Alternative Splicing in Human Physiology and Disease

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (18 October 2022) | Viewed by 95467

Special Issue Editors


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Guest Editor
Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
Interests: colorectal cancer; leukemia; tumor biomarkers; anticancer drugs; apoptosis; BCL2 family; alternative splicing; kallikrein-related peptidases (KLKs); nanopore sequencing; next-generation sequencing (NGS)
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Guest Editor
Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
Interests: alternative splicing; RNA biology; circular RNAs; pre-mRNAs; post-transcriptional analysis; apoptosis; BCL2 family; colorectal adenocarcinoma; molecular biomarkers
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Alternative splicing, first proposed by Gilbert in 1978, allows multi-exon genes to produce multiple splice variants. Several of the linear transcripts encode protein isoforms with distinct amino acid sequence, structure, and function(s). Alternatively spliced transcripts are generated from a single gene through selection of cassette exons, mutually exclusive exons, retained introns, alternative 3′ or 5′ splice sites, and/or usage of alternative promoters or polyadenylation sites. High-throughput sequencing has revolutionized transcriptomics, revealing that the post-transcriptional maturation of primary transcripts from more than 95% of human multi-exon genes involves alternative splicing. Examples of hundreds of alternative splicing events from a single gene have also been described. Besides linear transcripts, splicing generates also circular RNAs (circRNAs). They were initially discovered in RNA viroid analysis during the 1970s but were characterized as by-products of alternative splicing.

Alternative splice variants may contribute to the etiology of many human diseases, including cancer, since protein isoforms that arise by translation of splice variants often contain additional functional domains or lack some of the structural motifs of the classical protein isoform and consequently acquire new properties or are deprived of some of them, respectively. Furthermore, circRNAs—a neglected RNA type that derives from back-splicing—have been shown to play a pivotal role in the initiation and progression of cancer. From a clinical aspect, alternatively spliced linear and circular transcripts are highly important in oncology, as they may constitute promising drug targets or serve as molecular biomarkers for cancer diagnosis and/or prognosis.

This Special Issue aims to provide information to the readers regarding the mechanisms and/or products of alternative splicing in human physiological and pathological states, with emphasis on cancer, neurodegenerative diseases, and other diseases. Authors are encouraged to submit their original research studies concerning this topic. Review articles will also be taken into consideration. The Guest Editors are also willing to evaluate manuscripts describing other aspects of alternative splicing proposed by the authors. We hope that this Special Issue regarding the identity, biological role, and/or clinical utility of alternatively spliced linear and circular transcripts of human genes will attract the interest of the readers of this journal.

Dr. Christos K. Kontos
Dr. Pinelopi I. Artemaki
Guest Editors

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Keywords

  • alternative splicing
  • splice variants
  • spliceosome
  • circular RNA (circRNA)
  • long non-coding RNA (lncRNA)
  • pre-messenger RNA (pre-mRNA)
  • transcriptomics
  • cancer pathobiology
  • molecular biomarkers
  • therapeutic targets

Published Papers (23 papers)

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Editorial

Jump to: Research, Review

4 pages, 178 KiB  
Editorial
Alternative Splicing in Human Physiology and Disease
by Pinelopi I. Artemaki and Christos K. Kontos
Genes 2022, 13(10), 1820; https://doi.org/10.3390/genes13101820 - 8 Oct 2022
Cited by 2 | Viewed by 1519
Abstract
Since the discovery of alternative splicing in the late 1970s, a great number of alternatively spliced transcripts have emerged; this number has exponentially increased with the advances in transcriptomics and massive parallel sequencing technologies [...] Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)

