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Pandkar MR, Shukla S. Epigenetics and alternative splicing in cancer: old enemies, new perspectives. Biochem J 2024; 481:1497-1518. [PMID: 39422322 DOI: 10.1042/bcj20240221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 09/30/2024] [Accepted: 10/07/2024] [Indexed: 10/19/2024]
Abstract
In recent years, significant strides in both conceptual understanding and technological capabilities have bolstered our comprehension of the factors underpinning cancer initiation and progression. While substantial insights have unraveled the molecular mechanisms driving carcinogenesis, there has been an overshadowing of the critical contribution made by epigenetic pathways, which works in concert with genetics. Mounting evidence demonstrates cancer as a complex interplay between genetics and epigenetics. Notably, epigenetic elements play a pivotal role in governing alternative pre-mRNA splicing, a primary contributor to protein diversity. In this review, we have provided detailed insights into the bidirectional communication between epigenetic modifiers and alternative splicing, providing examples of specific genes and isoforms affected. Notably, succinct discussion on targeting epigenetic regulators and the potential of the emerging field of epigenome editing to modulate splicing patterns is also presented. In summary, this review offers valuable insights into the intricate interplay between epigenetics and alternative splicing in cancer, paving the way for novel approaches to understanding and targeting this critical process.
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Affiliation(s)
- Madhura R Pandkar
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh 462066, India
| | - Sanjeev Shukla
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh 462066, India
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2
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Du Y, Cao L, Wang S, Guo L, Tan L, Liu H, Feng Y, Wu W. Differences in alternative splicing and their potential underlying factors between animals and plants. J Adv Res 2024; 64:83-98. [PMID: 37981087 PMCID: PMC11464654 DOI: 10.1016/j.jare.2023.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/16/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Alternative splicing (AS), a posttranscriptional process, contributes to the complexity of transcripts from a limited number of genes in a genome, and AS is considered a great source of genetic and phenotypic diversity in eukaryotes. In animals, AS is tightly regulated during the processes of cell growth and differentiation, and its dysregulation is involved in many diseases, including cancers. Likewise, in plants, AS occurs in all stages of plant growth and development, and it seems to play important roles in the rapid reprogramming of genes in response to environmental stressors. To date, the prevalence and functional roles of AS have been extensively reviewed in animals and plants. However, AS differences between animals and plants, especially their underlying molecular mechanisms and impact factors, are anecdotal and rarely reviewed. AIM OF REVIEW This review aims to broaden our understanding of AS roles in a variety of biological processes and provide insights into the underlying mechanisms and impact factors likely leading to AS differences between animals and plants. KEY SCIENTIFIC CONCEPTS OF REVIEW We briefly summarize the roles of AS regulation in physiological and biochemical activities in animals and plants. Then, we underline the differences in the process of AS between plants and animals and especially analyze the potential impact factors, such as gene exon/intron architecture, 5'/3' untranslated regions (UTRs), spliceosome components, chromatin dynamics and transcription speeds, splicing factors [serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs)], noncoding RNAs, and environmental stimuli, which might lead to the differences. Moreover, we compare the nonsense-mediated mRNA decay (NMD)-mediated turnover of the transcripts with a premature termination codon (PTC) in animals and plants. Finally, we summarize the current AS knowledge published in animals versus plants and discuss the potential development of disease therapies and superior crops in the future.
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Affiliation(s)
- Yunfei Du
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Lu Cao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Lingling Tan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Hua Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Ying Feng
- Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health (SINH), Chinese Academy of Sciences (CAS), Shanghai 200032, China.
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China.
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Wu SL, Yang L, Huang C, Li Q, Ma C, Yuan F, Zhou Y, Wang X, Tong WM, Niu Y, Jin F. Genome-wide characterization of dynamic DNA 5-hydroxymethylcytosine and TET2-related DNA demethylation during breast tumorigenesis. Clin Epigenetics 2024; 16:125. [PMID: 39261937 PMCID: PMC11391647 DOI: 10.1186/s13148-024-01726-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 08/09/2024] [Indexed: 09/13/2024] Open
Abstract
BACKGROUND Breast tumorigenesis is a complex and multistep process accompanied by both genetic and epigenetic dysregulation. In contrast to the extensive studies on DNA epigenetic modifications 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) in malignant breast tumors, their roles in the early phases of breast tumorigenesis remain ambiguous. RESULTS DNA 5hmC and 5mC exhibited a consistent and significant decrease from usual ductal hyperplasia to atypical ductal hyperplasia and subsequently to ductal carcinoma in situ (DCIS). However, 5hmC showed a modest increase in invasive ductal breast cancer compared to DCIS. Genomic analyses showed that the changes in 5hmC and 5mC levels occurred around the transcription start sites (TSSs), and the modification levels were strongly correlated with gene expression levels. Meanwhile, it was found that differentially hydroxymethylated regions (DhMRs) and differentially methylated regions (DMRs) were overlapped in the early phases and accompanied by the enrichment of active histone marks. In addition, TET2-related DNA demethylation was found to be involved in breast tumorigenesis, and four transcription factor binding sites (TFs: ESR1, FOXA1, GATA3, FOS) were enriched in TET2-related DhMRs/DMRs. Intriguingly, we also identified a certain number of common DhMRs between tumor samples and cell-free DNA (cfDNA). CONCLUSIONS Our study reveals that dynamic changes in DNA 5hmC and 5mC play a vital role in propelling breast tumorigenesis. Both TFs and active histone marks are involved in TET2-related DNA demethylation. Concurrent changes in 5hmC signals in primary breast tumors and cfDNA may play a promising role in breast cancer screening.
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Affiliation(s)
- Shuang-Ling Wu
- Department of Surgical Oncology and Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, 110000, China
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Lin Yang
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Changcai Huang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Center for Bioinformatics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Qing Li
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Chunhui Ma
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Fang Yuan
- National Institute of Measurement and Testing Technology, Chengdu, 610021, China
| | - Yinglin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Xiaoyue Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Center for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine and Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100871, China
| | - Wei-Min Tong
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
- Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yamei Niu
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.
- Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Feng Jin
- Department of Surgical Oncology and Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, 110000, China.
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Yustis JC, Devoucoux M, Côté J. The Functional Relationship Between RNA Splicing and the Chromatin Landscape. J Mol Biol 2024; 436:168614. [PMID: 38762032 DOI: 10.1016/j.jmb.2024.168614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/27/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
Chromatin is a highly regulated and dynamic structure that has been shown to play an essential role in transcriptional and co-transcriptional regulation. In the context of RNA splicing, early evidence suggested a loose connection between the chromatin landscape and splicing. More recently, it has been shown that splicing occurs in a co-transcriptional manner, meaning that the splicing process occurs in the context of chromatin. Experimental and computational evidence have also shown that chromatin dynamics can influence the splicing process and vice versa. However, much of this evidence provides mainly correlative relationships between chromatin and splicing with just a few concrete examples providing defined molecular mechanisms by which these two processes are functionally related. Nevertheless, it is clear that chromatin and RNA splicing are tightly interconnected to one another. In this review, we highlight the current state of knowledge of the relationship between chromatin and splicing.
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Affiliation(s)
- Juan-Carlos Yustis
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of the CHU de Québec-Université Laval Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Maëva Devoucoux
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of the CHU de Québec-Université Laval Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of the CHU de Québec-Université Laval Research Center, Quebec City, Quebec G1R 3S3, Canada.
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Sha M, Parveen Rahamathulla M. Splice site recognition - deciphering Exon-Intron transitions for genetic insights using Enhanced integrated Block-Level gated LSTM model. Gene 2024; 915:148429. [PMID: 38575098 DOI: 10.1016/j.gene.2024.148429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Bioinformatics is a contemporary interdisciplinary area focused on analyzing the growing number of genome sequences. Gene variants are differences in DNA sequences among individuals within a population. Splice site recognition is a crucial step in the process of gene expression, where the coding sequences of genes are joined together to form mature messenger RNA (mRNA). These genetic variants that disrupt genes are believed to be the primary reason for neuro-developmental disorders like ASD (Autism Spectrum Disorder) is a neuro-developmental disorder that is diagnosed in individuals, families, and society and occurs as the developmental delay in one among the hundred genes that are associated with these disorders. Missense variants, premature stop codons, or deletions alter both the quality and quantity of encoded proteins. Predicting genes within exons and introns presents main challenges, such as dealing with sequencing errors, short reads, incomplete genes, overlapping, and more. Although many traditional techniques have been utilized in creating an exon prediction system, the primary challenge lies in accurately identifying the length and spliced strand location classification of exons in conjunction with introns. From now on, the suggested approach utilizes a Deep Learning algorithm to analyze intricate and extensive genomic datasets. M-LSTM is utilized to categorize three binary combinations (EI as 1, IE as 2, and none as 3) using spliced DNA strands. The M-LSTM system is able to sequence extensive datasets, ensuring that long information can be stored without any impact on the current input or output. This enables it to recognize and address long-term connections and problems with rapidly increasing gradients. The proposed model is compared internally with Naïve Bayes and Random Forest to assess its efficacy. Additionally, the proposed model's performance is forecasted by utilizing probabilistic parameters like recall, F1-score, precision, and accuracy to assess the effectiveness of the proposed system.
