Skip Content
You are currently on the new version of our website. Access the old version .

Non-Coding RNA

Non-Coding RNA is an international, peer-reviewed, open access journal on non-coding RNA research dealing with elucidating the structure, function and biology of regulatory non-coding RNAs, and published bimonthly online by MDPI. 

Indexed in PubMed | Quartile Ranking JCR - Q2 (Genetics and Heredity)

All Articles (592)

Mechanisms at the Intersection of lncRNA and m6A Biology

  • Samuel J. Gonzalez,
  • Edgardo Linares and
  • Aaron M. Johnson
  • + 1 author

This review provides a thorough survey of long noncoding RNAs that bear the RNA modification N6-methyladenosine (m6A) and current work to understand the resulting mechanistic and biological consequences. We give an overview of lncRNA and m6A biology first, describing the writers, erasers, and readers of m6A and their targeting of lncRNAs. Next, we give an in-depth review of the field of nuclear lncRNAs that regulate chromatin and their regulation via m6A. We then describe the growing appreciation of liquid–liquid phase separation properties in lncRNA and m6A biology. Finally, we cover examples of cytoplasmic lncRNAs regulated by m6A. Overall, this review aims to emphasize how epitranscriptomics influences noncoding RNA mechanisms to provide additional layers of regulation, integrated into downstream biological processes.

31 January 2026

General m6A machinery. The primary writer of m6A within mammalian cells is Mettl3/14, in complex with many regulatory subunits (WTAP, VIRMA, AC3H13, HAKAI, and RBM15) that make up the MACOM. Deposition of m6A marks on lncRNAs occurs co-transcriptionally. Readers of m6A can preferentially localize to the nucleus or the cytoplasm, coming in two main types: canonical readers and indirect readers. Canonical readers directly bind m6A, while indirect readers bind the RNA sequence that becomes available due to changes in the secondary structure of the RNA upon m6A methylation. The two primary erasers of m6A are ALKBH5 and FTO; ALKBH5 functions primarily in the nucleus, while FTO functions primarily in the cytoplasm. Created in BioRender. Gonzalez, S. (2025) https://BioRender.com/i0u2r64 (accedd on 21 November 2025).

Background/Objectives: In severe peripheral artery disease (PAD) with limb ischemia, hypercholesterolemia (HC) is associated with impaired neovascularization. Extracellular vesicles (EVs) are present within ischemic muscles, and they contain microRNAs (miRs) involved in several biological functions, including angiogenesis and neovascularization. Methods: We used a mouse model of PAD and compared the response to hindlimb ischemia in hypercholesterolemic ApoE−/− vs. normocholesterolemic mice. Next-generation sequencing (NGS) was used to perform full miR expression profiling in ischemic skeletal muscles and in EVs of varying sizes—large EVs (lEVs) and small EVs (sEVs)—within these muscles. Results: We identified several miRs with potential pro-angiogenic effects (angiomiRs) that are reduced by HC in lEVs (Let-7b-5p, miR-151-3p, Let-7c-5p) or sEVs (miR-21a-5p, miR-196b-5p, miR-340-5p). As proof of principle, we showed that the overexpression of Let-7b-5p in lEVs, or miR-21a-5p in sEVs, can significantly increase the angiogenic capacity of these EVs in vitro. HC also impaired the enrichment of specific angiomiRs in lEVs (miR-100-5p), sEVs (miR-142a-3p), or in both lEVs and sEVs (miR-146b-5p). In silico approaches, including the prediction of miR targets, pathway unions, and gene unions, identified the resulting predictive effects of HC-modulated miRs in EVs on processes with key roles in the modulation of angiogenesis and neovascularization, such as the regulation of the actin cytoskeleton and focal adhesion and the HIF-1, MAPK, AMPK, and PI3K-Akt signaling pathways. Conclusions: Our results constitute an important first step towards the identification of specific miRs that could be targeted to improve EV angiogenic function in hypercholesterolemic conditions and reduce tissue ischemia in patients with severe PAD.

26 January 2026

Effect of hypercholesterolemia on miR expression profile in whole ischemic skeletal muscles. (A,B). Expression profile of all miRs (A) or 50 most expressed miRs (B) isolated in whole ischemic skeletal muscles of hypercholesterolemic ApoE−/− mice (pool of 3) or normocholesterolemic control mice (CTL, pool of 4). (C). Fold change representation of effect of hypercholesterolemia on 50 most expressed miRs in ischemic muscles. (D). Representation of 4 miRs that were reduced by more than 20% in hypercholesterolemic conditions, including 1 potential angiomiR (miR-151-3p).