Research

Jump to: Editorial, Review

19 pages, 3386 KiB  
Article
Identification of Novel Circular RNAs of the Human Protein Arginine Methyltransferase 1 (PRMT1) Gene, Expressed in Breast Cancer Cells
by Maria Papatsirou, Marios A. Diamantopoulos, Katerina Katsaraki, Dimitris Kletsas, Christos K. Kontos and Andreas Scorilas
Genes 2022, 13(7), 1133; https://doi.org/10.3390/genes13071133 - 24 Jun 2022
Cited by 12 | Viewed by 2360
Abstract
Circular RNAs (circRNAs) constitute a type of RNA formed through back-splicing. In breast cancer, circRNAs are implicated in tumor onset and progression. Although histone methylation by PRMT1 is largely involved in breast cancer development and metastasis, the effect of circular transcripts deriving from [...] Read more.
Circular RNAs (circRNAs) constitute a type of RNA formed through back-splicing. In breast cancer, circRNAs are implicated in tumor onset and progression. Although histone methylation by PRMT1 is largely involved in breast cancer development and metastasis, the effect of circular transcripts deriving from this gene has not been examined. In this study, total RNA was extracted from four breast cancer cell lines and reversely transcribed using random hexamer primers. Next, first- and second-round PCRs were performed using gene-specific divergent primers. Sanger sequencing followed for the determination of the sequence of each novel PRMT1 circRNA. Lastly, bioinformatics analysis was conducted to predict the functions of the novel circRNAs. In total, nine novel circRNAs were identified, comprising both complete and truncated exons of the PRMT1 gene. Interestingly, we demonstrated that the back-splice junctions consist of novel splice sites of the PRMT1 exons. Moreover, the circRNA expression pattern differed among these four breast cancer cell lines. All the novel circRNAs are predicted to act as miRNA and/or protein sponges, while five circRNAs also possess an open reading frame. In summary, we described the complete sequence of nine novel circRNAs of the PRMT1 gene, comprising distinct back-splice junctions and probably having different molecular properties. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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12 pages, 1308 KiB  
Article
Lower Fractions of TCF4 Transcripts Spanning over the CTG18.1 Trinucleotide Repeat in Human Corneal Endothelium
by Ida Maria Westin, Andreas Viberg, Berit Byström and Irina Golovleva
Genes 2021, 12(12), 2006; https://doi.org/10.3390/genes12122006 - 17 Dec 2021
Cited by 4 | Viewed by 2205
Abstract
Fuchs’ endothelial corneal dystrophy (FECD) is a bilateral disease of the cornea caused by gradual loss of corneal endothelial cells. Late-onset FECD is strongly associated with the CTG18.1 trinucleotide repeat expansion in the Transcription Factor 4 gene (TCF4), which forms RNA [...] Read more.
Fuchs’ endothelial corneal dystrophy (FECD) is a bilateral disease of the cornea caused by gradual loss of corneal endothelial cells. Late-onset FECD is strongly associated with the CTG18.1 trinucleotide repeat expansion in the Transcription Factor 4 gene (TCF4), which forms RNA nuclear foci in corneal endothelial cells. To date, 46 RefSeq transcripts of TCF4 are annotated by the National Center of Biotechnology information (NCBI), however the effect of the CTG18.1 expansion on expression of alternative TCF4 transcripts is not completely understood. To investigate this, we used droplet digital PCR for quantification of TCF4 transcripts spanning over the CTG18.1 and transcripts with transcription start sites immediately downstream of the CTG18.1. TCF4 expression was analysed in corneal endothelium and in whole blood of FECD patients with and without CTG18.1 expansion, in non-FECD controls without CTG18.1 expansion, and in five additional control tissues. Subtle changes in transcription levels in groups of TCF4 transcripts were detected. In corneal endothelium, we found a lower fraction of transcripts spanning over the CTG18.1 tract compared to all other tissues investigated. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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11 pages, 1070 KiB  
Article
Performance Evaluation of SpliceAI for the Prediction of Splicing of NF1 Variants
by Changhee Ha, Jong-Won Kim and Ja-Hyun Jang
Genes 2021, 12(9), 1308; https://doi.org/10.3390/genes12091308 - 25 Aug 2021
Cited by 20 | Viewed by 4027
Abstract
Neurofibromatosis type 1, characterized by neurofibromas and café-au-lait macules, is one of the most common genetic disorders caused by pathogenic NF1 variants. Because of the high proportion of splicing mutations in NF1, identifying variants that alter splicing may be an essential issue [...] Read more.
Neurofibromatosis type 1, characterized by neurofibromas and café-au-lait macules, is one of the most common genetic disorders caused by pathogenic NF1 variants. Because of the high proportion of splicing mutations in NF1, identifying variants that alter splicing may be an essential issue for laboratories. Here, we investigated the sensitivity and specificity of SpliceAI, a recently introduced in silico splicing prediction algorithm in conjunction with other in silico tools. We evaluated 285 NF1 variants identified from 653 patients. The effect on variants on splicing alteration was confirmed by complementary DNA sequencing followed by genomic DNA sequencing. For in silico prediction of splicing effects, we used SpliceAI, MaxEntScan (MES), and Splice Site Finder-like (SSF). The sensitivity and specificity of SpliceAI were 94.5% and 94.3%, respectively, with a cut-off value of Δ Score > 0.22. The area under the curve of SpliceAI was 0.975 (p < 0.0001). Combined analysis of MES/SSF showed a sensitivity of 83.6% and specificity of 82.5%. The concordance rate between SpliceAI and MES/SSF was 84.2%. SpliceAI showed better performance for the prediction of splicing alteration for NF1 variants compared with MES/SSF. As a convenient web-based tool, SpliceAI may be helpful in clinical laboratories conducting DNA-based NF1 sequencing. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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15 pages, 3077 KiB  
Article
Extensive Changes in Transcription Dynamics Reflected on Alternative Splicing Events in Systemic Lupus Erythematosus Patients
by Sofia Papanikolaou, George K. Bertsias and Christoforos Nikolaou
Genes 2021, 12(8), 1260; https://doi.org/10.3390/genes12081260 - 18 Aug 2021
