scholarly journals Detection and Analysis of RNA Ribose 2′-O-Methylations: Challenges and Solutions

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 642 ◽  
Author(s):  
Yuri Motorin ◽  
Virginie Marchand
Keyword(s):  
Messenger Rnas ◽  
Small Nucleolar Rnas ◽  
Rna Modifications ◽  
Site Specific ◽  
Transfer Rnas ◽  
Small Nuclear Rnas ◽  
Regulatory Rnas ◽  
Traditional Approaches ◽  
Nucleolar Rnas ◽  
Made In

Ribose 2′-O-methylation is certainly one of the most common RNA modifications found in almost any type of cellular RNA. It decorates transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), small nuclear RNAs (snRNAs) (and most probably small nucleolar RNAs, snoRNAs), as well as regulatory RNAs like microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), and finally, eukaryotic messenger RNAs (mRNAs). Due to this exceptional widespread of RNA 2′-O-methylation, considerable efforts were made in order to precisely map these numerous modifications. Extensive studies of RNA 2′-O-methylation were also stimulated by the discovery of C/D-box snoRNA-guided machinery, which insures site-specific modification of hundreds 2′-O-methylated residues in archaeal and eukaryotic rRNAs and some other RNAs. In this brief review we discussed both traditional approaches of RNA biochemistry and also modern deep sequencing-based methods, used for detection/mapping and quantification of RNA 2′-O-methylations.

scholarly journals Site-Specific Pseudouridine Formation in Preribosomal RNA Is Guided by Small Nucleolar RNAs

Cell ◽  
1997 ◽  
Vol 89 (5) ◽  
pp. 799-809 ◽  
Author(s):  
Philippe Ganot ◽  
Marie-Line Bortolin ◽  
Tamás Kiss
Keyword(s):  
Small Nucleolar Rnas ◽  
Site Specific ◽  
Nucleolar Rnas

scholarly journals Emerging Roles and Potential Applications of Non-Coding RNAs in Glioblastoma

2020 ◽  
Vol 21 (7) ◽  
pp. 2611 ◽  
Author(s):  
Carlos DeOcesano-Pereira ◽  
Raquel A. C. Machado ◽  
Ana Marisa Chudzinski-Tavassi ◽  
Mari Cleide Sogayar
Keyword(s):  
Cancer Type ◽  
Biological Processes ◽  
Small Nucleolar Rnas ◽  
Physiological Conditions ◽  
Master Regulators ◽  
Potential Applications ◽  
Non Coding Rnas ◽  
Regulatory Rnas ◽  
Nucleolar Rnas ◽  
Substantial Effort

Non-coding RNAs (ncRNAs) comprise a diversity of RNA species, which do not have the potential to encode proteins. Non-coding RNAs include two classes of RNAs, namely: short regulatory ncRNAs and long non-coding RNAs (lncRNAs). The short regulatory RNAs, containing up to 200 nucleotides, include small RNAs, such as microRNAs (miRNA), short interfering RNAs (siRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNAs (snoRNAs). The lncRNAs include long antisense RNAs and long intergenic RNAs (lincRNAs). Non-coding RNAs have been implicated as master regulators of several biological processes, their expression being strictly regulated under physiological conditions. In recent years, particularly in the last decade, substantial effort has been made to investigate the function of ncRNAs in several human diseases, including cancer. Glioblastoma is the most common and aggressive type of brain cancer in adults, with deregulated expression of small and long ncRNAs having been implicated in onset, progression, invasiveness, and recurrence of this tumor. The aim of this review is to guide the reader through important aspects of miRNA and lncRNA biology, focusing on the molecular mechanism associated with the progression of this highly malignant cancer type.

scholarly journals Structure and biogenesis of small nucleolar RNAs acting as guides for ribosomal RNA modification.

1999 ◽  
Vol 46 (2) ◽  
pp. 377-389 ◽  
Author(s):  
W Filipowicz ◽  
P Pelczar ◽  
V Pogacic ◽  
F Dragon
Keyword(s):  
Ribosomal Rna ◽  
Structure And Function ◽  
Hydroxyl Group ◽  
Rna Modification ◽  
Small Nucleolar Rnas ◽  
Yeast Saccharomyces Cerevisiae ◽  
Site Specific ◽  
Alternative Pathways ◽  
And Function ◽  
Nucleolar Rnas