The Role of microRNAs as Potential Biomarkers in Diffuse Large B-Cell Lymphoma

  • Eirini Panteli,
  • Epameinondas Koumpis and
  • Eleftheria Hatzimichael
  • + 5 authors

Diffuse large B-cell lymphoma (DLBCL) is the most common and clinically aggressive subtype of non-Hodgkin lymphoma (NHL). While novel therapies such as rituximab and polatuzumab vedotin have led to improved outcomes, approximately 35% of patients eventually develop relapsed or refractory disease. MicroRNAs (miRNAs), a class of endogenous single-stranded RNAs approximately 22 nucleotides in length, play a pivotal role in the regulation of gene expression at the post-transcriptional level through interactions with complementary target RNAs and contribute significantly to the development, progression, and treatment response of DLBCL. Oncogenic miRNAs, such as miR-155, miR-21, and the miR-17–92 cluster, promote proliferation, survival, immune evasion, and therapy resistance by modulating pathways including PI3K/AKT, NF-κB, and MYC. Conversely, tumor-suppressive miRNAs such as miR-34a, miR-144, miR-181a, and miR-124-3p inhibit oncogene activity and enhance apoptosis, with their loss often associated with adverse outcomes. Among these, miR-155 and miR-21 are particularly well studied, playing central roles in both tumor progression and remodeling of the tumor microenvironment. This review summarizes current evidence on the biological and clinical relevance of miRNAs in DLBCL, emphasizing their diagnostic and prognostic potential.

7 January 2026

miRNAs are transcribed by RNA polymerase II as primary transcripts (pri-miRNAs), which are then processed in the nucleus by the enzyme Drosha along with its cofactor DGCR8 into precursor miRNAs (pre-miRNAs). These pre-miRNAs are transported to the cytoplasm via exportin 5, where they associate with the Dicer/TRBP complex and are cleaved into short double-stranded RNA molecules. One strand of this miRNA duplex is then incorporated into the Argonaute protein to form the RNA-induced silencing complex (RISC). RISC then binds to specific target mRNAs, leading to their degradation, destabilization, or inhibition of translation. In addition to the canonical pathway, miRNAs can be generated through non-canonical biogenesis routes, including Drosha-independent mechanisms (where pri-miRNAs are processed by the spliceosome) as well as Dicer-independent pathways. Abbreviations: Ago2: Argonaute 2, DGCR8: DiGeorge syndrome critical region 8, RISC: RNA-induced silencing complex, TRBP: Transactivation response element RNA-binding protein. Created in https://BioRender.com (accessed on 8 July 2025). Modified from Seyhan, Attila 2023 [51].

Background/Objectives: Bone marrow mesenchymal stromal cells (MSCs) are therapeutic cells that adopt an immunomodulatory phenotype when exposed to pro-inflammatory cytokines. Recent research efforts uncovered that many therapeutic benefits of MSCs can be attributed to the secretion of extracellular vesicles (EVs) such as exosomes, small membrane vesicles of endocytic origin present in the cellular secretome. EVs’ formation and release are impacted by the autophagy pathway, which recycles proteins and organelles via lysosomal degradation. Methods: To evaluate how modulation of autophagy affects properties of MSC EVs enriched in exosomes under pro-inflammatory conditions, we treated the cells with either tamoxifen (TX) or chloroquine (CQ), two drugs known to stimulate or inhibit autophagy, respectively, together with IFNγ. MSC EVs enriched in exosomes were then purified from serum-free media, and their immunoregulatory properties were evaluated ex vivo using activated CD4 T cells; small RNA sequencing was also conducted to determine EVs’ microRNA content. Results: Our data indicate that MSCs treated with CQ + IFNγ yield EVs that possess somewhat higher capacity to decrease T cell proliferation compared to other EVs. Small RNA sequencing revealed that, although similar microRNAs were found in EVs isolated from all treated cells, the treatments exerted more effect on the levels of multiple microRNAs that are known to regulate either cancer or inflammation-related biological pathways in target cells. Conclusions: Overall, we conclude that the co-treatment of MSCs with TX or CQ in the presence of pro-inflammatory cytokine IFNγ has the potential to modulate microRNA content of EVs, potentially affecting biological properties of such EVs and their effect on target cells.

24 December 2025

TX or CQ treatments cause accumulation of autophagic vehicles in MSCs without cytotoxicity or upregulation of apoptotic markers. MSCs were treated as indicated for 48 h to evaluate markers of apoptosis and autophagy (n = 3–4). (A) Assessment of autophagic vehicles using Cyto-ID staining of autophagic vesicles by flow cytometry and its quantification (bottom); (B) Annexin V and 7AAD staining of cells after exposure to TX, CQ, IFNg, or combinations (left) and light microscopy assessment of cells upon treatment (bar = 1000 mm); staurosporine was used as a positive control. Circles around bar graphs indicate individual data points (n = 3–5). Error bars represent the standard error between the replicates. n.s.: no statistical significance between the groups to the left of the line.

News & Conferences

Issues

Open for Submission

Editor's Choice

Get Alerted

Add your email address to receive forthcoming issues of this journal.

XFacebookLinkedIn
Non-Coding RNA - ISSN 2311-553X