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Affiliation(s)
- Mohemmed Sha
- Department of Software Engineering, College of Computer Engineering and Sciences, Prince Sattam bin Abdulaziz University, Al Kharj 11942, Kingdom of Saudi Arabia.
| | - Mohamudha Parveen Rahamathulla
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam bin Abdulaziz University, Al Kharj 11942, Kingdom of Saudi Arabia.
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Riccardi F, Romano G, Licastro D, Pagani F. Age-dependent regulation of ELP1 exon 20 splicing in Familial Dysautonomia by RNA Polymerase II kinetics and chromatin structure. PLoS One 2024; 19:e0298965. [PMID: 38829854 PMCID: PMC11146744 DOI: 10.1371/journal.pone.0298965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 02/01/2024] [Indexed: 06/05/2024] Open
Abstract
Familial Dysautonomia (FD) is a rare disease caused by ELP1 exon 20 skipping. Here we clarify the role of RNA Polymerase II (RNAPII) and chromatin on this splicing event. A slow RNAPII mutant and chromatin-modifying chemicals that reduce the rate of RNAPII elongation induce exon skipping whereas chemicals that create a more relaxed chromatin exon inclusion. In the brain of a mouse transgenic for the human FD-ELP1 we observed on this gene an age-dependent decrease in the RNAPII density profile that was most pronounced on the alternative exon, a robust increase in the repressive marks H3K27me3 and H3K9me3 and a decrease of H3K27Ac, together with a progressive reduction in ELP1 exon 20 inclusion level. In HEK 293T cells, selective drug-induced demethylation of H3K27 increased RNAPII elongation on ELP1 and SMN2, promoted the inclusion of the corresponding alternative exons, and, by RNA-sequencing analysis, induced changes in several alternative splicing events. These data suggest a co-transcriptional model of splicing regulation in which age-dependent changes in H3K27me3/Ac modify the rate of RNAPII elongation and affect processing of ELP1 alternative exon 20.
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Affiliation(s)
- Federico Riccardi
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano, Trieste, Italy
| | - Giulia Romano
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano, Trieste, Italy
| | - Danilo Licastro
- Laboratorio di Genomica ed Epigenomica, AREA Science Park, Padriciano, Trieste, Italy
| | - Franco Pagani
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano, Trieste, Italy
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7
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Carvalho L, Lasek AW. It is not just about transcription: involvement of brain RNA splicing in substance use disorders. J Neural Transm (Vienna) 2024; 131:495-503. [PMID: 38396082 PMCID: PMC11055753 DOI: 10.1007/s00702-024-02740-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 01/04/2024] [Indexed: 02/25/2024]
Abstract
Alternative splicing is a co-transcriptional process that significantly contributes to the molecular landscape of the cell. It plays a multifaceted role in shaping gene transcription, protein diversity, and functional adaptability in response to environmental cues. Recent studies demonstrate that drugs of abuse have a profound impact on alternative splicing patterns within different brain regions. Drugs like alcohol and cocaine modify the expression of genes responsible for encoding splicing factors, thereby influencing alternative splicing of crucial genes involved in neurotransmission, neurogenesis, and neuroinflammation. Notable examples of these alterations include alcohol-induced changes in splicing factors such as HSPA6 and PCBP1, as well as cocaine's impact on PTBP1 and SRSF11. Beyond the immediate effects of drug exposure, recent research has shed light on the role of alternative splicing in contributing to the risk of substance use disorders (SUDs). This is exemplified by exon skipping events in key genes like ELOVL7, which can elevate the risk of alcohol use disorder. Lastly, drugs of abuse can induce splicing alterations through epigenetic modifications. For example, cocaine exposure leads to alterations in levels of trimethylated lysine 36 of histone H3, which exhibits a robust association with alternative splicing and serves as a reliable predictor for exon exclusion. In summary, alternative splicing has emerged as a critical player in the complex interplay between drugs of abuse and the brain, offering insights into the molecular underpinnings of SUDs.
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Affiliation(s)
- Luana Carvalho
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, 1220 E. Broad ST, Box 980613, Richmond, VA, 23298, USA.
| | - Amy W Lasek
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, 1220 E. Broad ST, Box 980613, Richmond, VA, 23298, USA
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8
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Alfonso-Gonzalez C, Hilgers V. (Alternative) transcription start sites as regulators of RNA processing. Trends Cell Biol 2024:S0962-8924(24)00033-3. [PMID: 38531762 DOI: 10.1016/j.tcb.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/28/2024]
Abstract
Alternative transcription start site usage (ATSS) is a widespread regulatory strategy that enables genes to choose between multiple genomic loci for initiating transcription. This mechanism is tightly controlled during development and is often altered in disease states. In this review, we examine the growing evidence highlighting a role for transcription start sites (TSSs) in the regulation of mRNA isoform selection during and after transcription. We discuss how the choice of transcription initiation sites influences RNA processing and the importance of this crosstalk for cell identity and organism function. We also speculate on possible mechanisms underlying the integration of transcriptional and post-transcriptional processes.
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Affiliation(s)
- Carlos Alfonso-Gonzalez
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, Albert Ludwigs University, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS- MCB), 79108 Freiburg, Germany
| | - Valérie Hilgers
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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9
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Marie P, Bazire M, Ladet J, Ameur LB, Chahar S, Fontrodona N, Sexton T, Auboeuf D, Bourgeois CF, Mortreux F. Gene-to-gene coordinated regulation of transcription and alternative splicing by 3D chromatin remodeling upon NF-κB activation. Nucleic Acids Res 2024; 52:1527-1543. [PMID: 38272542 PMCID: PMC10899780 DOI: 10.1093/nar/gkae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 12/13/2023] [Accepted: 01/05/2024] [Indexed: 01/27/2024] Open
Abstract
The NF-κB protein p65/RelA plays a pivotal role in coordinating gene expression in response to diverse stimuli, including viral infections. At the chromatin level, p65/RelA regulates gene transcription and alternative splicing through promoter enrichment and genomic exon occupancy, respectively. The intricate ways in which p65/RelA simultaneously governs these functions across various genes remain to be fully elucidated. In this study, we employed the HTLV-1 Tax oncoprotein, a potent activator of NF-κB, to investigate its influence on the three-dimensional organization of the genome, a key factor in gene regulation. We discovered that Tax restructures the 3D genomic landscape, bringing together genes based on their regulation and splicing patterns. Notably, we found that the Tax-induced gene-gene contact between the two master genes NFKBIA and RELA is associated with their respective changes in gene expression and alternative splicing. Through dCas9-mediated approaches, we demonstrated that NFKBIA-RELA interaction is required for alternative splicing regulation and is caused by an intragenic enrichment of p65/RelA on RELA. Our findings shed light on new regulatory mechanisms upon HTLV-1 Tax and underscore the integral role of p65/RelA in coordinated regulation of NF-κB-responsive genes at both transcriptional and splicing levels in the context of the 3D genome.
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Affiliation(s)
- Paul Marie
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Matéo Bazire
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Julien Ladet
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Lamya Ben Ameur
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Sanjay Chahar
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Nicolas Fontrodona
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Tom Sexton
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Didier Auboeuf
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Cyril F Bourgeois
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Franck Mortreux
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
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10
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Ahmad H, Chetlangia N, Prasanth SG. Chromatin's Influence on Pre-Replication Complex Assembly and Function. BIOLOGY 2024; 13:152. [PMID: 38534422 DOI: 10.3390/biology13030152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024]
Abstract
In all eukaryotes, the initiation of DNA replication requires a stepwise assembly of factors onto the origins of DNA replication. This is pioneered by the Origin Recognition Complex, which recruits Cdc6. Together, they bring Cdt1, which shepherds MCM2-7 to form the OCCM complex. Sequentially, a second Cdt1-bound hexamer of MCM2-7 is recruited by ORC-Cdc6 to form an MCM double hexamer, which forms a part of the pre-RC. Although the mechanism of ORC binding to DNA varies across eukaryotes, how ORC is recruited to replication origins in human cells remains an area of intense investigation. This review discusses how the chromatin environment influences pre-RC assembly, function, and, eventually, origin activity.
