the last decade, however, understanding what role the biomolecules associated with lncRNA play and the nature of these interactions will allow us to better understand lncRNA's biological functions in the cell. We also describe a set of methods currently used for the detection of lncRNA interactome components and the analysis of their interactions. We think that such a holistic and integrated analysis of the lncRNA interactome will help to better understand its potential role in the development of organisms and cancers.

scholarly journals Highly Divergent Neuropeptide - non-coding RNA regulatory networks underpin variant host-finding behaviours in Steinernema species infective juveniles

2020 ◽  
Author(s):  
Neil D. Warnock ◽  
Erwan Atcheson ◽  
Ciaran McCoy ◽  
Johnathan J. Dalzell
Keyword(s):  
Gene Expression ◽  
Small Rna ◽  
Regulatory Networks ◽  
Host Finding ◽  
Protein Coding ◽  
Rna Analysis ◽  
New Family ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Shared Gene

AbstractWe conducted a transcriptomic and small RNA analysis of infective juveniles (IJs) from three behaviourally distinct Steinernema species. Substantial variation was found in the expression of shared gene orthologues, revealing gene expression signatures that correlate with behavioural states. 97% of predicted microRNAs are novel to each species. Surprisingly, our data provide evidence that isoform variation can effectively convert protein-coding neuropeptide genes into non-coding transcripts, which may represent a new family of long non-coding RNAs. These data suggest that differences in neuropeptide gene expression, isoform variation, and small RNA interactions could contribute to behavioural differences within the Steinernema genus.

scholarly journals Long Non-Coding RNA-Ribonucleoprotein Networks in the Post-Transcriptional Control of Gene Expression

2020 ◽  
Vol 6 (3) ◽  
pp. 40
Author(s):  
Paola Briata ◽  
Roberto Gherzi
Keyword(s):  
Transcriptional Control ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Huge Number ◽  
Protein Coding ◽  
Control Of Gene Expression ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
And Function ◽  
Long Non Coding Rna

Although mammals possess roughly the same number of protein-coding genes as worms, it is evident that the non-coding transcriptome content has become far broader and more sophisticated during evolution. Indeed, the vital regulatory importance of both short and long non-coding RNAs (lncRNAs) has been demonstrated during the last two decades. RNA binding proteins (RBPs) represent approximately 7.5% of all proteins and regulate the fate and function of a huge number of transcripts thus contributing to ensure cellular homeostasis. Transcriptomic and proteomic studies revealed that RBP-based complexes often include lncRNAs. This review will describe examples of how lncRNA-RBP networks can virtually control all the post-transcriptional events in the cell.

Non-coding RNA in cystic fibrosis

2018 ◽  
Vol 46 (3) ◽  
pp. 619-630 ◽  
Author(s):  
Arlene M.A. Glasgow ◽  
Chiara De Santi ◽  
Catherine M. Greene
Keyword(s):  
Cystic Fibrosis ◽  
Chloride Ion ◽  
Altered Expression ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Small Ncrnas ◽  
Non Coding Rnas ◽  
Regulatory Rnas ◽  
And Function ◽  
Near Future

Non-coding RNAs (ncRNAs) are an abundant class of RNAs that include small ncRNAs, long non-coding RNAs (lncRNA) and pseudogenes. The human ncRNA atlas includes thousands of these specialised RNA molecules that are further subcategorised based on their size or function. Two of the more well-known and widely studied ncRNA species are microRNAs (miRNAs) and lncRNAs. These are regulatory RNAs and their altered expression has been implicated in the pathogenesis of a variety of human diseases. Failure to express a functional cystic fibrosis (CF) transmembrane receptor (CFTR) chloride ion channel in epithelial cells underpins CF. Secondary to the CFTR defect, it is known that other pathways can be altered and these may contribute to the pathophysiology of CF lung disease in particular. For example, quantitative alterations in expression of some ncRNAs are associated with CF. In recent years, there has been a series of published studies exploring ncRNA expression and function in CF. The majority have focussed principally on miRNAs, with just a handful of reports to date on lncRNAs. The present study reviews what is currently known about ncRNA expression and function in CF, and discusses the possibility of applying this knowledge to the clinical management of CF in the near future.

scholarly journals The role of m6A, m5C and Ψ RNA modifications in cancer: Novel therapeutic opportunities

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Paz Nombela ◽  
Borja Miguel-López ◽  
Sandra Blanco
Keyword(s):  
Gene Expression ◽  
Rna Processing ◽  
Therapeutic Potential ◽  
Biological Processes ◽  
Rna Modifications ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
And Function ◽  
Made In

