scholarly journals Biogenesis and Function of Small Non-Coding RNAs Derived from Eukaryotic Ribosomal RNA

2018 ◽  
Author(s):  
Marine Lambert ◽  
Abderrahim Benmoussa ◽  
Patrick Provost
Keyword(s):  
Ribosomal Rna ◽  
Potential Role ◽  
A Priori ◽  
Biological Significance ◽  
Rna Seq ◽  
New Class ◽  
Scientific Mind ◽  
Non Coding Rnas ◽  
And Function ◽  
Rrna Sequences

The advent of RNA-sequencing (RNA-Seq) technologies has markedly improved our knowledge and expanded the compendium of small non-coding RNAs, most of which derive from the processing of longer RNA precursors. In this review article, we will discuss about the biogenesis and function of small non-coding RNAs derived from eukaryotic ribosomal RNA (rRNA), called rRNA fragments (rRFs), and their potential role(s) as regulator of gene expression. This relatively new class of ncRNAs remained poorly investigated and underappreciated until recently, due mainly to the a priori exclusion of rRNA sequences—because of their overabundance—from RNA-Seq datasets. The situation surrounding rRFs resembles that of microRNAs (miRNAs), which used to be readily discarded from further analyses, for more than five decades, because we could not believe that RNA of such a short length could bear biological significance. As if we had not yet learned our lesson not to restrain our investigative, scientific mind from challenging widely accepted beliefs or dogmas, and from looking for the hidden treasures in the most unexpected places.

scholarly journals Small Non-Coding RNAs Derived From Eukaryotic Ribosomal RNA

2019 ◽  
Vol 5 (1) ◽  
pp. 16 ◽  
Author(s):  
Marine Lambert ◽  
Abderrahim Benmoussa ◽  
Patrick Provost
Keyword(s):  
Ribosomal Rna ◽  
Potential Role ◽  
A Priori ◽  
Biological Significance ◽  
Regulatory Proteins ◽  
Rna Seq ◽  
New Class ◽  
Scientific Mind ◽  
Non Coding Rnas ◽  
Rrna Sequences

The advent of RNA-sequencing (RNA-Seq) technologies has markedly improved our knowledge and expanded the compendium of small non-coding RNAs, most of which derive from the processing of longer RNA precursors. In this review article, we will present a nonexhaustive list of referenced small non-coding RNAs (ncRNAs) derived from eukaryotic ribosomal RNA (rRNA), called rRNA fragments (rRFs). We will focus on the rRFs that are experimentally verified, and discuss their origin, length, structure, biogenesis, association with known regulatory proteins, and potential role(s) as regulator of gene expression. This relatively new class of ncRNAs remained poorly investigated and underappreciated until recently, due mainly to the a priori exclusion of rRNA sequences—because of their overabundance—from RNA-Seq datasets. The situation surrounding rRFs resembles that of microRNAs (miRNAs), which used to be readily discarded from further analyses, for more than five decades, because no one could believe that RNA of such a short length could bear biological significance. As if we had not yet learned our lesson not to restrain our investigative, scientific mind from challenging widely accepted beliefs or dogmas, and from looking for the hidden treasures in the most unexpected places.

scholarly journals Emerging Data on the Diversity of Molecular Mechanisms Involving C/D snoRNAs

2021 ◽  
Vol 7 (2) ◽  
pp. 30
Author(s):  
Laeya Baldini ◽  
Bruno Charpentier ◽  
Stéphane Labialle
Keyword(s):  
Ribosomal Rna ◽  
Molecular Mechanisms ◽  
Molecular Level ◽  
Accurate Description ◽  
Small Nucleolar Rnas ◽  
Age Of Maturity ◽  
Non Coding Rnas ◽  
And Function ◽  
Nucleolar Rnas

Box C/D small nucleolar RNAs (C/D snoRNAs) represent an ancient family of small non-coding RNAs that are classically viewed as housekeeping guides for the 2′-O-methylation of ribosomal RNA in Archaea and Eukaryotes. However, an extensive set of studies now argues that they are involved in mechanisms that go well beyond this function. Here, we present these pieces of evidence in light of the current comprehension of the molecular mechanisms that control C/D snoRNA expression and function. From this inventory emerges that an accurate description of these activities at a molecular level is required to let the snoRNA field enter in a second age of maturity.

scholarly journals Transcriptomic and ChIP-seq Integrative Analysis Reveals Important Roles of Epigenetically Regulated lncRNAs in Placental Development in Meishan Pigs

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 397
Author(s):  
Dadong Deng ◽  
Xihong Tan ◽  
Kun Han ◽  
Ruimin Ren ◽  
Jianhua Cao ◽  
...  
Keyword(s):  
Differentially Expressed ◽  
Rna Seq ◽  
Sequencing Data ◽  
Placental Development ◽  
Cytoskeleton Organization ◽  
New Class ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Non Coding Rnas ◽  
Two Stages ◽  
Regulatory Functions

