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Non-Coding RNA, Volume 8, Issue 3

2022 June - 15 articles

Cover Story: Small RNA sequencing (sRNA-Seq) approaches reveal potentially functional RNA sequences derived from longer non-coding RNAs. However, RNAs shorter than 16 nucleotides (nt) are often removed from sequencing libraries/analyses, although they may be functional. Here, we compiled a comprehensive repertoire of small RNAs from 6 different eukaryotic organisms in an extended window of 8 to 30 nt RNA length. Among others, we show in this study that unusually short RNAs <16 nt appear to be more abundant than those >16 nt in bilaterian organisms. Notably, RNAs between 8 and 15 nt predominantly represent non-coding RNA fragments, such as semi-microRNAs, pRFs, sdRNAs, tRFs, and rRFs. We propose that the lower threshold of RNA length be reduced in sRNA-Seq analyses and datasets, as their abundance and diversity support their potential role as biomarkers of disease and/or mediators of cell function. View this paper
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Articles (15)

  • Communication
  • Open Access
2 Citations
3,723 Views
15 Pages

The Role of miR-217-5p in the Puromycin Aminonucleoside-Induced Morphological Change of Podocytes

  • Osamu Ishibashi,
  • Mika Hayashi,
  • Aya Horikawa,
  • Hitoshi Owada,
  • Ryotaro Miyamoto,
  • Naoya Mizukami and
  • Takashi Inui

Podocytes, alternatively called glomerular epithelial cells, are terminally differentiated cells that wrap around glomerular capillaries and function as a part of the glomerular filtration barrier in the kidney. Therefore, podocyte injury with morpho...

  • Article
  • Open Access
5 Citations
3,984 Views
20 Pages

CRISPR/CasRx-Mediated RNA Knockdown Reveals That ACE2 Is Involved in the Regulation of Oligodendroglial Cell Morphological Differentiation

  • Yukino Kato,
  • Kenji Tago,
  • Shoya Fukatsu,
  • Miyu Okabe,
  • Remina Shirai,
  • Hiroaki Oizumi,
  • Katsuya Ohbuchi,
  • Masahiro Yamamoto,
  • Kazushige Mizoguchi and
  • Junji Yamauchi
  • + 1 author

Angiotensin-converting enzyme 2 (ACE2) plays a role in catalyzing angiotensin II conversion to angiotensin (1–7), which often counteracts the renin-angiotensin system. ACE2 is expressed not only in the cells of peripheral tissues such as the he...

  • Feature Paper
  • Article
  • Open Access
7 Citations
3,534 Views
12 Pages

This study explored the relationship between 3D genome organization and RNA–DNA triplex-forming sites of long noncoding RNAs (lncRNAs), a group of RNAs that do not code for proteins but are important factors regulating different aspects of geno...

  • Article
  • Open Access
10 Citations
4,278 Views
17 Pages

LINC00892 Is an lncRNA Induced by T Cell Activation and Expressed by Follicular Lymphoma-Resident T Helper Cells

  • Ingram Iaccarino,
  • Fatme Mourtada,
  • Sarah Reinke,
  • Paurnima Patil,
  • Gero Doose,
  • Gianni Monaco,
  • Steve Hoffmann,
  • Reiner Siebert and
  • Wolfram Klapper

Successful immunotherapy in both solid tumors and in hematological malignancies relies on the ability of T lymphocytes to infiltrate the cancer tissue and mount an immune response against the tumor. Biomarkers able to discern the amount and the types...

  • Review
  • Open Access
38 Citations
5,115 Views
15 Pages

Tumor Suppressive Effects of GAS5 in Cancer Cells

  • Jesminder Kaur,
  • Nur’ain Salehen,
  • Anwar Norazit,
  • Amirah Abdul Rahman,
  • Nor Azian Abdul Murad,
  • Nik Mohd Afizan Nik Abd. Rahman and
  • Kamariah Ibrahim

In recent years, long non-coding RNAs (lncRNAs) have been shown to play important regulatory roles in cellular processes. Growth arrests specific transcript 5 (GAS5) is a lncRNA that is highly expressed during the cell cycle arrest phase but is downr...

  • Review
  • Open Access
6 Citations
4,481 Views
12 Pages

The Functional Roles and Regulation of Circular RNAs during Cellular Stresses

  • Yueh-Chun Lee,
  • Wei-Yu Wang,
  • Hui-Hsuan Lin,
  • Yi-Ren Huang,
  • Ya-Chi Lin and
  • Kuei-Yang Hsiao

Circular RNAs (circRNAs) are a novel class of regulatory RNA involved in many biological, physiological and pathological processes by functioning as a molecular sponge, transcriptional/epigenetic/splicing regulator, modulator of protein–protein...

  • Review
  • Open Access
6 Citations
5,668 Views
19 Pages

tiRNAs: Insights into Their Biogenesis, Functions, and Future Applications in Livestock Research

  • Fabio Sarais,
  • Alvaro Perdomo-Sabogal,
  • Klaus Wimmers and
  • Siriluck Ponsuksili

Transfer RNA (tRNA)-derived small RNAs (tsRNAs) belong to a group of transfer ribonucleic acid (tRNA)-derived fragments that have recently gained interest as molecules with specific biological functions. Their involvement in the regulation of physiol...

