Long-read RNA sequencing can probe organelle genome pervasive transcription DOI
Matheus Sanitá Lima, Douglas Silva Domingues, Alexandre Rossi Paschoal

et al.

Briefings in Functional Genomics, Journal Year: 2024, Volume and Issue: 23(6), P. 695 - 701

Published: June 17, 2024

Abstract 40 years ago, organelle genomes were assumed to be streamlined and, perhaps, unexciting remnants of their prokaryotic past. However, the field genomics has exposed an unparallel diversity in genome architecture (i.e. size, structure, and content). The transcription these eccentric can just as elaborate – are pervasively transcribed into a plethora RNA types. while protein-coding genes known produce polycistronic transcripts that undergo heavy posttranscriptional processing, nature noncoding transcriptomes is still poorly resolved. Here, we review how wet-lab experiments second-generation sequencing data short reads) have been useful determine certain types RNAs, particularly RNAs. We then explain third-generation (long-read) RNA-Seq represent new frontier transcriptomics. show public repositories (e.g. NCBI SRA) already contain enough for inter-phyla comparative studies argue biologists benefit from such data. discuss prospects using publicly available organelle-focused examine challenges approach. highlight lack comprehensive database dedicated genomics/transcriptomics major impediment development with implications basic applied science.

Language: Английский

Comprehensive analysis of microRNA (miRNA) in cancer cells DOI Creative Commons

Naghmana Kanwal,

Othman Rashid Al Samarrai, Haider Majid Haider Al-Zaidi

et al.

Cellular Molecular and Biomedical Reports, Journal Year: 2023, Volume and Issue: 3(2), P. 89 - 97

Published: April 11, 2023

MicroRNAs (miRNA) are a group of small non-coding RNAs that regulate gene expression at the RNA level. have positive regulatory effects on protein translation processes and often induce their performance by binding to 3'-UTR mRNA region. Also, microRNAs involved in various cellular processes, including development, cell division, signaling, growth, generally play an effective role cycle control physiological pathology. Several studies confirm important initiation progression cancer, many them act as oncogenes tumor suppressors. On other hand, stimulating factors can biomarkers diagnosis prognosis types cases, occurrence mutations open-reading templates lead cancer. also regulating expression. Biological shown about 30% all genes majority genetic pathways regulated microRNAs. In general, target molecules potential biological goals for primary screening, targeted treatment, pharmaceutical resistance, identifying provides clear prospect better understanding leading

Language: Английский

Citations

77
CircRNAs in colorectal cancer: potential biomarkers and therapeutic targets DOI Creative Commons

Yuying Zhang,

Jingyan Luo,

Weikang Yang

et al.

Cell Death and Disease, Journal Year: 2023, Volume and Issue: 14(6)

Published: June 9, 2023

Abstract Globally, colorectal cancer (CRC) is the third most prevalent and second leading cause of cancer-related deaths. Circular RNAs (circRNAs) are single-stranded RNA with covalently closed-loop structures highly stable, conserved, abundantly expressed in various organs tissues. Recent research found abnormal circRNA expression CRC patients’ blood/serum, cells, tissues, exosomes. Furthermore, mounting data demonstrated that circRNAs crucial to development CRC. CircRNAs have been shown exert biological functions by acting as microRNA sponges, RNA-binding protein regulators gene splicing transcription, protein/peptide translators. These characteristics make potential markers for diagnosis prognosis, therapeutic targets, circRNA-based therapies. However, further studies still necessary improve understanding roles mechanisms In this review, up-to-date on role was examined, focusing their application targeted therapy, which would advance knowledge progression

Language: Английский

Citations

67
Long Non-Coding RNAs of Plants in Response to Abiotic Stresses and Their Regulating Roles in Promoting Environmental Adaption DOI Creative Commons
Hong Yang,

Yuting Cui,

Yanrong Feng

et al.