The development of the placental fold, which increases the maternal–fetal interacting surface area, is of primary importance for the growth of the fetus throughout the whole pregnancy. However, the mechanisms involved remain to be fully elucidated. Increasing evidence has revealed that long non-coding RNAs (lncRNAs) are a new class of RNAs with regulatory functions and could be epigenetically regulated by histone modifications. In this study, 141 lncRNAs (including 73 up-regulated and 68 down-regulated lncRNAs) were identified to be differentially expressed in the placentas of pigs during the establishment and expanding stages of placental fold development. The differentially expressed lncRNAs and genes (DElncRNA-DEgene) co-expression network analysis revealed that these differentially expressed lncRNAs (DElncRNAs) were mainly enriched in pathways of cell adhesion, cytoskeleton organization, epithelial cell differentiation and angiogenesis, indicating that the DElncRNAs are related to the major events that occur during placental fold development. In addition, we integrated the RNA-seq (RNA sequencing) data with the ChIP-seq (chromatin immunoprecipitation sequencing) data of H3K4me3/H3K27ac produced from the placental samples of pigs from the two stages (gestational days 50 and 95). The analysis revealed that the changes in H3K4me3 and/or H3K27ac levels were significantly associated with the changes in the expression levels of 37 DElncRNAs. Furthermore, several H3K4me3/H3K27ac-lncRNAs were characterized to be significantly correlated with genes functionally related to placental development. Thus, this study provides new insights into understanding the mechanisms for the placental development of pigs.

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 Emerging Roles of Estrogen-Regulated Enhancer and Long Non-Coding RNAs

2020 ◽  
Vol 21 (10) ◽  
pp. 3711
Author(s):  
Melina J. Sedano ◽  
Alana L. Harrison ◽  
Mina Zilaie ◽  
Chandrima Das ◽  
Ramesh Choudhari ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Expression Patterns ◽  
Biological Significance ◽  
Rna Seq ◽  
Biological Functions ◽  
Protein Coding ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Non Coding Rnas

Genome-wide RNA sequencing has shown that only a small fraction of the human genome is transcribed into protein-coding mRNAs. While once thought to be “junk” DNA, recent findings indicate that the rest of the genome encodes many types of non-coding RNA molecules with a myriad of functions still being determined. Among the non-coding RNAs, long non-coding RNAs (lncRNA) and enhancer RNAs (eRNA) are found to be most copious. While their exact biological functions and mechanisms of action are currently unknown, technologies such as next-generation RNA sequencing (RNA-seq) and global nuclear run-on sequencing (GRO-seq) have begun deciphering their expression patterns and biological significance. In addition to their identification, it has been shown that the expression of long non-coding RNAs and enhancer RNAs can vary due to spatial, temporal, developmental, or hormonal variations. In this review, we explore newly reported information on estrogen-regulated eRNAs and lncRNAs and their associated biological functions to help outline their markedly prominent roles in estrogen-dependent signaling.

scholarly journals Comparison of Poly-A+ Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq

2020 ◽  
Vol 6 (3) ◽  
pp. 32 ◽  
Author(s):  
Anna R. Dahlgren ◽  
Erica Y. Scott ◽  
Tamer Mansour ◽  
Erin N. Hales ◽  
Pablo J. Ross ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Preparation Method ◽  
Parietal Lobe ◽  
Library Preparation ◽  
Rna Seq ◽  
The Past ◽  
Rrna Depletion ◽  
Non Coding Rnas ◽  
Nucleolar Rna ◽  
Library Preparation Method

Long non-coding RNAs (lncRNAs) are untranslated regulatory transcripts longer than 200 nucleotides that can play a role in transcriptional, post-translational, and epigenetic regulation. Traditionally, RNA-sequencing (RNA-seq) libraries have been created by isolating transcriptomic RNA via poly-A+ selection. In the past 10 years, methods to perform ribosomal RNA (rRNA) depletion of total RNA have been developed as an alternative, aiming for better coverage of whole transcriptomic RNA, both polyadenylated and non-polyadenylated transcripts. The purpose of this study was to determine which library preparation method is optimal for lncRNA investigations in the horse. Using liver and cerebral parietal lobe tissues from two healthy Thoroughbred mares, RNA-seq libraries were prepared using standard poly-A+ selection and rRNA-depletion methods. Averaging the two biologic replicates, poly-A+ selection yielded 327 and 773 more unique lncRNA transcripts for liver and parietal lobe, respectively. More lncRNA were found to be unique to poly-A+ selected libraries, and rRNA-depletion identified small nucleolar RNA (snoRNA) to have a higher relative expression than in the poly-A+ selected libraries. Overall, poly-A+ selection provides a more thorough identification of total lncRNA in equine tissues while rRNA-depletion may allow for easier detection of snoRNAs.

scholarly journals tsRBase: a comprehensive database for expression and function of tsRNAs in multiple species