Cited by 7 | Viewed by 2797
Abstract
In addition to increasing the complexity of the transcriptional output, alternative RNA splicing can lead to the reduction of mRNA translation or the production of non-functional or malfunctional proteins, thus representing a vital component of the gene regulation process. Herein, we set out [...] Read more.
In addition to increasing the complexity of the transcriptional output, alternative RNA splicing can lead to the reduction of mRNA translation or the production of non-functional or malfunctional proteins, thus representing a vital component of the gene regulation process. Herein, we set out to detect and characterize alternative splicing events that occur in whole-blood samples of patients with Systemic Lupus Erythematosus (SLE) as compared to healthy counterparts. Through the implementation of a computational pipeline on published RNA-sequencing data, we identified extensive changes in the transcription dynamics affecting a large number of genes. We found a predominance of intron retention events, with the majority introducing premature stop codons, suggestive of gene repression, in both inactive and active SLE patient samples. Alternative splicing affected a distinct set of genes from the ones detected as differentially expressed in the same comparisons, while alternatively spliced genes tended to reside in genome areas associated with increased gene co-expression. Functional analysis of genes affected by alternative splicing pointed towards particular functions related to metabolism and histone acetylation as of potential interest. Together, our findings underline the importance of incorporating alternative splicing analyses in the context of molecular characterization of complex diseases such as SLE. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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17 pages, 7428 KiB  
Article
Upregulation of 15 Antisense Long Non-Coding RNAs in Osteosarcoma
by Emel Rothzerg, Xuan Dung Ho, Jiake Xu, David Wood, Aare Märtson and Sulev Kõks
Genes 2021, 12(8), 1132; https://doi.org/10.3390/genes12081132 - 26 Jul 2021
Cited by 28 | Viewed by 3760
Abstract
The human genome encodes thousands of natural antisense long noncoding RNAs (lncRNAs); they play the essential role in regulation of gene expression at multiple levels, including replication, transcription and translation. Dysregulation of antisense lncRNAs plays indispensable roles in numerous biological progress, such as [...] Read more.
The human genome encodes thousands of natural antisense long noncoding RNAs (lncRNAs); they play the essential role in regulation of gene expression at multiple levels, including replication, transcription and translation. Dysregulation of antisense lncRNAs plays indispensable roles in numerous biological progress, such as tumour progression, metastasis and resistance to therapeutic agents. To date, there have been several studies analysing antisense lncRNAs expression profiles in cancer, but not enough to highlight the complexity of the disease. In this study, we investigated the expression patterns of antisense lncRNAs from osteosarcoma and healthy bone samples (24 tumour-16 bone samples) using RNA sequencing. We identified 15 antisense lncRNAs (RUSC1-AS1, TBX2-AS1, PTOV1-AS1, UBE2D3-AS1, ERCC8-AS1, ZMIZ1-AS1, RNF144A-AS1, RDH10-AS1, TRG-AS1, GSN-AS1, HMGA2-AS1, ZNF528-AS1, OTUD6B-AS1, COX10-AS1 and SLC16A1-AS1) that were upregulated in tumour samples compared to bone sample controls. Further, we performed real-time polymerase chain reaction (RT-qPCR) to validate the expressions of the antisense lncRNAs in 8 different osteosarcoma cell lines (SaOS-2, G-292, HOS, U2-OS, 143B, SJSA-1, MG-63, and MNNG/HOS) compared to hFOB (human osteoblast cell line). These differentially expressed IncRNAs can be considered biomarkers and potential therapeutic targets for osteosarcoma. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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20 pages, 3650 KiB  
Article
Two RECK Splice Variants (Long and Short) Are Differentially Expressed in Patients with Stable and Unstable Coronary Artery Disease: A Pilot Study
by Chiara Vancheri, Elena Morini, Francesca Romana Prandi, Elie Alkhoury, Roberto Celotto, Francesco Romeo, Giuseppe Novelli and Francesca Amati
Genes 2021, 12(6), 939; https://doi.org/10.3390/genes12060939 - 19 Jun 2021
Cited by 3 | Viewed by 2665
Abstract
Primary prevention is crucial for coronary heart disease (CAD) and the identification of new reliable biomarkers might help risk stratification or predict adverse coronary events. Alternative splicing (AS) is a less investigated genetic factors implicated in CAD etiology. We performed an RNA-seq study [...] Read more.
Primary prevention is crucial for coronary heart disease (CAD) and the identification of new reliable biomarkers might help risk stratification or predict adverse coronary events. Alternative splicing (AS) is a less investigated genetic factors implicated in CAD etiology. We performed an RNA-seq study on PBMCs from CAD patients and control subjects (CTR) and observed 113 differentially regulated AS events (24 up and 89 downregulated) in 86 genes. The RECK (Reversion-inducing-cysteine-rich protein with Kazal motifs) gene was further analyzed in a larger case study (24 CTR subjects, 72 CAD and 32 AMI patients) for its Splicing-Index FC (FC = −2.64; p = 0.0217), the AS event involving an exon (exon 18), and its role in vascular inflammation and remodeling. We observed a significant downregulation of Long RECK splice variant (containing exon 18) in PBMCs of AMI compared to CTR subjects (FC = −3.3; p < 0.005). Interestingly, the Short RECK splice variant (lacking exon 18) was under-expressed in AMI compared to both CTR (FC = −4.5; p < 0.0001) and CAD patients (FC = −4.2; p < 0.0001). A ROC curve, constructed combining Long and Short RECK expression data, shows an AUC = 0.81 (p < 0.001) to distinguish AMI from stable CAD patients. A significant negative correlation between Long RECK and triglycerides in CTR group and a positive correlation in the AMI group was found. The combined evaluation of Long and Short RECK expression levels is a potential genomic biomarker for the discrimination of AMI from CAD patients. Our results underline the relevance of deeper studies on the expression of these two splice variants to elucidate their functional role in CAD development and progression. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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15 pages, 1475 KiB  
