Special Issue "Small RNAs – Big Roles: IsomiRs, tRNA Fragments, and rRNA Fragments in Human Health and Disease"

A special issue of Non-Coding RNA (ISSN 2311-553X).

Deadline for manuscript submissions: 30 December 2023 | Viewed by 2865

Special Issue Editors

Computational Medicine Center, Department of Pathology, Anatomy and Cellular Biology Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
Interests: next-generation sequencing; microRNAs; non-coding RNAs; transcriptome; bioinformatics
Special Issues, Collections and Topics in MDPI journals
Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia
Interests: microRNAs; noncoding RNA; gene expression; cell signalling
Special Issues, Collections and Topics in MDPI journals
Department of Biochemistry and Molecular Biology, and Computational Medicine Center at Thomas Jefferson University, Philadelphia, PA, USA
Interests: short non-coding RNA, cyclic phosphate-containing RNA, tRNA-derived RNA, tRNA half
Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
Interests: microRNAs (miRNAs) and miRNA isoforms (isomiRs); tRNA-derived fragments (tRFs); rRNA-derived fragments (rRFs); post-transcriptional regulation; pyknons; repetitive elements; genomic architecture

Special Issue Information

Dear Colleagues,

Small RNAs are known to play essential roles in numerous cellular contexts. Among the various RNA classes, the microRNAs (miRNAs) and their isoforms (isomiRs), the tRNA-derived fragments (tRFs), and the rRNA-derived fragments (rRFs) have been attracting much attention during the last decade. Quickly accumulating evidence suggests that all three classes are useful for designing powerful diagnostics and prognostics and as novel therapeutic targets. 

IsomiRs, tRFs, and rRFs arise non-randomly from miRNA precursors, tRNAs, and rRNAs, respectively. Which of these small RNAs are produced from a precursor molecule and at what abundance level depends on personal attributes (e.g., biological sex, ancestry, age) and context (e.g., cell type, disease type/subtype). Moreover, while some isomiRs, tRFs, and rRFs regulate mRNA and protein levels through RNA interference, it is unclear how most of them function.

This Special Issue of “Noncoding RNA” focuses on isomiRs, tRFs, and rRFs and the many open questions surrounding them. Manuscripts reporting original research, short communications, and methods will be of particular interest. Focused reviews will also be considered. 

The following is a non-exhaustive list of themes of interest:

  • Novel insights into the biogenesis of isomiRs, tRFs, and rRFs.
  • Novel insights into how isomiRs, tRFs, and rRFs regulate gene expression.
  • Previously unreported patterns of expression in health and disease.
  • Reports of novel disease biomarkers or prognostics based on these small RNAs.
  • Functionalization of specific small RNAs.
  • Evolutionary aspects of isomiRs, tRNA fragments, and rRNA fragments.
  • Experimental methods for the accurate detection and quantification of these small RNAs.

Dr. Eric Londin
Dr. Cameron Bracken
Dr. Yohei Kirino
Dr. Isidore Rigoutsos
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Non-Coding RNA is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microRNA
  • miRNA
  • miRNA isoform
  • isomiR
  • tRNA
  • tRNA-derived fragment
  • tRF
  • rRNA
  • rRNA-derived fragment
  • rRF
  • biomarker
  • diagnostic
  • prognostic
  • therapeutic
  • small RNA

Published Papers (2 papers)

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Research

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18 pages, 761 KiB  
Article
The Typical tRNA Co-Expresses Multiple 5′ tRNA Halves Whose Sequences and Abundances Depend on Isodecoder and Isoacceptor and Change with Tissue Type, Cell Type, and Disease
Non-Coding RNA 2023, 9(6), 69; https://doi.org/10.3390/ncrna9060069 - 06 Nov 2023
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Abstract
Transfer RNA-derived fragments (tRFs) are noncoding RNAs that arise from either mature transfer RNAs (tRNAs) or their precursors. One important category of tRFs comprises the tRNA halves, which are generated through cleavage at the anticodon. A given tRNA typically gives rise to several [...] Read more.
Transfer RNA-derived fragments (tRFs) are noncoding RNAs that arise from either mature transfer RNAs (tRNAs) or their precursors. One important category of tRFs comprises the tRNA halves, which are generated through cleavage at the anticodon. A given tRNA typically gives rise to several co-expressed 5’-tRNA halves (5′-tRHs) that differ in the location of their 3′ ends. These 5′-tRHs, even though distinct, have traditionally been treated as indistinguishable from one another due to their near-identical sequences and lengths. We focused on co-expressed 5′-tRHs that arise from the same tRNA and systematically examined their exact sequences and abundances across 10 different human tissues. To this end, we manually curated and analyzed several hundred human RNA-seq datasets from NCBI’s Sequence Run Archive (SRA). We grouped datasets from the same tissue into their own collection and examined each group separately. We found that a given tRNA produces different groups of co-expressed 5′-tRHs in different tissues, different cell lines, and different diseases. Importantly, the co-expressed 5′-tRHs differ in their sequences, absolute abundances, and relative abundances, even among tRNAs with near-identical sequences from the same isodecoder or isoacceptor group. The findings suggest that co-expressed 5′-tRHs that are produced from the same tRNA or closely related tRNAs have distinct, context-dependent roles. Moreover, our analyses show that cell lines modeling the same tissue type and disease may not be interchangeable when it comes to experimenting with tRFs. Full article
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Review

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20 pages, 1349 KiB  
Review
A Review of IsomiRs in Colorectal Cancer
Non-Coding RNA 2023, 9(3), 34; https://doi.org/10.3390/ncrna9030034 - 07 Jun 2023
Cited by 1 | Viewed by 1483
Abstract
As advancements in sequencing technology rapidly continue to develop, a new classification of microRNAs has occurred with the discovery of isomiRs, which are relatively common microRNAs with sequence variations compared to their established template microRNAs. This review article seeks to compile all known [...] Read more.
As advancements in sequencing technology rapidly continue to develop, a new classification of microRNAs has occurred with the discovery of isomiRs, which are relatively common microRNAs with sequence variations compared to their established template microRNAs. This review article seeks to compile all known information about isomiRs in colorectal cancer (CRC), which has not, to our knowledge, been gathered previously to any great extent. A brief overview is given of the history of microRNAs, their implications in colon cancer, the canonical pathway of biogenesis and isomiR classification. This is followed by a comprehensive review of the literature that is available on microRNA isoforms in CRC. The information on isomiRs presented herein shows that isomiRs hold great promise for translation into new diagnostics and therapeutics in clinical medicine. Full article
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