AbstractRNA modifications have recently emerged as critical posttranscriptional regulators of gene expression programmes. Significant advances have been made in understanding the functional role of RNA modifications in regulating coding and non-coding RNA processing and function, which in turn thoroughly shape distinct gene expression programmes. They affect diverse biological processes, and the correct deposition of many of these modifications is required for normal development. Alterations of their deposition are implicated in several diseases, including cancer. In this Review, we focus on the occurrence of N6-methyladenosine (m6A), 5-methylcytosine (m5C) and pseudouridine (Ψ) in coding and non-coding RNAs and describe their physiopathological role in cancer. We will highlight the latest insights into the mechanisms of how these posttranscriptional modifications influence tumour development, maintenance, and progression. Finally, we will summarize the latest advances on the development of small molecule inhibitors that target specific writers or erasers to rewind the epitranscriptome of a cancer cell and their therapeutic potential.

scholarly journals Emerging Role of Exosomal Long Non-coding RNAs in Spaceflight-Associated Risks in Astronauts

2022 ◽  
Vol 12 ◽  
Author(s):  
Malik Bisserier ◽  
Nathaniel Saffran ◽  
Agnieszka Brojakowska ◽  
Aimy Sebastian ◽  
Angela Clare Evans ◽  
...  
Keyword(s):  
Rna Splicing ◽  
Potential Role ◽  
Space Environment ◽  
Non Coding Rna ◽  
Peripheral Blood Plasma ◽  
Non Coding Rnas ◽  
Associated Risk Factors ◽  
And Function ◽  
Long Non Coding Rna

During spaceflight, astronauts are exposed to multiple unique environmental factors, particularly microgravity and ionizing radiation, that can cause a range of harmful health consequences. Over the past decades, increasing evidence demonstrates that the space environment can induce changes in gene expression and RNA processing. Long non-coding RNA (lncRNA) represent an emerging area of focus in molecular biology as they modulate chromatin structure and function, the transcription of neighboring genes, and affect RNA splicing, stability, and translation. They have been implicated in cancer development and associated with diverse cardiovascular conditions and associated risk factors. However, their role on astronauts’ health after spaceflight remains poorly understood. In this perspective article, we provide new insights into the potential role of exosomal lncRNA after spaceflight. We analyzed the transcriptional profile of exosomes isolated from peripheral blood plasma of three astronauts who flew on various Shuttle missions between 1998–2001 by RNA-sequencing. Computational analysis of the transcriptome of these exosomes identified 27 differentially expressed lncRNAs with a Log2 fold change, with molecular, cellular, and clinical implications.

scholarly journals The non-coding epitranscriptome in cancer

2021 ◽  
Author(s):  
Valentina Miano ◽  
Azzurra Codino ◽  
Luca Pandolfini ◽  
Isaia Barbieri
Keyword(s):  
Human Disease ◽  
Eukaryotic Cells ◽  
Structure Stability ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Post Synthesis ◽  
And Function

Abstract Post-synthesis modification of biomolecules is an efficient way of regulating and optimizing their functions. The human epitranscriptome includes a variety of more than 100 modifications known to exist in all RNA subtypes. Modifications of non-coding RNAs are particularly interesting since they can directly affect their structure, stability, interaction and function. Indeed, non-coding RNAs such as tRNA and rRNA are the most modified RNA species in eukaryotic cells. In the last 20 years, new functions of non-coding RNAs have been discovered and their involvement in human disease, including cancer, became clear. In this review, we will present the evidence connecting modifications of different non-coding RNA subtypes and their role in cancer.

scholarly journals Small RNA sequencing reveals distinct nuclear microRNAs in pig granulosa cells during ovarian follicle growth

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Derek Toms ◽  
Bo Pan ◽  
Yinshan Bai ◽  
Julang Li
Keyword(s):  
Granulosa Cells ◽  
Small Rna ◽  
High Throughput Sequencing ◽  
Ovarian Function ◽  
Ovarian Follicle ◽  
Small Rna Sequencing ◽  
Cell Fractionation ◽  
Steroid Synthesis ◽  
Non Coding Rna ◽  
Dna Binding Sites

AbstractNuclear small RNAs have emerged as an important subset of non-coding RNA species that are capable of regulating gene expression. A type of small RNA, microRNA (miRNA) have been shown to regulate development of the ovarian follicle via canonical targeting and translational repression. Little has been done to study these molecules at a subcellular level. Using cell fractionation and high throughput sequencing, we surveyed cytoplasmic and nuclear small RNA found in the granulosa cells of the pig ovarian antral preovulatory follicle. Bioinformatics analysis revealed a diverse network of small RNA that differ in their subcellular distribution and implied function. We identified predicted genomic DNA binding sites for nucleus-enriched miRNAs that may potentially be involved in transcriptional regulation. The small nucleolar RNA (snoRNA) SNORA73, known to be involved in steroid synthesis, was also found to be highly enriched in the cytoplasm, suggesting a role for snoRNA species in ovarian function. Taken together, these data provide an important resource to study the small RNAome in ovarian follicles and how they may impact fertility.

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