Article
Nanopore Sequencing Unveils Diverse Transcript Variants of the Epithelial Cell-Specific Transcription Factor Elf-3 in Human Malignancies
by Michaela A. Boti, Panagiotis G. Adamopoulos, Panagiotis Tsiakanikas and Andreas Scorilas
Genes 2021, 12(6), 839; https://doi.org/10.3390/genes12060839 - 29 May 2021
Cited by 7 | Viewed by 3584
Abstract
The human E74-like ETS transcription factor 3 (Elf-3) is an epithelium-specific member of the ETS family, all members of which are characterized by a highly conserved DNA-binding domain. Elf-3 plays a crucial role in epithelial cell differentiation by participating in morphogenesis and terminal [...] Read more.
The human E74-like ETS transcription factor 3 (Elf-3) is an epithelium-specific member of the ETS family, all members of which are characterized by a highly conserved DNA-binding domain. Elf-3 plays a crucial role in epithelial cell differentiation by participating in morphogenesis and terminal differentiation of the murine small intestinal epithelium, and also acts as an indispensable regulator of mesenchymal to epithelial transition, underlying its significant involvement in development and in pathological states, such as cancer. Although previous research works have deciphered the functional role of Elf-3 in normal physiology as well as in tumorigenesis, the present study highlights for the first time the wide spectrum of ELF3 mRNAs that are transcribed, providing an in-depth analysis of splicing events and exon/intron boundaries in a broad panel of human cell lines. The implementation of a versatile targeted nanopore sequencing approach led to the identification of 25 novel ELF3 mRNA transcript variants (ELF3 v.3–v.27) with new alternative splicing events, as well as two novel exons. Although the current study provides a qualitative transcriptional profile regarding ELF3, further studies must be conducted, so the biological function of all novel alternative transcript variants as well as the putative protein isoforms are elucidated. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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14 pages, 4943 KiB  
Article
Exploration of Alternative Splicing Events in Mesenchymal Stem Cells from Human Induced Pluripotent Stem Cells
by Ji-Eun Jeong, Binna Seol, Han-Seop Kim, Jae-Yun Kim and Yee-Sook Cho
Genes 2021, 12(5), 737; https://doi.org/10.3390/genes12050737 - 13 May 2021
Cited by 3 | Viewed by 2891
Abstract
Although comparative genome-wide transcriptomic analysis has provided insight into the biology of human induced pluripotent stem cell-derived mesenchymal stem cells (iMSCs), the distinct alternative splicing (AS) signatures of iMSCs remain elusive. Here, we performed Illumina RNA sequencing analysis to characterize AS events in [...] Read more.
Although comparative genome-wide transcriptomic analysis has provided insight into the biology of human induced pluripotent stem cell-derived mesenchymal stem cells (iMSCs), the distinct alternative splicing (AS) signatures of iMSCs remain elusive. Here, we performed Illumina RNA sequencing analysis to characterize AS events in iMSCs compared with tissue-derived MSCs. A total of 4586 differentially expressed genes (|FC| > 2) were identified between iMSCs and umbilical cord blood-derived MSCs (UCB-MSCs), including 2169 upregulated and 2417 downregulated genes. Of these, 164 differentially spliced events (BF > 20) in 112 genes were identified between iMSCs and UCB-MSCs. The predominant type of AS found in iMSCs was skipped exons (43.3%), followed by retained introns (19.5%), alternative 3′ (15.2%) and 5′ (12.8%) splice sites, and mutually exclusive exons (9.1%). Functional enrichment analysis showed that the differentially spliced genes (|FC| > 2 and BF > 20) were mainly enriched in functions associated with focal adhesion, extracellular exosomes, extracellular matrix organization, cell adhesion, and actin binding. Splice isoforms of selected genes including TRPT1, CNN2, and AP1G2, identified in sashimi plots, were further validated by RT-PCR analysis. This study provides valuable insight into the biology of iMSCs and the translation of mechanistic understanding of iMSCs into therapeutic applications. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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14 pages, 4451 KiB  
Article
Sp1-Mediated circRNA circHipk2 Regulates Myogenesis by Targeting Ribosomal Protein Rpl7
by Junyu Yan, Yalan Yang, Xinhao Fan, Yijie Tang and Zhonglin Tang
Genes 2021, 12(5), 696; https://doi.org/10.3390/genes12050696 - 8 May 2021
Cited by 18 | Viewed by 3262
Abstract
Circular RNAs (circRNAs) represent a class of covalently closed single-stranded RNA molecules that are emerging as essential regulators of various biological processes. The circRNA circHipk2 originates from exon 2 of the Hipk2 gene in mice and was reported to be involved in acute [...] Read more.
Circular RNAs (circRNAs) represent a class of covalently closed single-stranded RNA molecules that are emerging as essential regulators of various biological processes. The circRNA circHipk2 originates from exon 2 of the Hipk2 gene in mice and was reported to be involved in acute promyelocytic leukemia and myocardial injury. However, the functions and mechanisms of circHipk2 in myogenesis are largely unknown. Here, to deepen our knowledge about the role of circHipk2, we studied the expression and function of circHipk2 during skeletal myogenesis. We found that circHipk2 was mostly distributed in the cytoplasm, and dynamically and differentially expressed in various myogenesis systems in vitro and in vivo. Functionally, overexpression of circHipk2 inhibited myoblast proliferation and promoted myotube formation in C2C12 cells, whereas the opposite effects were observed after circHipk2 knockdown. Mechanistically, circHipk2 could directly bind to ribosomal protein Rpl7, an essential 60S preribosomal assembly factor, to inhibit ribosome translation. In addition, we verified that transcription factor Sp1 directly bound to the promoter of circHipk2 and affected the expression of Hipk2 and circHipk2 in C2C12 myoblasts. Collectively, these findings identify circHipk2 as a candidate circRNA regulating ribosome biogenesis and myogenesis proliferation and differentiation. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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14 pages, 17108 KiB  