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Affiliation(s)
- Hina Ahmad
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Neha Chetlangia
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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11
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Xie JQ, Zhou X, Jia ZC, Su CF, Zhang Y, Fernie AR, Zhang J, Du ZY, Chen MX. Alternative Splicing, An Overlooked Defense Frontier of Plants with Respect to Bacterial Infection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37916838 DOI: 10.1021/acs.jafc.3c04163] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Disease represents a major problem in sustainable agricultural development. Plants interact closely with various microorganisms during their development and in response to the prevailing environment. In particular, pathogenic microorganisms can cause plant diseases, affecting the fertility, yield, and longevity of plants. During the long coevolution of plants and their pathogens, plants have evolved both molecular pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) signaling networks in order to regulate host cells in response to pathogen infestation. Additionally, in the postgenomic era, alternative splicing (AS) has become uncovered as one of the major drivers of proteome diversity, and abnormal RNA splicing is closely associated with bacterial infections. Currently, the complexity of host-bacteria interactions is a much studied area of research that has shown steady progress over the past decade. Although the development of high-throughput sequencing technologies and their application in transcriptomes have revolutionized our understanding of AS, many mechanisms related to host-bacteria interactions remain still unclear. To this end, this review summarizes the changes observed in AS during host-bacteria interactions and outlines potential therapeutics for bacterial diseases based on existing studies. In doing so, we hope to provide guidelines for plant disease management in agriculture.
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Affiliation(s)
- Ji-Qin Xie
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou 550025, China
| | - Xiang Zhou
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Zi-Chang Jia
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Chang-Feng Su
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou 550025, China
| | - Youjun Zhang
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Golm, Germany
| | - Alisdair R Fernie
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Golm, Germany
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Zhi-Yan Du
- Department of Molecular Biosciences & Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Mo-Xian Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
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12
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Azhar M, Xu C, Jiang X, Li W, Cao Y, Zhu X, Xing X, Wu L, Zou J, Meng L, Cheng Y, Han W, Bao J. The arginine methyltransferase Prmt1 coordinates the germline arginine methylome essential for spermatogonial homeostasis and male fertility. Nucleic Acids Res 2023; 51:10428-10450. [PMID: 37739418 PMCID: PMC10602896 DOI: 10.1093/nar/gkad769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 08/30/2023] [Accepted: 09/08/2023] [Indexed: 09/24/2023] Open
Abstract
Arginine methylation, catalyzed by the protein arginine methyltransferases (PRMTs), is a common post-translational protein modification (PTM) that is engaged in a plethora of biological events. However, little is known about how the methylarginine-directed signaling functions in germline development. In this study, we discover that Prmt1 is predominantly distributed in the nuclei of spermatogonia but weakly in the spermatocytes throughout mouse spermatogenesis. By exploiting a combination of three Cre-mediated Prmt1 knockout mouse lines, we unravel that Prmt1 is essential for spermatogonial establishment and maintenance, and that Prmt1-catalyzed asymmetric methylarginine coordinates inherent transcriptional homeostasis within spermatogonial cells. In conjunction with high-throughput CUT&Tag profiling and modified mini-bulk Smart-seq2 analyses, we unveil that the Prmt1-deposited H4R3me2a mark is permissively enriched at promoter and exon/intron regions, and sculpts a distinctive transcriptomic landscape as well as the alternative splicing pattern, in the mouse spermatogonia. Collectively, our study provides the genetic and mechanistic evidence that connects the Prmt1-deposited methylarginine signaling to the establishment and maintenance of a high-fidelity transcriptomic identity in orchestrating spermatogonial development in the mammalian germline.
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Affiliation(s)
- Muhammad Azhar
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Caoling Xu
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Xue Jiang
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Wenqing Li
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Yuzhu Cao
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Xiaoli Zhu
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Xuemei Xing
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Limin Wu
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Jiaqi Zou
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Lan Meng
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Yu Cheng
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Wenjie Han
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Jianqiang Bao
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
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13
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Sanchez A, Lhuillier J, Grosjean G, Ayadi L, Maenner S. The Long Non-Coding RNA ANRIL in Cancers. Cancers (Basel) 2023; 15:4160. [PMID: 37627188 PMCID: PMC10453084 DOI: 10.3390/cancers15164160] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
ANRIL (Antisense Noncoding RNA in the INK4 Locus), a long non-coding RNA encoded in the human chromosome 9p21 region, is a critical factor for regulating gene expression by interacting with multiple proteins and miRNAs. It has been found to play important roles in various cellular processes, including cell cycle control and proliferation. Dysregulation of ANRIL has been associated with several diseases like cancers and cardiovascular diseases, for instance. Understanding the oncogenic role of ANRIL and its potential as a diagnostic and prognostic biomarker in cancer is crucial. This review provides insights into the regulatory mechanisms and oncogenic significance of the 9p21 locus and ANRIL in cancer.
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Affiliation(s)
| | | | | | - Lilia Ayadi
- CNRS, Université de Lorraine, IMoPA, F-54000 Nancy, France
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14
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Ray M, Conard AM, Urban J, Mahableshwarkar P, Aguilera J, Huang A, Vaidyanathan S, Larschan E. Sex-specific splicing occurs genome-wide during early Drosophila embryogenesis. eLife 2023; 12:e87865. [PMID: 37466240 PMCID: PMC10400075 DOI: 10.7554/elife.87865] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
Sex-specific splicing is an essential process that regulates sex determination and drives sexual dimorphism. Yet, how early in development widespread sex-specific transcript diversity occurs was unknown because it had yet to be studied at the genome-wide level. We use the powerful Drosophila model to show that widespread sex-specific transcript diversity occurs early in development, concurrent with zygotic genome activation. We also present a new pipeline called time2Splice to quantify changes in alternative splicing over time. Furthermore, we determine that one of the consequences of losing an essential maternally deposited pioneer factor called CLAMP (chromatin-linked adapter for MSL proteins) is altered sex-specific splicing of genes involved in diverse biological processes that drive development. Overall, we show that sex-specific differences in transcript diversity exist even at the earliest stages of development..
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Affiliation(s)
- Mukulika Ray
- MCB department, Brown UniversityProvidenceUnited States
| | | | - Jennifer Urban
- Biology department, Johns Hopkins UniversityBaltimoreUnited States
| | - Pranav Mahableshwarkar
- MCB department, Brown UniversityProvidenceUnited States
- CCMB department, Brown UniversityProvidenceUnited States
| | | | - Annie Huang
- MCB department, Brown UniversityProvidenceUnited States
| | - Smriti Vaidyanathan
- MCB department, Brown UniversityProvidenceUnited States
- CCMB department, Brown UniversityProvidenceUnited States
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15
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Gohr A, Iñiguez LP, Torres-Méndez A, Bonnal S, Irimia M. Insplico: effective computational tool for studying splicing order of adjacent introns genome-wide with short and long RNA-seq reads. Nucleic Acids Res 2023; 51:e56. [PMID: 37026474 PMCID: PMC10250204 DOI: 10.1093/nar/gkad244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 03/13/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Although splicing occurs largely co-transcriptionally, the order by which introns are removed does not necessarily follow the order in which they are transcribed. Whereas several genomic features are known to influence whether or not an intron is spliced before its downstream neighbor, multiple questions related to adjacent introns' splicing order (AISO) remain unanswered. Here, we present Insplico, the first standalone software for quantifying AISO that works with both short and long read sequencing technologies. We first demonstrate its applicability and effectiveness using simulated reads and by recapitulating previously reported AISO patterns, which unveiled overlooked biases associated with long read sequencing. We next show that AISO around individual exons is remarkably constant across cell and tissue types and even upon major spliceosomal disruption, and it is evolutionarily conserved between human and mouse brains. We also establish a set of universal features associated with AISO patterns across various animal and plant species. Finally, we used Insplico to investigate AISO in the context of tissue-specific exons, particularly focusing on SRRM4-dependent microexons. We found that the majority of such microexons have non-canonical AISO, in which the downstream intron is spliced first, and we suggest two potential modes of SRRM4 regulation of microexons related to their AISO and various splicing-related features. Insplico is available on gitlab.com/aghr/insplico.