Maturation of pre-ribosomal RNA (pre-rRNA) in eukaryotic cells takes place in the nucleolus and involves a large number of cleavage events, which frequently follow alternative pathways. In addition, rRNAs are extensively modified, with the methylation of the 2'-hydroxyl group of sugar residues and conversion of uridines to pseudouridines being the most frequent modifications. Both cleavage and modification reactions of pre-rRNAs are assisted by a variety of small nucleolar RNAs (snoRNAs), which function in the form of ribonucleoprotein particles (snoRNPs). The majority of snoRNAs acts as guides directing site-specific 2'-O-ribose methylation or pseudouridine formation. Over one hundred RNAs of this type have been identified to date in vertebrates and the yeast Saccharomyces cerevisiae. This number is readily explained by the findings that one snoRNA acts as a guide usually for one or at most two modifications, and human rRNAs contain 91 pseudouridines and 106 2'-O-methyl residues. In this article we review information about the biogenesis, structure and function of guide snoRNAs.

scholarly journals Epigenetic Regulation by Non-Coding RNAs in the Avian Immune System

Life ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 148
Author(s):  
Xiaolan Chen ◽  
Bahareldin Ali Abdalla ◽  
Zhenhui Li ◽  
Qinghua Nie
Keyword(s):  
Immune System ◽  
Circular Rnas ◽  
Biological Processes ◽  
Small Interfering Rnas ◽  
Transfer Rnas ◽  
Small Nuclear Rnas ◽  
Non Coding Rnas ◽  
Avian Diseases ◽  
Regulatory Rnas ◽  
Functional Mechanisms

The identified non-coding RNAs (ncRNAs) include circular RNAs, long non-coding RNAs, microRNAs, ribosomal RNAs, small interfering RNAs, small nuclear RNAs, piwi-interacting RNAs, and transfer RNAs, etc. Among them, long non-coding RNAs, circular RNAs, and microRNAs are regulatory RNAs that have different functional mechanisms and were extensively participated in various biological processes. Numerous research studies have found that circular RNAs, long non-coding RNAs, and microRNAs played their important roles in avian immune system during the infection of parasites, virus, or bacterium. Here, we specifically review and expand this knowledge with current advances of circular RNAs, long non-coding RNAs, and microRNAs in the regulation of different avian diseases and discuss their functional mechanisms in response to avian diseases.

scholarly journals Site-Specific Ribose Methylation of Preribosomal RNA: A Novel Function for Small Nucleolar RNAs

Cell ◽  
1996 ◽  
Vol 85 (7) ◽  
pp. 1077-1088 ◽  
Author(s):  
Zsuzsanna Kiss-László ◽  
Yves Henry ◽  
Jean-Pierre Bachellerie ◽  
Michèle Caizergues-Ferrer ◽  
Tamás Kiss
Keyword(s):  
Small Nucleolar Rnas ◽  
Site Specific ◽  
Nucleolar Rnas

scholarly journals The Emerging Roles of RNA Modifications in Glioblastoma

Cancers ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 736 ◽  
Author(s):  
Zhen Dong ◽  
Hongjuan Cui
Keyword(s):  
Tumor Type ◽  
Messenger Rnas ◽  
Rna Modifications ◽  
Transfer Rnas ◽  
Pathological Mechanism ◽  
Fast Development ◽  
Living Organisms ◽  
Almost All ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Glioblastoma (GBM) is a grade IV glioma that is the most malignant brain tumor type. Currently, there are no effective and sufficient therapeutic strategies for its treatment because its pathological mechanism is not fully characterized. With the fast development of the Next Generation Sequencing (NGS) technology, more than 170 kinds of covalent ribonucleic acid (RNA) modifications are found to be extensively present in almost all living organisms and all kinds of RNAs, including ribosomal RNAs (rRNAs), transfer RNAs (tRNAs) and messenger RNAs (mRNAs). RNA modifications are also emerging as important modulators in the regulation of biological processes and pathological progression, and study of the epi-transcriptome has been a new area for researchers to explore their connections with the initiation and progression of cancers. Recently, RNA modifications, especially m6A, and their RNA-modifying proteins (RMPs) such as methyltransferase like 3 (METTL3) and α-ketoglutarate-dependent dioxygenase alkB homolog 5 (ALKBH5), have also emerged as important epigenetic mechanisms for the aggressiveness and malignancy of GBM, especially the pluripotency of glioma stem-like cells (GSCs). Although the current study is just the tip of an iceberg, these new evidences will provide new insights for possible GBM treatments. In this review, we summarize the recent studies about RNA modifications, such as N6-methyladenosine (m6A), N6,2′O-dimethyladenosine (m6Am), 5-methylcytosine (m5C), N1-methyladenosine (m1A), inosine (I) and pseudouridine (ψ) as well as the corresponding RMPs including the writers, erasers and readers that participate in the tumorigenesis and development of GBM, so as to provide some clues for GBM treatment.