Article
Landscape of Chimeric RNAs in Non-Cancerous Cells
by Chen Chen, Samuel Haddox, Yue Tang, Fujun Qin and Hui Li
Genes 2021, 12(4), 466; https://doi.org/10.3390/genes12040466 - 24 Mar 2021
Cited by 5 | Viewed by 2548
Abstract
Gene fusions and their products (RNA and protein) have been traditionally recognized as unique features of cancer cells and are used as ideal biomarkers and drug targets for multiple cancer types. However, recent studies have demonstrated that chimeric RNAs generated by intergenic alternative [...] Read more.
Gene fusions and their products (RNA and protein) have been traditionally recognized as unique features of cancer cells and are used as ideal biomarkers and drug targets for multiple cancer types. However, recent studies have demonstrated that chimeric RNAs generated by intergenic alternative splicing can also be found in normal cells and tissues. In this study, we aim to identify chimeric RNAs in different non-neoplastic cell lines and investigate the landscape and expression of these novel candidate chimeric RNAs. To do so, we used HEK-293T, HUVEC, and LO2 cell lines as models, performed paired-end RNA sequencing, and conducted analyses for chimeric RNA profiles. Several filtering criteria were applied, and the landscape of chimeric RNAs was characterized at multiple levels and from various angles. Further, we experimentally validated 17 chimeric RNAs from different classifications. Finally, we examined a number of validated chimeric RNAs in different cancer and non-cancer cells, including blood from healthy donors, and demonstrated their ubiquitous expression pattern. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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11 pages, 1808 KiB  
Article
BAF57/SMARCE1 Interacting with Splicing Factor SRSF1 Regulates Mechanical Stress-Induced Alternative Splicing of Cyclin D1
by Jianguo Feng, Xichao Xu, Xin Fan, Qian Yi and Liling Tang
Genes 2021, 12(2), 306; https://doi.org/10.3390/genes12020306 - 21 Feb 2021
Cited by 14 | Viewed by 2866
Abstract
Background: Cyclin D1 regulates cyclin-dependent protein kinase activity of the cell cycle, and cyclin D1 alternative splicing generates a cyclin D1b isoform, acting as a mediator of aberrant cellular proliferation. As alternative splicing processes are sensitive to mechanical stimuli, whether the alternative splicing [...] Read more.
Background: Cyclin D1 regulates cyclin-dependent protein kinase activity of the cell cycle, and cyclin D1 alternative splicing generates a cyclin D1b isoform, acting as a mediator of aberrant cellular proliferation. As alternative splicing processes are sensitive to mechanical stimuli, whether the alternative splicing of cyclin D1 is regulated by mechanical stress and what kinds of factors may act as the regulator of mechano-induced alternative splicing remain unknown. Methods: The alternative splicing of Cyclin D1 was examined using reverse transcription polymerase chain reaction (RT-PCR) in osteoblast cell lines and keratinocyte cells loaded by a cyclic stretch. The expression of splicing factors and switching defective/sucrose non-fermenting (SWI/SNF) complex subunits were detected in stretched cells using real-time quantitative PCR (RT-qPCR). The protein interaction was tested by co-immunoprecipitation assay (Co-IP). Results:Cyclin D1 expression decreased with its splice variant upregulated in stretched cells. Serine/arginine-rich splicing factor 1 (SRSF1) and SWI/SNF complex subunit Brahma-related gene-1-associated factor 57 (BAF57), also named SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 (SMARCE1), could respond to mechanical stimuli. Overexpression and knockdown experiments indicated the BAF57/SMARCE1 is probably a critical factor regulating the alternative splicing of cyclin D1. Co-IP showed an interaction between BAF57/SMARCE1 and SRSF1, implying a possible underlying mechanism of the regulator role of BAF57/SMARCE1 in the splicing process of cyclin D1. Conclusions: The splicing factor SRSF1 and BAF57/SMARCE1 are possibly responsible for the mechanical stress-induced alternative splicing of cyclin D1. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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18 pages, 3634 KiB  
Article
Bisphenol A Exposure Changes the Transcriptomic and Proteomic Dynamics of Human Retinoblastoma Y79 Cells
by Chul-Hong Kim, Mi Jin Kim, Jinhong Park, Jinho Kim, Ji-Young Kim, Mi-Jin An, Geun-Seup Shin, Hyun-Min Lee and Jung-Woong Kim
Genes 2021, 12(2), 264; https://doi.org/10.3390/genes12020264 - 11 Feb 2021
Cited by 9 | Viewed by 2541
Abstract
Bisphenol A (BPA) is a xenoestrogen chemical commonly used to manufacture polycarbonate plastics and epoxy resin and might affect various human organs. However, the cellular effects of BPA on the eyes have not been widely investigated. This study aimed to investigate the cellular [...] Read more.
Bisphenol A (BPA) is a xenoestrogen chemical commonly used to manufacture polycarbonate plastics and epoxy resin and might affect various human organs. However, the cellular effects of BPA on the eyes have not been widely investigated. This study aimed to investigate the cellular cytotoxicity by BPA exposure on human retinoblastoma cells. BPA did not show cytotoxic effects, such as apoptosis, alterations to cell viability and cell cycle regulation. Comparative analysis of the transcriptome and proteome profiles were investigated after long-term exposure of Y79 cells to low doses of BPA. Transcriptome analysis using RNA-seq revealed that mRNA expression of the post-transcriptional regulation-associated gene sets was significantly upregulated in the BPA-treated group. Cell cycle regulation-associated gene sets were significantly downregulated by exposure to BPA. Interestingly, RNA-seq analysis at the transcript level indicated that alternative splicing events, particularly retained introns, were noticeably altered by low-dose BPA treatment. Additionally, proteome profiling using MALDI-TOF-MS identified a total of nine differentially expressed proteins. These results suggest that alternative splicing events and altered gene/protein expression patterns are critical phenomena affected by long-term low-dose BPA exposure. This represents a novel marker for the detection of various diseases associated with environmental pollutants such as BPA. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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Review