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Affiliation(s)
- André Gohr
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luis P Iñiguez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antonio Torres-Méndez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sophie Bonnal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
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16
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Mehlferber MM, Kuyumcu-Martinez M, Miller CL, Sheynkman GM. Transcription factors and splice factors - interconnected regulators of stem cell differentiation. CURRENT STEM CELL REPORTS 2023; 9:31-41. [PMID: 38939410 PMCID: PMC11210451 DOI: 10.1007/s40778-023-00227-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2023] [Indexed: 06/29/2024]
Abstract
Purpose of review The underlying molecular mechanisms that direct stem cell differentiation into fully functional, mature cells remain an area of ongoing investigation. Cell state is the product of the combinatorial effect of individual factors operating within a coordinated regulatory network. Here, we discuss the contribution of both gene regulatory and splicing regulatory networks in defining stem cell fate during differentiation and the critical role of protein isoforms in this process. Recent findings We review recent experimental and computational approaches that characterize gene regulatory networks, splice regulatory networks, and the resulting transcriptome and proteome they mediate during differentiation. Such approaches include long-read RNA sequencing, which has demonstrated high-resolution profiling of mRNA isoforms, and Cas13-based CRISPR, which could make possible high-throughput isoform screening. Collectively, these developments enable systems-level profiling of factors contributing to cell state. Summary Overall, gene and splice regulatory networks are important in defining cell state. The emerging high-throughput systems-level approaches will characterize the gene regulatory network components necessary in driving stem cell differentiation.
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Affiliation(s)
- Madison M Mehlferber
- Department of Biochemistry and Molecular Genetics, University Virginia, Charlottesville, VA 22903
| | - Muge Kuyumcu-Martinez
- Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Fontaine Medical Office Building 1, 415 Ray C. Hunt Dr, Charlottesville, VA 22903
| | - Clint L Miller
- Department of Public Health Sciences, Department of Biochemistry and Molecular Genetics, and Department of Biomedical Engineering, University of Virginia, Multistory Building, West Complex, 1335 Lee St, Charlottesville, VA 22908, PO Box 800717, Charlottesville, Virginia 22908
| | - Gloria M Sheynkman
- Department of Molecular Physiology and Biological Physics, Center for Public Health Genomics, UVA Comprehensive Cancer Center, Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22903
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17
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Girardini KN, Olthof AM, Kanadia RN. Introns: the "dark matter" of the eukaryotic genome. Front Genet 2023; 14:1150212. [PMID: 37260773 PMCID: PMC10228655 DOI: 10.3389/fgene.2023.1150212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/28/2023] [Indexed: 06/02/2023] Open
Abstract
The emergence of introns was a significant evolutionary leap that is a major distinguishing feature between prokaryotic and eukaryotic genomes. While historically introns were regarded merely as the sequences that are removed to produce spliced transcripts encoding functional products, increasingly data suggests that introns play important roles in the regulation of gene expression. Here, we use an intron-centric lens to review the role of introns in eukaryotic gene expression. First, we focus on intron architecture and how it may influence mechanisms of splicing. Second, we focus on the implications of spliceosomal snRNAs and their variants on intron splicing. Finally, we discuss how the presence of introns and the need to splice them influences transcription regulation. Despite the abundance of introns in the eukaryotic genome and their emerging role regulating gene expression, a lot remains unexplored. Therefore, here we refer to introns as the "dark matter" of the eukaryotic genome and discuss some of the outstanding questions in the field.
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Affiliation(s)
- Kaitlin N. Girardini
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
| | - Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
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18
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Bhatnagar A, Krick K, Karisetty BC, Armour EM, Heller EA, Elefant F. Tip60's Novel RNA-Binding Function Modulates Alternative Splicing of Pre-mRNA Targets Implicated in Alzheimer's Disease. J Neurosci 2023; 43:2398-2423. [PMID: 36849418 PMCID: PMC10072303 DOI: 10.1523/jneurosci.2331-22.2023] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
The severity of Alzheimer's disease (AD) progression involves a complex interplay of genetics, age, and environmental factors orchestrated by histone acetyltransferase (HAT)-mediated neuroepigenetic mechanisms. While disruption of Tip60 HAT action in neural gene control is implicated in AD, alternative mechanisms underlying Tip60 function remain unexplored. Here, we report a novel RNA binding function for Tip60 in addition to its HAT function. We show that Tip60 preferentially interacts with pre-mRNAs emanating from its chromatin neural gene targets in the Drosophila brain and this RNA binding function is conserved in human hippocampus and disrupted in Drosophila brains that model AD pathology and in AD patient hippocampus of either sex. Since RNA splicing occurs co-transcriptionally and alternative splicing (AS) defects are implicated in AD, we investigated whether Tip60-RNA targeting modulates splicing decisions and whether this function is altered in AD. Replicate multivariate analysis of transcript splicing (rMATS) analysis of RNA-Seq datasets from wild-type and AD fly brains revealed a multitude of mammalian-like AS defects. Strikingly, over half of these altered RNAs are identified as bona-fide Tip60-RNA targets that are enriched for in the AD-gene curated database, with some of these AS alterations prevented against by increasing Tip60 in the fly brain. Further, human orthologs of several Tip60-modulated splicing genes in Drosophila are well characterized aberrantly spliced genes in human AD brains, implicating disruption of Tip60's splicing function in AD pathogenesis. Our results support a novel RNA interaction and splicing regulatory function for Tip60 that may underly AS impairments that hallmark AD etiology.SIGNIFICANCE STATEMENT Alzheimer's disease (AD) has recently emerged as a hotbed for RNA alternative splicing (AS) defects that alter protein function in the brain yet causes remain unclear. Although recent findings suggest convergence of epigenetics with co-transcriptional AS, whether epigenetic dysregulation in AD pathology underlies AS defects remains unknown. Here, we identify a novel RNA interaction and splicing regulatory function for Tip60 histone acetyltransferase (HAT) that is disrupted in Drosophila brains modeling AD pathology and in human AD hippocampus. Importantly, mammalian orthologs of several Tip60-modulated splicing genes in Drosophila are well characterized aberrantly spliced genes in human AD brain. We propose that Tip60-mediated AS modulation is a conserved critical posttranscriptional step that may underlie AS defects now characterized as hallmarks of AD.
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Affiliation(s)
- Akanksha Bhatnagar
- Department of Biology, Drexel University, Philadelphia, Pennsylvania 19104
| | - Keegan Krick
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | | | - Ellen M Armour
- Department of Biology, Drexel University, Philadelphia, Pennsylvania 19104
| | - Elizabeth A Heller
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Felice Elefant
- Department of Biology, Drexel University, Philadelphia, Pennsylvania 19104
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19
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Agosto LM, Mallory MJ, Ferretti MB, Blake D, Krick KS, Gazzara MR, Garcia BA, Lynch KW. Alternative splicing of HDAC7 regulates its interaction with 14-3-3 proteins to alter histone marks and target gene expression. Cell Rep 2023; 42:112273. [PMID: 36933216 PMCID: PMC10113009 DOI: 10.1016/j.celrep.2023.112273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/28/2023] [Accepted: 03/02/2023] [Indexed: 03/19/2023] Open
Abstract
Chromatin regulation and alternative splicing are both critical mechanisms guiding gene expression. Studies have demonstrated that histone modifications can influence alternative splicing decisions, but less is known about how alternative splicing may impact chromatin. Here, we demonstrate that several genes encoding histone-modifying enzymes are alternatively spliced downstream of T cell signaling pathways, including HDAC7, a gene previously implicated in controlling gene expression and differentiation in T cells. Using CRISPR-Cas9 gene editing and cDNA expression, we show that differential inclusion of HDAC7 exon 9 controls the interaction of HDAC7 with protein chaperones, resulting in changes to histone modifications and gene expression. Notably, the long isoform, which is induced by the RNA-binding protein CELF2, promotes expression of several critical T cell surface proteins including CD3, CD28, and CD69. Thus, we demonstrate that alternative splicing of HDAC7 has a global impact on histone modification and gene expression that contributes to T cell development.
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Affiliation(s)
- Laura M Agosto
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael J Mallory
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Max B Ferretti
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Davia Blake
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Keegan S Krick
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew R Gazzara
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Genomic and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA; Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA.