Cells, Journal Year: 2023, Volume and Issue: 12(5), P. 729 - 729

Published: Feb. 24, 2023

Abiotic stresses triggered by climate change and human activity cause substantial agricultural environmental problems which hamper plant growth. Plants have evolved sophisticated mechanisms in response to abiotic stresses, such as stress perception, epigenetic modification, regulation of transcription translation. Over the past decade, a large body literature has revealed various regulatory roles long non-coding RNAs (lncRNAs) their irreplaceable functions adaptation. LncRNAs are recognized class ncRNAs that longer than 200 nucleotides, influencing variety biological processes. In this review, we mainly focused on recent progress lncRNAs, outlining features, evolution, lncRNAs drought, low or high temperature, salt, heavy metal stress. The approaches characterize function how they regulate responses were further reviewed. Moreover, discuss accumulating discoveries regarding memory well. present review provides updated information directions for us potential future.

Language: Английский

Citations

47
Non-coding RNAs and neuroinflammation: implications for neurological disorders DOI Creative Commons
Yvonne Chen,

Julia Mateski,

Linda Gerace

et al.

Experimental Biology and Medicine, Journal Year: 2024, Volume and Issue: 249

Published: Feb. 28, 2024

Neuroinflammation is considered a balanced inflammatory response important in the intrinsic repair process after injury or infection. Under chronic states of disease, injury, infection, persistent neuroinflammation results heightened presence cytokines, chemokines, and reactive oxygen species that result tissue damage. In CNS, surrounding microglia normally contain macrophages other innate immune cells perform active surveillance. The resulting cytokines produced by these affect growth, development, responsiveness present both white gray matter regions CNS. Controlling levels ultimately improves neurocognitive function lesions associated with neurologic disease. MicroRNAs (miRNAs) are master regulators genome subsequently control activity responses crucial sustaining robust acute immunological towards an infection while dampening pathways chemokines neuroinflammation. Numerous reports have directly implicated miRNAs controlling abundance interleukins, TGF-B, NF-kB, toll-like receptor-signaling intrinsically linked development neurological disorders such as Parkinson’s, ALS, epilepsy, Alzheimer’s, neuromuscular degeneration. This review focused on discussing role play regulating initiating states, many which maintain level and/or neuron-specific secondary messengers. Dysregulated microglia, astrocytes, oligodendrocytes, epididymal cells, contribute to overall glial-specific niche impacts neuronal conductivity, signaling action potentials, neurotransmitter robustness, neuron-neuron specific communication, neuron-muscular connections. Understanding regulate microglial activation step forward developing non-coding RNA-based therapeutics treat potentially correct behavioral cognitive deficits typically found patients suffering from

Language: Английский

Citations

14
CircRNA-mediated ceRNA regulatory networks: transcriptomic insights into obesity type 2 diabetes progression and treatment strategies DOI Creative Commons

Xianjie Zhen,

Ruying Hu, Nannan Liu

et al.

Diabetology & Metabolic Syndrome, Journal Year: 2025, Volume and Issue: 17(1)

Published: Feb. 14, 2025

The aim of this study was to deeply explore the pathogenesis obesity type 2 diabetes mellitus (O-T2DM) and search for potential biomarkers through high-throughput RNA sequencing technology. included 15 patients with O-T2DM healthy controls, peripheral blood samples were collected transcriptome analysis. results showed that compared control group, there 442 circRNAs 2756 mRNAs significant differential expression in group. Through weighted gene co-expression network analysis (WGCNA) pathway enrichment analysis, it found differentially expressed mainly enriched signaling pathways such as T cell receptor, senescence, cytotoxicity mediated by NK cells, IL-17, lipids atherosclerosis, oxidative phosphorylation activated, apoptosis inhibited. Based on ceRNA theory, a regulatory constructed, key hsa_circ_0060614 screened out, which may regulate MT2A adsorbing hsa-mir-4668-3p, levels three significantly increased patients. This provides new perspective research molecular mechanism an important theoretical basis development personalized treatment precision medicine it.

Language: Английский

Citations

1
Physiological and pathological functions of circular RNAs in the nervous system DOI Creative Commons
Min Zhou,

Shi Li,

Chuan Huang

et al.