Jump to: Editorial, Research

11 pages, 1237 KiB  
Review
Alternative Splicing and Isoforms: From Mechanisms to Diseases
by Qi Liu, Leiming Fang and Chengjun Wu
Genes 2022, 13(3), 401; https://doi.org/10.3390/genes13030401 - 24 Feb 2022
Cited by 37 | Viewed by 14515
Abstract
Alternative splicing of pre-mRNA is a key mechanism for increasing the complexity of proteins in humans, causing a diversity of expression of transcriptomes and proteomes in a tissue-specific manner. Alternative splicing is regulated by a variety of splicing factors. However, the changes and [...] Read more.
Alternative splicing of pre-mRNA is a key mechanism for increasing the complexity of proteins in humans, causing a diversity of expression of transcriptomes and proteomes in a tissue-specific manner. Alternative splicing is regulated by a variety of splicing factors. However, the changes and errors of splicing regulation caused by splicing factors are strongly related to many diseases, something which represents one of this study’s main interests. Further understanding of alternative splicing regulation mediated by cellular factors is also a prospective choice to develop specific drugs for targeting the dynamic RNA splicing process. In this review, we firstly concluded the basic principle of alternative splicing. Afterwards, we showed how splicing isoforms affect physiological activities through specific disease examples. Finally, the available treatment methods relative to adjusting splicing activities have been summarized. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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11 pages, 1010 KiB  
Review
Splicing Variants, Protein-Protein Interactions, and Drug Targeting in Hutchinson-Gilford Progeria Syndrome and Small Cell Lung Cancer
by Bae-Hoon Kim, Tae-Gyun Woo, So-Mi Kang, Soyoung Park and Bum-Joon Park
Genes 2022, 13(2), 165; https://doi.org/10.3390/genes13020165 - 18 Jan 2022
Cited by 4 | Viewed by 4766
Abstract
Alternative splicing (AS) is a biological operation that enables a messenger RNA to encode protein variants (isoforms) that give one gene several functions or properties. This process provides one of the major sources of use for understanding the proteomic diversity of multicellular organisms. [...] Read more.
Alternative splicing (AS) is a biological operation that enables a messenger RNA to encode protein variants (isoforms) that give one gene several functions or properties. This process provides one of the major sources of use for understanding the proteomic diversity of multicellular organisms. In combination with post-translational modifications, it contributes to generating a variety of protein–protein interactions (PPIs) that are essential to cellular homeostasis or proteostasis. However, cells exposed to many kinds of stresses (aging, genetic changes, carcinogens, etc.) sometimes derive cancer or disease onset from aberrant PPIs caused by DNA mutations. In this review, we summarize how splicing variants may form a neomorphic protein complex and cause diseases such as Hutchinson-Gilford progeria syndrome (HGPS) and small cell lung cancer (SCLC), and we discuss how protein–protein interfaces obtained from the variants may represent efficient therapeutic target sites to treat HGPS and SCLC. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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14 pages, 770 KiB  
Review
Alternative Splicing in Cardiovascular Disease—A Survey of Recent Findings
by Ena Hasimbegovic, Victor Schweiger, Nina Kastner, Andreas Spannbauer, Denise Traxler, Dominika Lukovic, Mariann Gyöngyösi and Julia Mester-Tonczar
Genes 2021, 12(9), 1457; https://doi.org/10.3390/genes12091457 - 21 Sep 2021
Cited by 22 | Viewed by 3629
Abstract
Alternative splicing, a driver of posttranscriptional variance, differs from canonical splicing by arranging the introns and exons of an immature pre-mRNA transcript in a multitude of different ways. Although alternative splicing was discovered almost half a century ago, estimates of the proportion of [...] Read more.
Alternative splicing, a driver of posttranscriptional variance, differs from canonical splicing by arranging the introns and exons of an immature pre-mRNA transcript in a multitude of different ways. Although alternative splicing was discovered almost half a century ago, estimates of the proportion of genes that undergo alternative splicing have risen drastically over the last two decades. Deep sequencing methods and novel bioinformatic algorithms have led to new insights into the prevalence of spliced variants, tissue-specific splicing patterns and the significance of alternative splicing in development and disease. Thus far, the role of alternative splicing has been uncovered in areas ranging from heart development, the response to myocardial infarction to cardiac structural disease. Circular RNAs, a product of alternative back-splicing, were initially discovered in 1976, but landmark publications have only recently identified their regulatory role, tissue-specific expression, and transcriptomic abundance, spurring a renewed interest in the topic. The aim of this review is to provide a brief insight into some of the available findings on the role of alternative splicing in cardiovascular disease, with a focus on atherosclerosis, myocardial infarction, heart failure, dilated cardiomyopathy and circular RNAs in myocardial infarction. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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17 pages, 2259 KiB  
Review
Alternative Splicing Role in New Therapies of Spinal Muscular Atrophy
by Jan Lejman, Grzegorz Zieliński, Piotr Gawda and Monika Lejman
Genes 2021, 12(9), 1346; https://doi.org/10.3390/genes12091346 - 28 Aug 2021
Cited by 7 | Viewed by 5894
Abstract
It has been estimated that 80% of the pre-mRNA undergoes alternative splicing, which exponentially increases the flow of biological information in cellular processes and can be an attractive therapeutic target. It is a crucial mechanism to increase genetic diversity. Disturbed alternative splicing is [...] Read more.
