Intron Retention (IR): RNA Processing, Post-Transcriptional Regulation in Stress Response, Genomic Function
A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".
Deadline for manuscript submissions: 30 November 2026 | Viewed by 1097
Special Issue Editor
Special Issue Information
Dear Colleagues,
Intron retention (IR) has emerged as a prevalent and regulated mode of RNA processing rather than a mere splicing byproduct. Across diverse stress conditions—oxidative, genotoxic, inflammatory, metabolic, proteotoxic, hypoxic, and mechanical—IR can reshape gene output by modulating nuclear detention, mRNA stability, translation competence, and the balance between productive and non-productive isoforms. Increasing evidence links stress-responsive IR programs to cell-fate decisions, immune adaptation, tissue regeneration, aging, and disease, including cancer, neurodegeneration, cardiometabolic disorders, and infection.
This Special Issue welcomes original research, reviews, and methodological advances that elucidate mechanisms, functions, and translational implications of IR. We particularly encourage studies integrating multi-omics and modern transcriptomics (long-read sequencing, single-cell/spatial approaches), quantitative modeling, and rigorous computational frameworks for IR detection and interpretation. This Special Issue will cover a wide range of research topics, such as the following:
- Mechanistic control of IR under stress: co-transcriptional splicing kinetics, Pol II elongation, chromatin/epigenetic coupling, and spliceosome dynamics.
- Neuropsychiatric and neurodegenerative applications: IR-based biomarkers for depression and dementia, including patient stratification and treatment-response monitoring.
- Stress signaling to splicing: ISR/ATF4, MAPK, mTOR, NF-κB, and post-translational regulation of splicing factors/RBPs.
- IR as an RNA output gate: nuclear detention/export licensing, RNA surveillance (NMD), mRNA stability, and translation competence.
- Cis–trans logic of IR: regulatory elements, RNA structure, and SR/hnRNP networks shaping IR propensity and specificity.
- Subcellular RNA fate programs: stress granules/P-bodies, phase separation, and translational reprogramming in acute vs chronic stress.
- Proteostasis, redox, and metabolism: coupling of IR to UPS/ER stress, mitochondrial function, oxidative stress, and metabolic remodeling.
- Genome maintenance links: IR responses to DNA damage/replication stress and consequences for cell-cycle and genome stability.
- Mechanobiology and IR: cytoskeletal tension, focal-adhesion pathways, nuclear lamina mechanics, and mechanotransduction impacts on RNA processing.
- Immune context: IR programs in thymus/spleen/lymph nodes and immune-state transitions (tolerance, inflammation, immunometabolism).
Dr. Norihiro Okada
Guest Editor
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Keywords
- intron retention
- alternative splicing
- RNA processing
- stress response
- post-transcriptional regulation
- nuclear export
- nonsense-mediated decay
- RNA surveillance
- RNA-binding proteins
- long-read sequencing
- single-cell transcriptomics
- biomarker
- systems biology
- disease mechanisms
- proteostasis
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