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20
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Boumpas P, Merabet S, Carnesecchi J. Integrating transcription and splicing into cell fate: Transcription factors on the block. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1752. [PMID: 35899407 DOI: 10.1002/wrna.1752] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/22/2022] [Accepted: 07/01/2022] [Indexed: 11/10/2022]
Abstract
Transcription factors (TFs) are present in all life forms and conserved across great evolutionary distances in eukaryotes. From yeast to complex multicellular organisms, they are pivotal players of cell fate decision by orchestrating gene expression at diverse molecular layers. Notably, TFs fine-tune gene expression by coordinating RNA fate at both the expression and splicing levels. They regulate alternative splicing, an essential mechanism for cell plasticity, allowing the production of many mRNA and protein isoforms in precise cell and tissue contexts. Despite this apparent role in splicing, how TFs integrate transcription and splicing to ultimately orchestrate diverse cell functions and cell fate decisions remains puzzling. We depict substantial studies in various model organisms underlining the key role of TFs in alternative splicing for promoting tissue-specific functions and cell fate. Furthermore, we emphasize recent advances describing the molecular link between the transcriptional and splicing activities of TFs. As TFs can bind both DNA and/or RNA to regulate transcription and splicing, we further discuss their flexibility and compatibility for DNA and RNA substrates. Finally, we propose several models integrating transcription and splicing activities of TFs in the coordination and diversification of cell and tissue identities. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Splicing Mechanisms.
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Affiliation(s)
- Panagiotis Boumpas
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard-Lyon 1, Lyon, France
| | - Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard-Lyon 1, Lyon, France
| | - Julie Carnesecchi
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard-Lyon 1, Lyon, France
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21
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Arfelli VC, Chang YC, Bagnoli JW, Kerbs P, Ciamponi FE, Paz LMDS, Pankivskyi S, de Matha Salone J, Maucuer A, Massirer KB, Enard W, Kuster B, Greif PA, Archangelo LF. UHMK1 is a novel splicing regulatory kinase. J Biol Chem 2023; 299:103041. [PMID: 36803961 PMCID: PMC10033318 DOI: 10.1016/j.jbc.2023.103041] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 01/18/2023] [Accepted: 02/04/2023] [Indexed: 02/19/2023] Open
Abstract
The U2AF Homology Motif Kinase 1 (UHMK1) is the only kinase that contains the U2AF homology motif, a common protein interaction domain among splicing factors. Through this motif, UHMK1 interacts with the splicing factors SF1 and SF3B1, known to participate in the 3' splice site recognition during the early steps of spliceosome assembly. Although UHMK1 phosphorylates these splicing factors in vitro, the involvement of UHMK1 in RNA processing has not previously been demonstrated. Here, we identify novel putative substrates of this kinase and evaluate UHMK1 contribution to overall gene expression and splicing, by integrating global phosphoproteomics, RNA-seq, and bioinformatics approaches. Upon UHMK1 modulation, 163 unique phosphosites were differentially phosphorylated in 117 proteins, of which 106 are novel potential substrates of this kinase. Gene Ontology analysis showed enrichment of terms previously associated with UHMK1 function, such as mRNA splicing, cell cycle, cell division, and microtubule organization. The majority of the annotated RNA-related proteins are components of the spliceosome but are also involved in several steps of gene expression. Comprehensive analysis of splicing showed that UHMK1 affected over 270 alternative splicing events. Moreover, splicing reporter assay further supported UHMK1 function on splicing. Overall, RNA-seq data demonstrated that UHMK1 knockdown had a minor impact on transcript expression and pointed to UHMK1 function in epithelial-mesenchymal transition. Functional assays demonstrated that UHMK1 modulation affects proliferation, colony formation, and migration. Taken together, our data implicate UHMK1 as a splicing regulatory kinase, connecting protein regulation through phosphorylation and gene expression in key cellular processes.
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Affiliation(s)
- Vanessa C Arfelli
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, São Paulo, Brazil
| | - Yun-Chien Chang
- Proteomics and Bioanalytics, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Johannes W Bagnoli
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University (LMU), Martinsried, Germany
| | - Paul Kerbs
- Laboratory for Experimental Leukemia and Lymphoma Research, Munich University Hospital, Ludwig-Maximilians University (LMU), Munich, Germany; German Cancer Consortium (DKTK), partner site Munich, Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felipe E Ciamponi
- Center for Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Laissa M da S Paz
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, São Paulo, Brazil
| | - Serhii Pankivskyi
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | | | - Alexandre Maucuer
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Katlin B Massirer
- Center for Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Wolfgang Enard
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University (LMU), Martinsried, Germany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Philipp A Greif
- Laboratory for Experimental Leukemia and Lymphoma Research, Munich University Hospital, Ludwig-Maximilians University (LMU), Munich, Germany; German Cancer Consortium (DKTK), partner site Munich, Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Leticia Fröhlich Archangelo
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, São Paulo, Brazil.
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22
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Del Giudice M, Foster JG, Peirone S, Rissone A, Caizzi L, Gaudino F, Parlato C, Anselmi F, Arkell R, Guarrera S, Oliviero S, Basso G, Rajan P, Cereda M. FOXA1 regulates alternative splicing in prostate cancer. Cell Rep 2022; 40:111404. [PMID: 36170835 PMCID: PMC9532847 DOI: 10.1016/j.celrep.2022.111404] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/28/2022] [Accepted: 09/01/2022] [Indexed: 11/25/2022] Open
Abstract
Dysregulation of alternative splicing in prostate cancer is linked to transcriptional programs activated by AR, ERG, FOXA1, and MYC. Here, we show that FOXA1 functions as the primary orchestrator of alternative splicing dysregulation across 500 primary and metastatic prostate cancer transcriptomes. We demonstrate that FOXA1 binds to the regulatory regions of splicing-related genes, including HNRNPK and SRSF1. By controlling trans-acting factor expression, FOXA1 exploits an "exon definition" mechanism calibrating alternative splicing toward dominant isoform production. This regulation especially impacts splicing factors themselves and leads to a reduction of nonsense-mediated decay (NMD)-targeted isoforms. Inclusion of the NMD-determinant FLNA exon 30 by FOXA1-controlled oncogene SRSF1 promotes cell growth in vitro and predicts disease recurrence. Overall, we report a role for FOXA1 in rewiring the alternative splicing landscape in prostate cancer through a cascade of events from chromatin access, to splicing factor regulation, and, finally, to alternative splicing of exons influencing patient survival.
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Affiliation(s)
- Marco Del Giudice
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - John G Foster
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Cancer Research UK Barts Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Serena Peirone
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Alberto Rissone
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - Livia Caizzi
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - Federica Gaudino
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - Caterina Parlato
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - Francesca Anselmi
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Department of Life Science and System Biology, Università degli Studi di Torino, via Accademia Albertina 13, 10123 Turin, Italy
| | - Rebecca Arkell
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Cancer Research UK Barts Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Simonetta Guarrera
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - Salvatore Oliviero
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Department of Life Science and System Biology, Università degli Studi di Torino, via Accademia Albertina 13, 10123 Turin, Italy
| | - Giuseppe Basso
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - Prabhakar Rajan
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Cancer Research UK Barts Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; Division of Surgery and Interventional Science, University College London, Charles Bell House, 3 Road Floor, 43-45 Foley Street, London W1W 7TS, UK; The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK; Department of Urology, Barts Health NHS Trust, the Royal London Hospital, Whitechapel Road, London E1 1BB, UK; Department of Uro-oncology, University College London NHS Foundation Trust, 47 Wimpole Street, London W1G 8SE, UK.
| | - Matteo Cereda
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.
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23
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De Kesel J, Fijalkowski I, Taylor J, Ntziachristos P. Splicing dysregulation in human hematologic malignancies: beyond splicing mutations. Trends Immunol 2022; 43:674-686. [PMID: 35850914 DOI: 10.1016/j.it.2022.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022]
Abstract
Splicing is a fundamental process in pre-mRNA maturation. Whereas alternative splicing (AS) enriches the diversity of the proteome, its aberrant regulation can drive oncogenesis. So far, most attention has been given to spliceosome mutations (SMs) in the context of splicing dysregulation in hematologic diseases. However, in recent years, post-translational modifications (PTMs) and transcriptional alterations of splicing factors (SFs), just as epigenetic signatures, have all been shown to contribute to global splicing dysregulation as well. In addition, the contribution of aberrant splicing to the neoantigen repertoire of cancers has been recognized. With the pressing need for novel therapeutics to combat blood cancers, this article provides an overview of emerging mechanisms that contribute to aberrant splicing, as well as their clinical potential.
