Aberrant splicing in human cancer: An RNA structural code point of view

Apostolidi, Maria; Stamatopoulou, Vassiliki

doi:10.3389/fphar.2023.1137154

Cited by 3 publications

(2 citation statements)

References 97 publications

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“…The accurate regulation of AS needs the cooperation of trans-factors and cis-elements [26,34]. Increasing evidences show that additional mechanisms help generate plastic AS events with high specificity and fidelity, including the regulators of spliceosome assembly, chromatin remodeling, epigenetic modification, RNA structure and so on [2,24].…”

Section: Introductionmentioning

confidence: 99%

The Importance of Stiff Change of U(T) Content Around Splicing Sites in Efficient Plant Intron Splicing -- A Case Study in Rice

Zhang,

Wang

et al. 2023

CBB

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Pre-mRNAs splicing is one of the fundamental process which generates multiple transcripts from a single gene, contributing to transcriptome and proteome diversity. AS is regulated by the cooperation of trans-factors and cis-elements. In plants, extensive alternative splicing occurs not only in tissue-specific manner but also in response to stress conditions. Intron retention is the most predominant splicing type. However, the cis-elements regulating intron retention are still ambiguous in plants, especially under environmental stresses. This study aimed to elucidate the cis-elements underlying intron retention in plants under adverse enrironments. Using RNA-seq data of rice cultivars IRAT109 and ZS97 under drought environments, we compared the sequence characteristics between constitutive and retained introns. The results show that the main AS types include intron retention (IR), alternative acceptor sites (AA), alternative donor sites (AD) and cassette exon (exon skipping, ES). Among of them, IR was the prevelent pattern with frequencies of 30.8-31.2%. Motif analysis of 5' and 3' 200bp intron sequences found rich U(T) in the motifs for both constitutive and retained introns. By further analysis of base composition of sequences flanking splice sites, we detected a notable difference in U(T) content between introns and their neighboring exons in constitutive introns, but not in retained introns. The results in this study suggested that the lack of significant changes in U(T) content between retained introns and neighboring exons might be a potential cis feature of intron retention.

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Section: Introductionmentioning

confidence: 99%

The Importance of Stiff Change of U(T) Content Around Splicing Sites in Efficient Plant Intron Splicing -- A Case Study in Rice

Zhang,

Wang

et al. 2023

CBB

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“…This was of course the net that saved my fall. Many mutations and compensatory mutations later, the model was partially proven [11], and secondary structures of the primary transcript are now believed to have important roles in alternative splicing [12][13][14][15].…”

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confidence: 99%

Memories of a young student: the early days of splicing regulation with François Gros

Libri

2024

C R Biol.

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I joined the laboratory of François Gros as a young student in the mid-1980s and worked on the characterization of the β-tropomyosin gene in chicken and the regulation of alternative splicing of its transcript, under the supervision of Marc Fiszman. In particular, I was interested in how secondary structures of the RNA influence the recognition of exons specifically used in muscle cells. I will recall a few memories on how interacting with François on this project shaped my perception of the scientific process and of the relationships between models and data. Later I worked on many aspects of RNA biology, from transcription to mRNP biogenesis and non-coding RNAs.

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RNA structure in alternative splicing regulation: from mechanism to therapy

Bao,

Wang,

et al. 2024

ABBS

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Alternative splicing is a highly intricate process that plays a crucial role in post-transcriptional regulation and significantly expands the functional proteome of a limited number of coding genes in eukaryotes. Its regulation is multifactorial, with RNA structure exerting a significant impact. Aberrant RNA conformations lead to dysregulation of splicing patterns, which directly affects the manifestation of disease symptoms. In this review, the molecular mechanisms of RNA secondary structure-mediated splicing regulation are summarized, with a focus on the complex interplay between aberrant RNA conformations and disease phenotypes resulted from splicing defects. This study also explores additional factors that reshape structural conformations, enriching our understanding of the mechanistic network underlying structure-mediated splicing regulation. In addition, an emphasis has been placed on the clinical role of targeting aberrant splicing corrections in human diseases. The principal mechanisms of action behind this phenomenon are described, followed by a discussion of prospective development strategies and pertinent challenges.

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Aberrant splicing in human cancer: An RNA structural code point of view

Cited by 3 publications

References 97 publications

The Importance of Stiff Change of U(T) Content Around Splicing Sites in Efficient Plant Intron Splicing -- A Case Study in Rice

The Importance of Stiff Change of U(T) Content Around Splicing Sites in Efficient Plant Intron Splicing -- A Case Study in Rice

Memories of a young student: the early days of splicing regulation with François Gros

RNA structure in alternative splicing regulation: from mechanism to therapy

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