  • Review
  • Open Access
21 Citations
4,909 Views
23 Pages

LncRNA-Dependent Mechanisms of Transforming Growth Factor-β: From Tissue Fibrosis to Cancer Progression

  • Philip Chiu-Tsun Tang,
  • Ying-Ying Zhang,
  • Jane Siu-Fan Li,
  • Max Kam-Kwan Chan,
  • Jiaoyi Chen,
  • Ying Tang,
  • Yiming Zhou,
  • Dongmei Zhang,
  • Kam-Tong Leung and
  • Patrick Ming-Kuen Tang
  • + 3 authors

Transforming growth factor-β (TGF-β) is a crucial pathogenic mediator of inflammatory diseases. In tissue fibrosis, TGF-β regulates the pathogenic activity of infiltrated immunocytes and promotes extracellular matrix production via de...

  • Perspective
  • Open Access
3 Citations
3,226 Views
5 Pages

Non-Coding RNAs in Rheumatoid Arthritis: Implications for Biomarker Discovery

  • Julio Enrique Castañeda-Delgado,
  • Noé Macias-Segura and
  • Cesar Ramos-Remus

Recent advances in gene expression analysis techniques and increased access to technologies such as microarrays, qPCR arrays, and next-generation sequencing, in the last decade, have led to increased awareness of the complexity of the inflammatory re...

  • Article
  • Open Access
3 Citations
3,792 Views
23 Pages

An Expanded Landscape of Unusually Short RNAs in 11 Samples from Six Eukaryotic Organisms

  • Marine Lambert,
  • Sara Guellal,
  • Jeffrey Ho,
  • Abderrahim Benmoussa,
  • Benoit Laffont,
  • Richard Bélanger and
  • Patrick Provost

Small RNA sequencing (sRNA-Seq) approaches unveiled sequences derived from longer non-coding RNAs, such as transfer RNA (tRNA) and ribosomal RNA (rRNA) fragments, known as tRFs and rRFs, respectively. However, rRNAs and RNAs shorter than 16 nt are of...

  • Article
  • Open Access
3,739 Views
12 Pages

Identification of Two Exosomal miRNAs in Circulating Blood of Cancer Patients by Using Integrative Transcriptome and Network Analysis

  • Andrés Rincón-Riveros,
  • Josefa Antonia Rodríguez,
  • Victoria E. Villegas and
  • Liliana López-Kleine

Exosomes carry molecules of great biological and clinical interest, such as miRNAs. The contents of exosomes vary between healthy controls and cancer patients. Therefore, miRNAs and other molecules transported in exosomes are considered a potential s...

  • Article
  • Open Access
7 Citations
4,540 Views
19 Pages

Comprehensive Transcriptional Profiling and Mouse Phenotyping Reveals Dispensable Role for Adipose Tissue Selective Long Noncoding RNA Gm15551

  • Christoph Andreas Engelhard,
  • Chien Huang,
  • Sajjad Khani,
  • Petr Kasparek,
  • Jan Prochazka,
  • Jan Rozman,
  • David Pajuelo Reguera,
  • Radislav Sedlacek and
  • Jan-Wilhelm Kornfeld

Cold and nutrient-activated brown adipose tissue (BAT) is capable of increasing systemic energy expenditure via the uncoupled respiration and secretion of endocrine factors, thereby protecting mice against diet-induced obesity and improving insulin r...

  • Editorial
  • Open Access
1 Citations
3,368 Views
5 Pages

The Non-Coding RNA Journal Club: Highlights on Recent Papers—11

  • Hélène Bonnet,
  • Baptiste Bogard,
  • Florent Hubé,
  • Mirolyuba Ilieva,
  • Shziuka Uchida,
  • Maria Ascensión Ariza-Mateos,
  • Alexander Serganov,
  • Barbara Pardini,
  • Alessio Naccarati and
  • Patrick K. T. Shiu
  • + 3 authors

We are delighted to share with you our eleventh Journal Club and highlight some of the most interesting papers published recently [...]

  • Article
  • Open Access
5 Citations
4,565 Views
16 Pages

ITAS: Integrated Transcript Annotation for Small RNA

  • Alexey Stupnikov,
  • Vitaly Bezuglov,
  • Ivan Skakov,
  • Victoria Shtratnikova,
  • J. Richard Pilsner,
  • Alexander Suvorov and
  • Oleg Sergeyev

Transcriptomics analysis of various small RNA (sRNA) biotypes is a new and rapidly developing field. Annotations for microRNAs, tRNAs, piRNAs and rRNAs contain information on transcript sequences and loci that is vital for downstream analyses. Severa...

  • Review
  • Open Access
20 Citations
6,749 Views
28 Pages

In recent functional genomics studies, a large number of non-coding RNAs have been identified. It has become increasingly apparent that noncoding RNAs are crucial players in a wide range of cellular and physiological functions. They have been shown t...

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Non-Coding RNA - ISSN 2311-553X