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Affiliation(s)
- Jonas De Kesel
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent, Ghent, Belgium; Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Igor Fijalkowski
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent, Ghent, Belgium; Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Justin Taylor
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Panagiotis Ntziachristos
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent, Ghent, Belgium; Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
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24
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Imbriano C, Belluti S. Histone Marks-Dependent Effect on Alternative Splicing: New Perspectives for Targeted Splicing Modulation in Cancer? Int J Mol Sci 2022; 23:ijms23158304. [PMID: 35955433 PMCID: PMC9368390 DOI: 10.3390/ijms23158304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Alternative splicing (AS) is a tightly regulated mechanism that generates the complex human proteome from a small number of genes. Cis-regulatory RNA motifs in exons and introns control AS, recruiting positive and negative trans-acting splicing regulators. At a higher level, chromatin affects splicing events. Growing evidence indicates that the popular histone code hypothesis can be extended to RNA-level processes, such as AS. In addition to nucleosome positioning, which can generate transcriptional barriers to shape the final splicing outcome, histone post-translational modifications can contribute to the detailed regulation of single exon inclusion/exclusion. A histone-based system can identify alternatively spliced chromatin stretches, affecting RNAPII elongation locally or recruiting splicing components via adaptor complexes. In tumor cells, several mechanisms trigger misregulated AS events and produce cancer-associated transcripts. On a genome-wide level, aberrant AS can be the consequence of dysfunctional epigenetic splicing code, including altered enrichment in histone post-translational modifications. This review describes the main findings related to the effect of histone modifications and variants on splicing outcome and how a dysfunctional epigenetic splicing code triggers aberrant AS in cancer. In addition, it highlights recent advances in programmable DNA-targeting technologies and their possible application for AS targeted epigenetic modulation.
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25
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Yu H, Chen M, Hu Y, Ou S, Yu X, Liang S, Li N, Yang M, Kong X, Sun C, Jia S, Zhang Q, Liu L, Hurst LD, Li R, Wang W, Wang J. Dynamic reprogramming of H3K9me3 at hominoid-specific retrotransposons during human preimplantation development. Cell Stem Cell 2022; 29:1031-1050.e12. [PMID: 35803225 DOI: 10.1016/j.stem.2022.06.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 04/06/2022] [Accepted: 06/08/2022] [Indexed: 12/13/2022]
Abstract
Reprogramming of H3K9me3-dependent heterochromatin is required for early development. How H3K9me3 is involved in early human development remains, however, largely unclear. Here, we resolve the temporal landscape of H3K9me3 during human preimplantation development and its regulation for diverse hominoid-specific retrotransposons. At the 8-cell stage, H3K9me3 reprogramming at hominoid-specific retrotransposons termed SINE-VNTR-Alu (SVA) facilitates interaction between certain promoters and SVA-derived enhancers, promoting the zygotic genome activation. In trophectoderm, de novo H3K9me3 domains prevent pluripotent transcription factors from binding to hominoid-specific retrotransposons-derived regulatory elements for inner cell mass (ICM)-specific genes. H3K9me3 re-establishment at SVA elements in the ICM is associated with higher transcription of DNA repair genes, when compared with naive human pluripotent stem cells. Our data demonstrate that species-specific reorganization of H3K9me3-dependent heterochromatin at hominoid-specific retrotransposons plays important roles during early human development, shedding light on how the epigenetic regulation for early development has evolved in mammals.
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Affiliation(s)
- Hanwen Yu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Manqi Chen
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Yuanlang Hu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China; The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Songbang Ou
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xiu Yu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Shiqi Liang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Niannian Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Mingzhu Yang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Xuhui Kong
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Chuanbo Sun
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Shiqi Jia
- The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Qingxue Zhang
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Laurence D Hurst
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Ruiqi Li
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Wenjun Wang
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Jichang Wang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China.
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26
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Reixachs‐Solé M, Eyras E. Uncovering the impacts of alternative splicing on the proteome with current omics techniques. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1707. [PMID: 34979593 PMCID: PMC9542554 DOI: 10.1002/wrna.1707] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 12/15/2022]
Abstract
The high-throughput sequencing of cellular RNAs has underscored a broad effect of isoform diversification through alternative splicing on the transcriptome. Moreover, the differential production of transcript isoforms from gene loci has been recognized as a critical mechanism in cell differentiation, organismal development, and disease. Yet, the extent of the impact of alternative splicing on protein production and cellular function remains a matter of debate. Multiple experimental and computational approaches have been developed in recent years to address this question. These studies have unveiled how molecular changes at different steps in the RNA processing pathway can lead to differences in protein production and have functional effects. New and emerging experimental technologies open exciting new opportunities to develop new methods to fully establish the connection between messenger RNA expression and protein production and to further investigate how RNA variation impacts the proteome and cell function. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing Translation > Regulation RNA Evolution and Genomics > Computational Analyses of RNA.
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Affiliation(s)
- Marina Reixachs‐Solé
- The John Curtin School of Medical ResearchAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
- EMBL Australia Partner Laboratory Network and the Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Eduardo Eyras
- The John Curtin School of Medical ResearchAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
- EMBL Australia Partner Laboratory Network and the Australian National UniversityCanberraAustralian Capital TerritoryAustralia
- Catalan Institution for Research and Advanced StudiesBarcelonaSpain
- Hospital del Mar Medical Research Institute (IMIM)BarcelonaSpain
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27
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Corrêa-Velloso JC, Linardi AM, Glaser T, Velloso FJ, Rivas MP, Leite REP, Grinberg LT, Ulrich H, Akins MR, Chiavegatto S, Haddad LA. Fmr1 exon 14 skipping in late embryonic development of the rat forebrain. BMC Neurosci 2022; 23:32. [PMID: 35641906 PMCID: PMC9158170 DOI: 10.1186/s12868-022-00711-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 04/24/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fragile X syndrome, the major cause of inherited intellectual disability among men, is due to deficiency of the synaptic functional regulator FMR1 protein (FMRP), encoded by the FMRP translational regulator 1 (FMR1) gene. FMR1 alternative splicing produces distinct transcripts that may consequently impact FMRP functional roles. In transcripts without exon 14 the translational reading frame is shifted. For deepening current knowledge of the differential expression of Fmr1 exon 14 along the rat nervous system development, we conducted a descriptive study employing quantitative RT-PCR and BLAST of RNA-Seq datasets. RESULTS We observed in the rat forebrain progressive decline of total Fmr1 mRNA from E11 to P112 albeit an elevation on P3; and exon-14 skipping in E17-E20 with downregulation of the resulting mRNA. We tested if the reduced detection of messages without exon 14 could be explained by nonsense-mediated mRNA decay (NMD) vulnerability, but knocking down UPF1, a major component of this pathway, did not increase their quantities. Conversely, it significantly decreased FMR1 mRNA having exon 13 joined with either exon 14 or exon 15 site A. CONCLUSIONS The forebrain in the third embryonic week of the rat development is a period with significant skipping of Fmr1 exon 14. This alternative splicing event chronologically precedes a reduction of total Fmr1 mRNA, suggesting that it may be part of combinatorial mechanisms downregulating the gene's expression in the late embryonic period. The decay of FMR1 mRNA without exon 14 should be mediated by a pathway different from NMD. Finally, we provide evidence of FMR1 mRNA stabilization by UPF1, likely depending on FMRP.
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Affiliation(s)
- Juliana C Corrêa-Velloso
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277 # 327, São Paulo, SP, 05508-090, Brazil
| | - Alessandra M Linardi
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277 # 327, São Paulo, SP, 05508-090, Brazil
| | - Talita Glaser
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Fernando J Velloso
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277 # 327, São Paulo, SP, 05508-090, Brazil
| | - Maria P Rivas
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277 # 327, São Paulo, SP, 05508-090, Brazil
| | - Renata E P Leite
- Department of Pathology, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Lea T Grinberg
- Department of Pathology, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Henning Ulrich
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Michael R Akins
- Department of Biology, Drexel University, Philadelphia, PA, USA
| | - Silvana Chiavegatto
- Department of Pharmacology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil.,Department of Psychiatry, Instituto de Psiquiatria, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Luciana A Haddad
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277 # 327, São Paulo, SP, 05508-090, Brazil.
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28
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Furth N, Shema E. It's all in the combination: decoding the epigenome for cancer research and diagnostics. Curr Opin Genet Dev 2022; 73:101899. [PMID: 35091256 PMCID: PMC9168437 DOI: 10.1016/j.gde.2022.101899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/20/2021] [Accepted: 12/28/2021] [Indexed: 12/14/2022]
Abstract
Genome regulation is governed by the dynamics of chromatin modifications. The extensive and diverse array of DNA and histone modifications allow multiple elements to act combinatorically and direct tissue-specific and cell-specific outcomes. Yet, our ability to elucidate these complex combinations and link them to normal genome regulation, as well as understand their deregulation in cancer, has been hindered by the lack of suitable technologies. Here, we describe recent findings indicating the importance of the combinatorial epigenome, and novel methodologies to measure and characterize these combinations. These complementary methods span multiple disciplines, providing a means to decode epigenetic combinations and link them to biological outcomes. Finally, we discuss the promise of harnessing the rich combinatorial epigenetic information to improve cancer diagnostics and monitoring.