2020 ◽  
Vol 49 (D1) ◽  
pp. D1038-D1045
Author(s):  
Yuanli Zuo ◽  
Lei Zhu ◽  
Zhixin Guo ◽  
Wenrong Liu ◽  
Jiting Zhang ◽  
...  
Keyword(s):  
Small Rnas ◽  
Expression Patterns ◽  
Biological Significance ◽  
Biological Processes ◽  
Rna Seq ◽  
Specific Expression ◽  
Spatiotemporal Expression ◽  
Multiple Species ◽  
And Function ◽  
Diverse Data

Abstract tRNA-derived small RNAs (tsRNAs) are a class of novel small RNAs, ubiquitously present in prokaryotes and eukaryotes. It has been reported that tsRNAs exhibit spatiotemporal expression patterns and can function as regulatory molecules in many biological processes. Current tsRNA databases only cover limited organisms and ignore tsRNA functional characteristics. Thus, integrating more relevant tsRNA information is helpful for further exploration. Here, we present a tsRNA database, named tsRBase, which integrates the expression pattern and functional information of tsRNAs in multiple species. In tsRBase, we identified 121 942 tsRNAs by analyzing more than 14 000 publicly available small RNA-seq data covering 20 species. This database collects samples from different tissues/cell-lines, or under different treatments and genetic backgrounds, thus helps depict specific expression patterns of tsRNAs under different conditions. Importantly, to enrich our understanding of biological significance, we collected tsRNAs experimentally validated from published literatures, obtained protein-binding tsRNAs from CLIP/RIP-seq data, and identified targets of tsRNAs from CLASH and CLEAR-CLIP data. Taken together, tsRBase is the most comprehensive and systematic tsRNA repository, exhibiting all-inclusive information of tsRNAs from diverse data sources of multiple species. tsRBase is freely available at http://www.tsrbase.org.

Identification and function of long non-coding RNAs

2013 ◽  
Vol 54 ◽  
pp. 113-126 ◽  
Author(s):  
Robert S. Young ◽  
Chris P. Ponting
Keyword(s):  
Gene Expression ◽  
Experimental Investigation ◽  
Eukaryotic Cells ◽  
Functional Roles ◽  
New Class ◽  
Biological Relevance ◽  
Genome Wide ◽  
Non Coding Rnas ◽  
And Function ◽  
Different Levels

It is now clear that eukaryotic cells produce many thousands of non-coding RNAs. The least well-studied of these are longer than 200 nt and are known as lncRNAs (long non-coding RNAs). These loci are of particular interest as their biological relevance remains uncertain. Sequencing projects have identified thousands of these loci in a variety of species, from flies to humans. Genome-wide scans for functionality, such as evolutionary and expression analyses, suggest that many of these molecules have functional roles to play in the cell. Nevertheless, only a handful of lncRNAs have been experimentally investigated, and most of these appear to possess roles in regulating gene expression at a variety of different levels. Several lncRNAs have also been implicated in cancer. This evidence suggests that lncRNAs represent a new class of non-coding gene whose importance should become clearer upon further experimental investigation.

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 Efficient and specific oligo-based depletion of rRNA

2019 ◽  
Author(s):  
Amelie J. Kraus ◽  
Benedikt G. Brink ◽  
T. Nicolai Siegel
Keyword(s):  
Oligonucleotide Probes ◽  
Rna Seq ◽  
Rrna Depletion ◽  
Non Coding Rnas ◽  
Paramagnetic Beads ◽  
Commercial Kits ◽  
High Degree ◽  
Target Rna ◽  
Rrna Sequences ◽  
Target Effects

SummaryIn most organisms, ribosomal RNA (rRNA) contributes to >85% of total RNA. Thus, to obtain useful information from RNA-sequencing (RNA-seq) analyses at reasonable sequencing depth, typically, mature polyadenylated transcripts are enriched or rRNA molecules are depleted. Targeted depletion of rRNA or other highly abundant transcripts is particularly useful when studying transcripts lacking a poly(A) tail, such as some non-coding RNAs (ncRNAs), most bacterial RNAs and partially degraded or immature transcripts. While several commercially available kits allow effective rRNA depletion, their efficiency relies on a high degree of sequence homology between oligonucleotide probes and the target RNA. This restricts the use of such kits to a limited number of organisms with conserved rRNA sequences.In this study we describe the use of biotinylated oligos and streptavidin-coated paramagnetic beads for the efficient and specific depletion of trypanosomal rRNA. Our approach reduces the levels of the most abundant rRNA transcripts to less than 5% with minimal off-target effects.By adjusting the sequence of the oligonucleotide probes, our approach can be used to deplete rRNAs or other abundant transcripts independent of species. Thus, our protocol provides a useful alternative for rRNA removal where enrichment of polyadenylated transcripts is not an option and commercial kits for rRNA are not available.

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