Neural Regeneration Research, Journal Year: 2023, Volume and Issue: 19(2), P. 342 - 349

Published: July 7, 2023

Abstract Circular RNAs (circRNAs) are a class of covalently closed single-stranded that expressed during the development specific cells and tissues. CircRNAs play crucial roles in physiological pathological processes by sponging microRNAs, modulating gene transcription, controlling activity certain RNA-binding proteins, producing functional peptides. A key focus research at present is functionality circRNAs nervous system several advances have emerged over last 2 years. However, precise role has yet to be comprehensively reviewed. In this review, we first summarize recently described brain development, maturity, aging. Then, on involvement various diseases central system, such as cancer, chronic neurodegenerative diseases, acute injuries neuropathic pain. better understanding will help us develop potential diagnostic, prognostic, therapeutic strategies treat system.

Language: Английский

Citations

21
Mitochondrial nucleic acids in innate immunity and beyond DOI Creative Commons
Jimin Yoon, Sujin Kim, Mihye Lee

et al.

Experimental & Molecular Medicine, Journal Year: 2023, Volume and Issue: 55(12), P. 2508 - 2518

Published: Dec. 1, 2023

Abstract Mitochondria participate in a wide range of cellular processes. One essential function mitochondria is to be platform for antiviral signaling proteins during the innate immune response viral infection. Recently, studies have revealed that mitochondrion-derived DNAs and RNAs are recognized as non-self molecules act immunogenic ligands. More importantly, cytosolic release these mitochondrial nucleic acids (mt-NAs) closely associated with pathogenesis human diseases accompanying aberrant activation. The (mtDNAs) via BAX/BAK activation and/or VDAC1 oligomerization activates inflammasome assembly. In addition, double-stranded (mt-dsRNAs) sensed by pattern recognition receptors cytosol induce type I interferon expression initiate apoptotic programs. Notably, mt-NAs also mediate adipocyte differentiation contribute mitogenesis thermogenesis. this review, we summarize recent pathways regulated mt-NAs, emerging physiological roles mt-NAs.

Language: Английский

Citations

17
Mitochondria in biology and medicine – 2023 DOI
B. Disha, Rohan Peter Mathew, Ashwin Dalal

et al.

Mitochondrion, Journal Year: 2024, Volume and Issue: 76, P. 101853 - 101853

Published: Feb. 28, 2024

Language: Английский

Citations

8
The Roles of CircRNAs in Mitochondria DOI Creative Commons
Donghong Liu, Xinyu Zhou,

Yida He

et al.

Journal of Cancer, Journal Year: 2024, Volume and Issue: 15(9), P. 2759 - 2769

Published: Jan. 1, 2024

Mitochondria participate in varieties of cellular events.It is widely accepted that human mitochondrial genome encodes 13 proteins, 2 rRNAs, and 22 tRNAs.Gene variation derived from nuclear cannot completely explain diseases.The advent high-throughput sequencing coupled with novel bioinformatic analyses decode the complexity mitochondria-derived transcripts.Recently, circular RNAs (circRNAs) both have been found to be located at mitochondria.Studies about roles molecular mechanisms underlying trafficking nucleus encoded circRNAs mitochondria or cytoplasm mammals are only beginning emerge.These associated a variety diseases, especially cancers.Here, we discuss emerging field mitochondria-located by reviewing their identification, expression patterns, regulatory roles, functional mechanisms.Mitochondria-located physiology pathology.We also highlight future perspectives challenges studying circRNAs, as well potential biomedical applications.

Language: Английский

Citations

6
RNA G-quadruplex in functional regulation of noncoding RNA: Challenges and emerging opportunities DOI Creative Commons

Vinodh J. Sahayasheela,

Hiroshi Sugiyama

Cell chemical biology, Journal Year: 2023, Volume and Issue: 31(1), P. 53 - 70

Published: Oct. 30, 2023

Language: Английский

Citations

12