Nucleolar RNPs: from genes to functional snoRNAs in plants

2010 ◽  
Vol 38 (2) ◽  
pp. 672-676 ◽  
Author(s):  
Julie Rodor ◽  
Ingrid Letelier ◽  
Loreto Holuigue ◽  
Manuel Echeverria
Keyword(s):  
Protein Interactions ◽  
Small Rnas ◽  
Small Nucleolar Rnas ◽  
Protein Protein Interactions ◽  
Nucleolar Proteins ◽  
Rna Targets ◽  
Complex Process ◽  
Small Nuclear Rnas ◽  
Nucleolar Rnas

The snoRNAs (small nucleolar RNAs) and related scaRNAs (small RNAs in the Cajal bodies) represent a major class of nuclear RNAs that guide 2′-O-ribose methylation and pseudouridylation of rRNAs, snRNAs (small nuclear RNAs) and other RNA targets. In vivo, all snoRNAs associate with a set of four highly conserved nucleolar proteins, forming the functional snoRNPs (small nucleolar ribonucleoproteins). The core structure of these mature snoRNPs has now been well described in eukaryotes, but less is known of their biogenesis. Recent data in animals and yeast reveal that assembly of the snoRNPs is a complex process that implicates several auxiliary proteins and transient protein–protein interactions. This new level of snoRNP regulation is now beginning to be unravelled in animals and yeast, but remains unexplored in plants. In the present paper, we review recent data from genomic and functional analysis allowing the identification and study of factors controlling the biogenesis of plant snoRNPs and their impact on plant development.

scholarly journals Regulatory Role of Small Nucleolar RNAs in Human Diseases

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Grigory A. Stepanov ◽  
Julia A. Filippova ◽  
Andrey B. Komissarov ◽  
Elena V. Kuligina ◽  
Vladimir A. Richter ◽  
...  
Keyword(s):  
Gene Expression Regulation ◽  
Human Cells ◽  
Small Nucleolar Rnas ◽  
Posttranscriptional Modification ◽  
Cellular Processes ◽  
Promising Target ◽  
Regulatory Rnas ◽  
Nucleolar Rnas ◽  
Artificial Stress

Small nucleolar RNAs (snoRNAs) are appreciable players in gene expression regulation in human cells. The canonical function of box C/D and box H/ACA snoRNAs is posttranscriptional modification of ribosomal RNAs (rRNAs), namely, 2′-O-methylation and pseudouridylation, respectively. A series of independent studies demonstrated that snoRNAs, as well as other noncoding RNAs, serve as the source of various short regulatory RNAs. Some snoRNAs and their fragments can also participate in the regulation of alternative splicing and posttranscriptional modification of mRNA. Alterations in snoRNA expression in human cells can affect numerous vital cellular processes. SnoRNA level in human cells, blood serum, and plasma presents a promising target for diagnostics and treatment of human pathologies. Here we discuss the relation between snoRNAs and oncological, neurodegenerative, and viral diseases and also describe changes in snoRNA level in response to artificial stress and some drugs.

scholarly journals Are Argonaute-Associated Tiny RNAs Junk, Inferior miRNAs, or a New Type of Functional RNAs?

2021 ◽  
Vol 8 ◽  
Author(s):  
Kotaro Nakanishi
Keyword(s):  
Small Rnas ◽  
Mature Mirnas ◽  
Small Nucleolar Rnas ◽  
Transfer Rnas ◽  
Mirna Genes ◽  
New Type ◽  
Mirna Degradation ◽  
Physiological Benefits ◽  
Functional Rnas ◽  
Nucleolar Rnas

The biosynthesis pathways of microRNAs (miRNAs) have been well characterized with the identification of the required components. miRNAs are synthesized from the transcripts of miRNA genes and other RNAs, such as introns, transfer RNAs, ribosomal RNAs, small nucleolar RNAs, and even viral miRNAs. These small RNAs are loaded into Argonaute (AGO) proteins and recruit the effector complexes to target mRNAs, repressing their gene expression post-transcriptionally. While mature miRNAs were defined as 19–23 nucleotides (nt), tiny RNAs (tyRNAs) shorter than 19 nt have been found to bind AGOs as equivalent or lesser miRNAs compared to their full-length mature miRNAs. In contrast, my recent study revealed that when human AGO3 loads 14 nt cleavage-inducing tyRNAs (cityRNAs), comprised of the first 14 nt of their corresponding mature miRNA, it can become a comparable slicer to AGO2. This observation raises the possibility that tyRNAs play distinct roles from their mature form. This minireview focuses on human AGO-associated tyRNAs shorter than 19 nt and discusses their possible biosynthesis pathways and physiological benefits, including how tyRNAs could avoid target-directed miRNA degradation accompanied by AGO polyubiquitination.

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