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Affiliation(s)
- Noa Furth
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Efrat Shema
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
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29
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Hinkle ER, Wiedner HJ, Torres EV, Jackson M, Black AJ, Blue RE, Harris SE, Guzman BB, Gentile GM, Lee EY, Tsai YH, Parker J, Dominguez D, Giudice J. Alternative splicing regulation of membrane trafficking genes during myogenesis. RNA (NEW YORK, N.Y.) 2022; 28:523-540. [PMID: 35082143 PMCID: PMC8925968 DOI: 10.1261/rna.078993.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Alternative splicing transitions occur during organ development, and, in numerous diseases, splicing programs revert to fetal isoform expression. We previously found that extensive splicing changes occur during postnatal mouse heart development in genes encoding proteins involved in vesicle-mediated trafficking. However, the regulatory mechanisms of this splicing-trafficking network are unknown. Here, we found that membrane trafficking genes are alternatively spliced in a tissue-specific manner, with striated muscles exhibiting the highest levels of alternative exon inclusion. Treatment of differentiated muscle cells with chromatin-modifying drugs altered exon inclusion in muscle cells. Examination of several RNA-binding proteins revealed that the poly-pyrimidine tract binding protein 1 (PTBP1) and quaking regulate splicing of trafficking genes during myogenesis, and that removal of PTBP1 motifs prevented PTBP1 from binding its RNA target. These findings enhance our understanding of developmental splicing regulation of membrane trafficking proteins which might have implications for muscle disease pathogenesis.
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Affiliation(s)
- Emma R Hinkle
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Hannah J Wiedner
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Eduardo V Torres
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Micaela Jackson
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Adam J Black
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - R Eric Blue
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Sarah E Harris
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Bryan B Guzman
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Gabrielle M Gentile
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Eunice Y Lee
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Joel Parker
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Daniel Dominguez
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jimena Giudice
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- McAllister Heart Institute, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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30
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Epigenetic regulation of human non-coding RNA gene transcription. Biochem Soc Trans 2022; 50:723-736. [PMID: 35285478 DOI: 10.1042/bst20210860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022]
Abstract
Recent investigations on the non-protein-coding transcriptome of human cells have revealed previously hidden layers of gene regulation relying on regulatory non-protein-coding (nc) RNAs, including the widespread ncRNA-dependent regulation of epigenetic chromatin states and of mRNA translation and stability. However, despite its centrality, the epigenetic regulation of ncRNA genes has received relatively little attention. In this mini-review, we attempt to provide a synthetic account of recent literature suggesting an unexpected complexity in chromatin-dependent regulation of ncRNA gene transcription by the three human nuclear RNA polymerases. Emerging common features, like the heterogeneity of chromatin states within ncRNA multigene families and their influence on 3D genome organization, point to unexplored issues whose investigation could lead to a better understanding of the whole human epigenomic network.
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Exploring New Functional Aspects of HTLV-1 RNA-Binding Protein Rex: How Does Rex Control Viral Replication? Viruses 2022; 14:v14020407. [PMID: 35216000 PMCID: PMC8877913 DOI: 10.3390/v14020407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 01/27/2023] Open
Abstract
After integration to the human genome as a provirus, human T-cell leukemia virus type 1 (HTLV-1) utilizes host T cell gene expression machinery for viral replication. The viral RNA-binding protein, Rex, is known to transport unspliced/incompletely spliced viral mRNAs encoding viral structural proteins out of the nucleus to enhance virus particle formation. However, the detailed mechanism of how Rex avoids extra splicing of unspliced/incompletely spliced viral mRNAs and stabilizes them for effective translation is still unclear. To elucidate the underlying molecular mechanism of Rex function, we comprehensively analyzed the changes in gene expression and splicing patterns in Rex-overexpressing T cells. In addition, we identified 81 human proteins interacting with Rex, involved in transcription, splicing, translation, and mRNA quality control. In particular, Rex interacts with NONO and SFPQ, which play important roles in the regulation of transcription and splicing. Accordingly, expression profiles and splicing patterns of a wide variety of genes are significantly changed in Rex-expressing T cells. Especially, the level of vPD-L1 mRNA that lacks the part of exon 4, thus encodes soluble PD-L1 was significantly increased in Rex-expressing cells. Overall, by integrated analysis of these three datasets, we showed for the first time that Rex intervenes the host gene expression machinery throughout the pathway, probably to escort viral unstable mRNAs from transcription (start) to translation (end). Upon exerting its function, Rex may alter the expression level and splicing patterns of various genes, thus influencing the phenotype of the host cell.
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32
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Segelle A, Núñez-Álvarez Y, Oldfield AJ, Webb KM, Voigt P, Luco RF. Histone marks regulate the epithelial-to-mesenchymal transition via alternative splicing. Cell Rep 2022; 38:110357. [PMID: 35172149 DOI: 10.1016/j.celrep.2022.110357] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/20/2021] [Accepted: 01/19/2022] [Indexed: 12/15/2022] Open
Abstract
Histone modifications impact final splicing decisions. However, there is little evidence of the driving role of these marks in inducing cell-specific splicing changes. Using CRISPR epigenome editing tools, we show in an epithelial-to-mesenchymal cell reprogramming system (epithelial-to-mesenchymal transition [EMT]) that a single change in H3K27ac or H3K27me3 levels right at the alternatively spliced exon is necessary and sufficient to induce a splicing change capable of recapitulating important aspects of EMT, such as cell motility and invasiveness. This histone-mark-dependent splicing effect is highly dynamic and mediated by direct recruitment of the splicing regulator PTB to its RNA binding sites. These results support a role for H3K27 marks in inducing a change in the cell's phenotype via regulation of alternative splicing. We propose the dynamic nature of chromatin as a rapid and reversible mechanism to coordinate the splicing response to cell-extrinsic cues, such as induction of EMT.
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Affiliation(s)
- Alexandre Segelle
- Institute of Human Genetics, University of Montpellier, Centre National de la Recherche Scientifique, Montpellier, France
| | - Yaiza Núñez-Álvarez
- Institute of Human Genetics, University of Montpellier, Centre National de la Recherche Scientifique, Montpellier, France
| | - Andrew J Oldfield
- Institute of Human Genetics, University of Montpellier, Centre National de la Recherche Scientifique, Montpellier, France
| | - Kimberly M Webb
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Reini F Luco
- Institute of Human Genetics, University of Montpellier, Centre National de la Recherche Scientifique, Montpellier, France.
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Sergeeva OV, Shcherbinina EY, Shomron N, Zatsepin TS. Modulation of RNA Splicing by Oligonucleotides: Mechanisms of Action and Therapeutic Implications. Nucleic Acid Ther 2022; 32:123-138. [PMID: 35166605 DOI: 10.1089/nat.2021.0067] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Dysregulation of RNA splicing causes many diseases and disorders. Several therapeutic approaches have been developed to correct aberrant alternative splicing events for the treatment of cancers and hereditary diseases, including gene therapy and redirecting splicing, using small molecules or splice switching oligonucleotides (SSO). Significant advances in the chemistry and pharmacology of nucleic acid have led to the development of clinically approved SSO drugs for the treatment of spinal muscular dystrophy and Duchenne muscular dystrophy (DMD). In this review, we discuss the mechanisms of SSO action with emphasis on "less common" approaches to modulate alternative splicing, including bipartite and bifunctional SSO, oligonucleotide decoys for splice factors and SSO-mediated mRNA degradation via AS-NMD and NGD pathways. We briefly discuss the current progress and future perspectives of SSO therapy for rare and ultrarare diseases.
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Affiliation(s)
- Olga V Sergeeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Timofei S Zatsepin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Department of Chemistry, Moscow State University, Moscow, Russia
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34
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Zhang X, Wagner S, Holleley CE, Deakin JE, Matsubara K, Deveson IW, O'Meally D, Patel HR, Ezaz T, Li Z, Wang C, Edwards M, Graves JAM, Georges A. Sex-specific splicing of Z- and W-borne nr5a1 alleles suggests sex determination is controlled by chromosome conformation. Proc Natl Acad Sci U S A 2022; 119:e2116475119. [PMID: 35074916 PMCID: PMC8795496 DOI: 10.1073/pnas.2116475119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/03/2021] [Indexed: 11/18/2022] Open
Abstract
Pogona vitticeps has female heterogamety (ZZ/ZW), but the master sex-determining gene is unknown, as it is for all reptiles. We show that nr5a1 (Nuclear Receptor Subfamily 5 Group A Member 1), a gene that is essential in mammalian sex determination, has alleles on the Z and W chromosomes (Z-nr5a1 and W-nr5a1), which are both expressed and can recombine. Three transcript isoforms of Z-nr5a1 were detected in gonads of adult ZZ males, two of which encode a functional protein. However, ZW females produced 16 isoforms, most of which contained premature stop codons. The array of transcripts produced by the W-borne allele (W-nr5a1) is likely to produce truncated polypeptides that contain a structurally normal DNA-binding domain and could act as a competitive inhibitor to the full-length intact protein. We hypothesize that an altered configuration of the W chromosome affects the conformation of the primary transcript generating inhibitory W-borne isoforms that suppress testis determination. Under this hypothesis, the genetic sex determination (GSD) system of P. vitticeps is a W-borne dominant female-determining gene that may be controlled epigenetically.
