Research Topic

Intron-centric transcription and its role in normal physiology and disease

About this Research Topic

Introns have long been kept in the famous “junk DNA” drawer. Because they are eliminated to allow formation of messenger RNA and are inherently non-coding, they have often been neglected in high throughput analyses. However, and maybe against all odds, high sequence conservation among homologous introns of closely related species suggests functional constraints on intronic sequences throughout evolution. Many studies have now added to the weight of evidence showing that introns can serve a considerable range of biological functions such as increasing protein or ncRNA diversity by intron retaining in long mRNA or ncRNA isoforms, or act as precursor for miRNAs.

Introns represent almost half of the human genome, yet they are generally eliminated from the pre-mRNA. Their role has been widely neglected and intron retention (IR) was long considered as a fault in the splicing mechanism. In opposition with this belief, IR affects over 80% of all protein coding genes, making IR a major regulator of gene expression.

Interestingly, there are cases where small regulatory RNAs are directly produced by way of splicing of the intron from the host transcript and thus, are strictly dependant on both transcription and splicing of the host gene. The most studied examples are the small nucleolar RNAs (snoRNAs) that are all by-products of intron splicing.

In addition, functional annotation of introns is required to understand their role in shaping transcriptional outputs and how perturbations to their processing can lead to disease. Indeed, nearly 30% of splicing mutations that are associated with cancer affect IR and IR is a well-known mechanism of tumour-suppressor genes inactivation. The release of functional elements derived from introns (mirtrons, snoRNAs...) is also perturbed in splicing diseases such as muscular dystrophy type 1, cancer and various neuropathies.

We propose a Research Topic in Frontiers in Genetic section RNA that is specifically dedicated to the publication of manuscripts dealing with introns as a source of transcriptional output involved in normal physiology and pathophysiology.

Potential emphasis would focus on different categories of RNA modifications, and include, but are not limited to, the following:

- What are the various functions of introns and what is the proportion of functional introns?
- Introns as precursor of small non-coding RNAs
- Introns with enzymatic activity; no need for proteins anymore?
- The fate of retained introns
- The fate of the introns that are spliced
- Introns and transcriptional output, enrichment or regulation?
- Nested intronic genes, what definition for an intron that contains other exonic sequences...
- Evolution of intronic regions during evolution
- Half-life of intron in cell (retained or spliced)
- How do we define introns: “are introns non-coding RNA or untranslated RNA?”
- Role of intron in disease


Keywords: Antisense RNA, BioInformatic, Genomic, intron, lncRNA, miRNA, snoRNA, Multifonctional RNA, ncRNA, RNA Splicing, RNA Stability, sncRNA, Untranslated RNA


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

Introns have long been kept in the famous “junk DNA” drawer. Because they are eliminated to allow formation of messenger RNA and are inherently non-coding, they have often been neglected in high throughput analyses. However, and maybe against all odds, high sequence conservation among homologous introns of closely related species suggests functional constraints on intronic sequences throughout evolution. Many studies have now added to the weight of evidence showing that introns can serve a considerable range of biological functions such as increasing protein or ncRNA diversity by intron retaining in long mRNA or ncRNA isoforms, or act as precursor for miRNAs.

Introns represent almost half of the human genome, yet they are generally eliminated from the pre-mRNA. Their role has been widely neglected and intron retention (IR) was long considered as a fault in the splicing mechanism. In opposition with this belief, IR affects over 80% of all protein coding genes, making IR a major regulator of gene expression.

Interestingly, there are cases where small regulatory RNAs are directly produced by way of splicing of the intron from the host transcript and thus, are strictly dependant on both transcription and splicing of the host gene. The most studied examples are the small nucleolar RNAs (snoRNAs) that are all by-products of intron splicing.

In addition, functional annotation of introns is required to understand their role in shaping transcriptional outputs and how perturbations to their processing can lead to disease. Indeed, nearly 30% of splicing mutations that are associated with cancer affect IR and IR is a well-known mechanism of tumour-suppressor genes inactivation. The release of functional elements derived from introns (mirtrons, snoRNAs...) is also perturbed in splicing diseases such as muscular dystrophy type 1, cancer and various neuropathies.

We propose a Research Topic in Frontiers in Genetic section RNA that is specifically dedicated to the publication of manuscripts dealing with introns as a source of transcriptional output involved in normal physiology and pathophysiology.

Potential emphasis would focus on different categories of RNA modifications, and include, but are not limited to, the following:

- What are the various functions of introns and what is the proportion of functional introns?
- Introns as precursor of small non-coding RNAs
- Introns with enzymatic activity; no need for proteins anymore?
- The fate of retained introns
- The fate of the introns that are spliced
- Introns and transcriptional output, enrichment or regulation?
- Nested intronic genes, what definition for an intron that contains other exonic sequences...
- Evolution of intronic regions during evolution
- Half-life of intron in cell (retained or spliced)
- How do we define introns: “are introns non-coding RNA or untranslated RNA?”
- Role of intron in disease


Keywords: Antisense RNA, BioInformatic, Genomic, intron, lncRNA, miRNA, snoRNA, Multifonctional RNA, ncRNA, RNA Splicing, RNA Stability, sncRNA, Untranslated RNA


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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Submission Deadlines

14 July 2018 Abstract
28 September 2018 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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Topic Editors

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Submission Deadlines

14 July 2018 Abstract
28 September 2018 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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