It has been estimated that 80% of the pre-mRNA undergoes alternative splicing, which exponentially increases the flow of biological information in cellular processes and can be an attractive therapeutic target. It is a crucial mechanism to increase genetic diversity. Disturbed alternative splicing is observed in many disorders, including neuromuscular diseases and carcinomas. Spinal Muscular Atrophy (SMA) is an autosomal recessive neurodegenerative disease. Homozygous deletion in 5q13 (the region coding for the motor neuron survival gene (SMN1)) is responsible for 95% of SMA cases. The nearly identical SMN2 gene does not compensate for SMN loss caused by SMN1 gene mutation due to different splicing of exon 7. A pathologically low level of survival motor neuron protein (SMN) causes degeneration of the anterior horn cells in the spinal cord with associated destruction of α-motor cells and manifested by muscle weakness and loss. Understanding the regulation of the SMN2 pre-mRNA splicing process has allowed for innovative treatment and the introduction of new medicines for SMA. After describing the concept of splicing modulation, this review will cover the progress achieved in this field, by highlighting the breakthrough accomplished recently for the treatment of SMA using the mechanism of alternative splicing. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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13 pages, 1839 KiB  
Review
Alternative Splicing: A Key Mediator of Diabetic Vasculopathy
by Victoria A. Cornelius, Jenna R. Fulton and Andriana Margariti
Genes 2021, 12(9), 1332; https://doi.org/10.3390/genes12091332 - 27 Aug 2021
Cited by 5 | Viewed by 2977
Abstract
Cardiovascular disease is the leading cause of death amongst diabetic individuals. Atherosclerosis is the prominent driver of diabetic vascular complications, which is triggered by the detrimental effects of hyperglycemia and oxidative stress on the vasculature. Research has extensively shown diabetes to result in [...] Read more.
Cardiovascular disease is the leading cause of death amongst diabetic individuals. Atherosclerosis is the prominent driver of diabetic vascular complications, which is triggered by the detrimental effects of hyperglycemia and oxidative stress on the vasculature. Research has extensively shown diabetes to result in the malfunction of the endothelium, the main component of blood vessels, causing severe vascular complications. The pathogenic mechanism in which diabetes induces vascular dysfunction, however, remains largely unclear. Alternative splicing of protein coding pre-mRNAs is an essential regulatory mechanism of gene expression and is accepted to be intertwined with cellular physiology. Recently, a role for alternative splicing has arisen within vascular health, with aberrant mis-splicing having a critical role in disease development, including in atherosclerosis. This review focuses on the current knowledge of alternative splicing and the roles of alternatively spliced isoforms within the vasculature, with a particular focus on disease states. Furthermore, we explore the recent elucidation of the alternatively spliced QKI gene within vascular cell physiology and the onset of diabetic vasculopathy. Potential therapeutic strategies to restore aberrant splicing are also discussed. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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10 pages, 1276 KiB  
Review
Alternative Splicing and Hypoxia Puzzle in Alzheimer’s and Parkinson’s Diseases
by Eglė Jakubauskienė and Arvydas Kanopka
Genes 2021, 12(8), 1272; https://doi.org/10.3390/genes12081272 - 20 Aug 2021
Cited by 9 | Viewed by 3572
Abstract
Alternative pre-mRNA splicing plays a very important role in expanding protein diversity as it generates numerous transcripts from a single protein-coding gene. Therefore, alterations lead this process to neurological human disorders, including Alzheimer’s and Parkinson’s diseases. Moreover, accumulating evidence indicates that the splicing [...] Read more.
Alternative pre-mRNA splicing plays a very important role in expanding protein diversity as it generates numerous transcripts from a single protein-coding gene. Therefore, alterations lead this process to neurological human disorders, including Alzheimer’s and Parkinson’s diseases. Moreover, accumulating evidence indicates that the splicing machinery highly contributes to the cells’ ability to adapt to different altered cellular microenvironments, such as hypoxia. Hypoxia is known to have an effect on the expression of proteins involved in a multiple of biological processes, such as erythropoiesis, angiogenesis, and neurogenesis, and is one of the important risk factors in neuropathogenesis. In this review, we discuss the current knowledge of alternatively spliced genes, which, as it is reported, are associated with Alzheimer’s and Parkinson’s diseases. Additionally, we highlight the possible influence of cellular hypoxic microenvironment for the formation of mRNA isoforms contributing to the development of these neurodegenerative diseases. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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21 pages, 2868 KiB  
Review
Adding Some “Splice” to Stress Eating: Autophagy, ESCRT and Alternative Splicing Orchestrate the Cellular Stress Response
by Elias Habib, Allyson Cook, Sabateeshan Mathavarajah and Graham Dellaire
Genes 2021, 12(8), 1196; https://doi.org/10.3390/genes12081196 - 31 Jul 2021
Cited by 4 | Viewed by 4833
Abstract
Autophagy is a widely studied self-renewal pathway that is essential for degrading damaged cellular organelles or recycling biomolecules to maintain cellular homeostasis, particularly under cellular stress. This pathway initiates with formation of an autophagosome, which is a double-membrane structure that envelopes cytosolic components [...] Read more.
Autophagy is a widely studied self-renewal pathway that is essential for degrading damaged cellular organelles or recycling biomolecules to maintain cellular homeostasis, particularly under cellular stress. This pathway initiates with formation of an autophagosome, which is a double-membrane structure that envelopes cytosolic components and fuses with a lysosome to facilitate degradation of the contents. The endosomal sorting complexes required for transport (ESCRT) proteins play an integral role in controlling autophagosome fusion events and disruption to this machinery leads to autophagosome accumulation. Given the central role of autophagy in maintaining cellular health, it is unsurprising that dysfunction of this process is associated with many human maladies including cancer and neurodegenerative diseases. The cell can also rapidly respond to cellular stress through alternative pre-mRNA splicing that enables adaptive changes to the cell’s proteome in response to stress. Thus, alternative pre-mRNA splicing of genes that are involved in autophagy adds another layer of complexity to the cell’s stress response. Consequently, the dysregulation of alternative splicing of genes associated with autophagy and ESCRT may also precipitate disease states by either reducing the ability of the cell to respond to stress or triggering a maladaptive response that is pathogenic. In this review, we summarize the diverse roles of the ESCRT machinery and alternative splicing in regulating autophagy and how their dysfunction can have implications for human disease. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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18 pages, 2023 KiB  