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Affiliation(s)
- Xiuwen Zhang
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Susan Wagner
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Clare E Holleley
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
- Australian National Wildlife Collection, Commonwealth Scientific and Industrial Research Organisation, Crace, ACT 2911, Australia
| | - Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Kazumi Matsubara
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Denis O'Meally
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Hardip R Patel
- Genome Sciences Department, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Zhao Li
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Chexu Wang
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Melanie Edwards
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Jennifer A Marshall Graves
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia;
- School of Life Sciences, La Trobe University, Bundoora, VIC 3186, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia;
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35
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Verta JP, Jacobs A. The role of alternative splicing in adaptation and evolution. Trends Ecol Evol 2021; 37:299-308. [PMID: 34920907 DOI: 10.1016/j.tree.2021.11.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/26/2021] [Accepted: 11/19/2021] [Indexed: 01/02/2023]
Abstract
Regulation of gene expression plays a central role in adaptive divergence and evolution. Although the role of gene regulation in microevolutionary processes is gaining wide acceptance, most studies have only investigated the evolution of transcript levels, ignoring the potentially significant role of transcript structures. We argue that variation in alternative splicing plays an important and widely unexplored role in adaptation (e.g., by increasing transcriptome and/or proteome diversity, or buffering potentially deleterious genetic variation). New studies increasingly highlight the potential for independent evolution in alternative splicing and transcript level, providing alternative paths for selection to act upon. We propose that alternative splicing and transcript levels can provide contrasting, nonredundant mechanisms of equal importance for adaptive diversification of gene function and regulation.
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Affiliation(s)
- Jukka-Pekka Verta
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 9, 00790, Helsinki, Finland.
| | - Arne Jacobs
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, G12 8QQ, Glasgow, UK.
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He X, Yu J, Shi H. Pan-Cancer Analysis Reveals Alternative Splicing Characteristics Associated With Immune-Related Adverse Events Elicited by Checkpoint Immunotherapy. Front Pharmacol 2021; 12:797852. [PMID: 34899357 PMCID: PMC8652050 DOI: 10.3389/fphar.2021.797852] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/08/2021] [Indexed: 02/05/2023] Open
Abstract
Immune-related adverse events (irAEs) can impair the effectiveness and safety of immune checkpoint inhibitors (ICIs) and restrict the clinical applications of ICIs in oncology. The predictive biomarkers of irAE are urgently required for early diagnosis and subsequent management. The exact mechanism underlying irAEs remains to be fully elucidated, and the availability of predictive biomarkers is limited. Herein, we performed data mining by combining pharmacovigilance data and pan-cancer transcriptomic information to illustrate the relationships between alternative splicing characteristics and irAE risk of ICIs. Four distinct classes of splicing characteristics considered were associated with splicing factors, neoantigens, splicing isoforms, and splicing levels. Correlation analysis confirmed that expression levels of splicing factors were predictive of irAE risk. Adding DHX16 expression to the bivariate PD-L1 protein expression-fPD1 model markedly enhanced the prediction for irAE. Furthermore, we identified 668 and 1,131 potential predictors based on the correlation of the incidence of irAEs with splicing frequency and isoform expression, respectively. The functional analysis revealed that alternative splicing might contribute to irAE pathogenesis via coordinating innate and adaptive immunity. Remarkably, autoimmune-related genes and autoantigens were preferentially over-represented in these predictors for irAE, suggesting a close link between autoimmunity and irAE occurrence. In addition, we established a trivariate model composed of CDC42EP3-206, TMEM138-211, and IRX3-202, that could better predict the risk of irAE across various cancer types, indicating a potential application as promising biomarkers for irAE. Our study not only highlights the clinical relevance of alternative splicing for irAE development during checkpoint immunotherapy but also sheds new light on the mechanisms underlying irAEs.
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Affiliation(s)
| | | | - Hubing Shi
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
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37
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Leo L, Colonna Romano N. Emerging Single-Cell Technological Approaches to Investigate Chromatin Dynamics and Centromere Regulation in Human Health and Disease. Int J Mol Sci 2021; 22:ijms22168809. [PMID: 34445507 PMCID: PMC8395756 DOI: 10.3390/ijms22168809] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic regulators play a crucial role in establishing and maintaining gene expression states. To date, the main efforts to study cellular heterogeneity have focused on elucidating the variable nature of the chromatin landscape. Specific chromatin organisation is fundamental for normal organogenesis and developmental homeostasis and can be affected by different environmental factors. The latter can lead to detrimental alterations in gene transcription, as well as pathological conditions such as cancer. Epigenetic marks regulate the transcriptional output of cells. Centromeres are chromosome structures that are epigenetically regulated and are crucial for accurate segregation. The advent of single-cell epigenetic profiling has provided finer analytical resolution, exposing the intrinsic peculiarities of different cells within an apparently homogenous population. In this review, we discuss recent advances in methodologies applied to epigenetics, such as CUT&RUN and CUT&TAG. Then, we compare standard and emerging single-cell techniques and their relevance for investigating human diseases. Finally, we describe emerging methodologies that investigate centromeric chromatin specification and neocentromere formation.
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38
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Igamberdiev AU. The drawbridge of nature: Evolutionary complexification as a generation and novel interpretation of coding systems. Biosystems 2021; 207:104454. [PMID: 34126191 DOI: 10.1016/j.biosystems.2021.104454] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 01/25/2023]
Abstract
The phenomenon of evolutionary complexification corresponds to the generation of new coding systems (defined as а codepoiesis by Marcello Barbieri). The whole process of generating novel coding statements that substantiate organizational complexification leads to an expansion of the system that incorporates externality to support newly generated complex structures. During complexifying evolution, the values are assigned to the previously unproven statements via their encoding by using new codes or rearranging the old ones. In this perspective, living systems during evolution continuously realize the proof of Gödel's theorem. In the real physical world, this realization is grounded in the irreversible reduction of the fundamental uncertainty appearing in the self-referential process of internal measurement performed by living systems. It leads to the formation of reflexive loops that establish novel interrelations between the biosystem and the external world and provide a possibility of active anticipatory transformation of externality. We propose a metamathematical framework that can account for the underlying logic of codepoiesis, outline the basic principles of the generation of new coding systems, and describe main codepoietic events in the course of progressive biological evolution. The evolutionary complexification is viewed as a metasystem transition that results in the increase of external work by the system based on the division of labor between its components.
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Affiliation(s)
- Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada.
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39
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TOMM40 RNA Transcription in Alzheimer's Disease Brain and Its Implication in Mitochondrial Dysfunction. Genes (Basel) 2021; 12:genes12060871. [PMID: 34204109 PMCID: PMC8226536 DOI: 10.3390/genes12060871] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 11/24/2022] Open
Abstract
Increasing evidence suggests that the Translocase of Outer Mitochondria Membrane 40 (TOMM40) gene may contribute to the risk of Alzheimer’s disease (AD). Currently, there is no consensus as to whether TOMM40 expression is up- or down-regulated in AD brains, hindering a clear interpretation of TOMM40’s role in this disease. The aim of this study was to determine if TOMM40 RNA levels differ between AD and control brains. We applied RT-qPCR to study TOMM40 transcription in human postmortem brain (PMB) and assessed associations of these RNA levels with genetic variants in APOE and TOMM40. We also compared TOMM40 RNA levels with mitochondrial functions in human cell lines. Initially, we found that the human genome carries multiple TOMM40 pseudogenes capable of producing highly homologous RNAs that can obscure precise TOMM40 RNA measurements. To circumvent this obstacle, we developed a novel RNA expression assay targeting the primary transcript of TOMM40. Using this assay, we showed that TOMM40 RNA was upregulated in AD PMB. Additionally, elevated TOMM40 RNA levels were associated with decreases in mitochondrial DNA copy number and mitochondrial membrane potential in oxidative stress-challenged cells. Overall, differential transcription of TOMM40 RNA in the brain is associated with AD and could be an indicator of mitochondrial dysfunction.
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