Review
Intermixing the OPN1LW and OPN1MW Genes Disrupts the Exonic Splicing Code Causing an Array of Vision Disorders
by Maureen Neitz and Jay Neitz
Genes 2021, 12(8), 1180; https://doi.org/10.3390/genes12081180 - 29 Jul 2021
Cited by 16 | Viewed by 5077
Abstract
Light absorption by photopigment molecules expressed in the photoreceptors in the retina is the first step in seeing. Two types of photoreceptors in the human retina are responsible for image formation: rods, and cones. Except at very low light levels when rods are [...] Read more.
Light absorption by photopigment molecules expressed in the photoreceptors in the retina is the first step in seeing. Two types of photoreceptors in the human retina are responsible for image formation: rods, and cones. Except at very low light levels when rods are active, all vision is based on cones. Cones mediate high acuity vision and color vision. Furthermore, they are critically important in the visual feedback mechanism that regulates refractive development of the eye during childhood. The human retina contains a mosaic of three cone types, short-wavelength (S), long-wavelength (L), and middle-wavelength (M) sensitive; however, the vast majority (~94%) are L and M cones. The OPN1LW and OPN1MW genes, located on the X-chromosome at Xq28, encode the protein component of the light-sensitive photopigments expressed in the L and M cones. Diverse haplotypes of exon 3 of the OPN1LW and OPN1MW genes arose thru unequal recombination mechanisms that have intermixed the genes. A subset of the haplotypes causes exon 3- skipping during pre-messenger RNA splicing and are associated with vision disorders. Here, we review the mechanism by which splicing defects in these genes cause vision disorders. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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29 pages, 1262 KiB  
Review
Alternative RNA Splicing—The Trojan Horse of Cancer Cells in Chemotherapy
by Nikolay Mehterov, Maria Kazakova, Yordan Sbirkov, Boyan Vladimirov, Nikolay Belev, Galina Yaneva, Krassimira Todorova, Soren Hayrabedyan and Victoria Sarafian
Genes 2021, 12(7), 1085; https://doi.org/10.3390/genes12071085 - 18 Jul 2021
Cited by 15 | Viewed by 5467
Abstract
Almost all transcribed human genes undergo alternative RNA splicing, which increases the diversity of the coding and non-coding cellular landscape. The resultant gene products might have distinctly different and, in some cases, even opposite functions. Therefore, the abnormal regulation of alternative splicing plays [...] Read more.
Almost all transcribed human genes undergo alternative RNA splicing, which increases the diversity of the coding and non-coding cellular landscape. The resultant gene products might have distinctly different and, in some cases, even opposite functions. Therefore, the abnormal regulation of alternative splicing plays a crucial role in malignant transformation, development, and progression, a fact supported by the distinct splicing profiles identified in both healthy and tumor cells. Drug resistance, resulting in treatment failure, still remains a major challenge for current cancer therapy. Furthermore, tumor cells often take advantage of aberrant RNA splicing to overcome the toxicity of the administered chemotherapeutic agents. Thus, deciphering the alternative RNA splicing variants in tumor cells would provide opportunities for designing novel therapeutics combating cancer more efficiently. In the present review, we provide a comprehensive outline of the recent findings in alternative splicing in the most common neoplasms, including lung, breast, prostate, head and neck, glioma, colon, and blood malignancies. Molecular mechanisms developed by cancer cells to promote oncogenesis as well as to evade anticancer drug treatment and the subsequent chemotherapy failure are also discussed. Taken together, these findings offer novel opportunities for future studies and the development of targeted therapy for cancer-specific splicing variants. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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15 pages, 1266 KiB  
Review
Alternative Splicing of Pre-mRNA in the Control of Immune Activity
by Zhongjing Su and Dongyang Huang
Genes 2021, 12(4), 574; https://doi.org/10.3390/genes12040574 - 15 Apr 2021
Cited by 19 | Viewed by 4544
Abstract
The human immune response is a complex process that responds to numerous exogenous antigens in preventing infection by microorganisms, as well as to endogenous components in the surveillance of tumors and autoimmune diseases, and a great number of molecules are necessary to carry [...] Read more.
The human immune response is a complex process that responds to numerous exogenous antigens in preventing infection by microorganisms, as well as to endogenous components in the surveillance of tumors and autoimmune diseases, and a great number of molecules are necessary to carry the functional complexity of immune activity. Alternative splicing of pre-mRNA plays an important role in immune cell development and regulation of immune activity through yielding diverse transcriptional isoforms to supplement the function of limited genes associated with the immune reaction. In addition, multiple factors have been identified as being involved in the control of alternative splicing at the cis, trans, or co-transcriptional level, and the aberrant splicing of RNA leads to the abnormal modulation of immune activity in infections, immune diseases, and tumors. In this review, we summarize the recent discoveries on the generation of immune-associated alternative splice variants, clinical disorders, and possible regulatory mechanisms. We also discuss the immune responses to the neoantigens produced by alternative splicing, and finally, we issue some alternative splicing and immunity correlated questions based on our knowledge. Full article
(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)
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