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The methyltransferase SETD2 couples transcription and splicing by engaging mRNA processing factors through its SHI domain. Nat Commun 2021; 12:1443. [PMID: 33664260 PMCID: PMC7933334 DOI: 10.1038/s41467-021-21663-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
Heterogeneous ribonucleoproteins (hnRNPs) are RNA binding molecules that are involved in key processes such as RNA splicing and transcription. One such hnRNP protein, hnRNP L, regulates alternative splicing (AS) by binding to pre-mRNA transcripts. However, it is unclear what factors contribute to hnRNP L-regulated AS events. Using proteomic approaches, we identified several key factors that co-purify with hnRNP L. We demonstrate that one such factor, the histone methyltransferase SETD2, specifically interacts with hnRNP L in vitro and in vivo. This interaction occurs through a previously uncharacterized domain in SETD2, the SETD2-hnRNP Interaction (SHI) domain, the deletion of which, leads to a reduced H3K36me3 deposition. Functionally, SETD2 regulates a subset of hnRNP L-targeted AS events. Our findings demonstrate that SETD2, by interacting with Pol II as well as hnRNP L, can mediate the crosstalk between the transcription and the splicing machinery. The methylation of Histone 3 at Lysine 36 (H3K36) has been implicated in the regulation of transcription and coupled processes such as mRNA splicing. Here the authors show that the histone methyltransferase SETD2 interacts with hnRNP L to mediate the crosstalk between the transcription and splicing machineries.
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TNFR1-d2 carrying the p.(Thr79Met) pathogenic variant is a potential novel actor of TNFα/TNFR1 signalling regulation in the pathophysiology of TRAPS. Sci Rep 2021; 11:4172. [PMID: 33603056 PMCID: PMC7893027 DOI: 10.1038/s41598-021-83539-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/29/2021] [Indexed: 11/09/2022] Open
Abstract
Binding of tumour necrosis factor α (TNFα) to its receptor (TNFR1) is critical for both survival and death cellular pathways. TNFα/TNFR1 signalling is complex and tightly regulated at different levels to control cell fate decisions. Previously, we identified TNFR1-d2, an exon 2-spliced transcript of TNFRSF1A gene encoding TNFR1, whose splicing may be modulated by polymorphisms associated with inflammatory disorders. Here, we investigated the impact of TNFRSF1A variants involved in TNFR-associated periodic syndrome (TRAPS) on TNFR1-d2 protein expression and activity. We found that TNFR1-d2 could be translated by using an internal translation initiation codon and a de novo internal ribosome entry site (IRES), which resulted in a putative TNFR1 isoform lacking its N-terminal region. The kinetic of assembly of TNFR1-d2 clusters at the cell surface was reduced as compared with full-length TNFR1. Although co-localized with the full-length TNFR1, TNFR1-d2 neither activated nuclear factor (NF)-κB signalling, nor interfered with TNFR1-induced NF-κB activation. Translation of TNFR1-d2 carrying the severe p.(Thr79Met) pathogenic variant (also known as T50M) was initiated at the mutated codon, resulting in an elongated extracellular domain, increased speed to form preassembled clusters in absence of TNFα, and constitutive NF-κB activation. Overall, TNFR1-d2 might reflect the complexity of the TNFR1 signalling pathways and could be involved in TRAPS pathophysiology of patients carrying the p.(Thr79Met) disease-causing variant.
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Léveillé M, Besse-Patin A, Jouvet N, Gunes A, Sczelecki S, Jeromson S, Khan NP, Baldwin C, Dumouchel A, Correia JC, Jannig PR, Boulais J, Ruas JL, Estall JL. PGC-1α isoforms coordinate to balance hepatic metabolism and apoptosis in inflammatory environments. Mol Metab 2020; 34:72-84. [PMID: 32180561 PMCID: PMC7011010 DOI: 10.1016/j.molmet.2020.01.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/31/2019] [Accepted: 01/07/2020] [Indexed: 12/14/2022] Open
Abstract
Objective The liver is regularly exposed to changing metabolic and inflammatory environments. It must sense and adapt to metabolic need while balancing resources required to protect itself from insult. Peroxisome proliferator activated receptor gamma coactivator-1 alpha (PGC-1α) is a transcriptional coactivator expressed as multiple, alternatively spliced variants transcribed from different promoters that coordinate metabolic adaptation and protect against inflammation. It is not known how PGC-1α integrates extracellular signals to balance metabolic and anti-inflammatory outcomes. Methods Primary mouse hepatocytes were used to evaluate the role(s) of different PGC-1α proteins in regulating hepatic metabolism and inflammatory signaling downstream of tumor necrosis factor alpha (TNFα). Gene expression and signaling analysis were combined with biochemical measurement of apoptosis using gain- and loss-of-function in vitro and in vivo. Results Hepatocytes expressed multiple isoforms of PGC-1α, including PGC-1α4, which microarray analysis showed had common and isoform-specific functions linked to metabolism and inflammation compared with canonical PGC-1α1. Whereas PGC-1α1 primarily impacted gene programs of nutrient metabolism and mitochondrial biology, TNFα signaling showed several pathways related to innate immunity and cell death downstream of PGC-1α4. Gain- and loss-of-function models illustrated that PGC-1α4 uniquely enhanced expression of anti-apoptotic gene programs and attenuated hepatocyte apoptosis in response to TNFα or lipopolysaccharide (LPS). This was in contrast to PGC-1α1, which decreased the expression of a wide inflammatory gene network but did not prevent hepatocyte death in response to cytokines. Conclusions PGC-1α variants have distinct, yet complementary roles in hepatic responses to metabolism and inflammation, and we identify PGC-1α4 as an important mitigator of apoptosis. Multiple isoforms of PGC-1α are expressed in hepatocytes, including PGC-1α4. PGC-1α1 and PGC-1α4 share many metabolic targets, but PGC-1α4 has unique functions linked to hepatic inflammatory signalling. PGC-1α4 attenuates hepatocyte apoptosis in response to TNFα and LPS in vitro and in vivo. Inflammatory signaling influences PGC-1α4 localization in hepatocytes.
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Affiliation(s)
- Mélissa Léveillé
- Institut de recherches cliniques de Montreal (IRCM), Montreal, Quebec, Canada; Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Aurèle Besse-Patin
- Institut de recherches cliniques de Montreal (IRCM), Montreal, Quebec, Canada; Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Nathalie Jouvet
- Institut de recherches cliniques de Montreal (IRCM), Montreal, Quebec, Canada; Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Aysim Gunes
- Institut de recherches cliniques de Montreal (IRCM), Montreal, Quebec, Canada; Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Sarah Sczelecki
- Institut de recherches cliniques de Montreal (IRCM), Montreal, Quebec, Canada; Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Stewart Jeromson
- Institut de recherches cliniques de Montreal (IRCM), Montreal, Quebec, Canada
| | - Naveen P Khan
- Institut de recherches cliniques de Montreal (IRCM), Montreal, Quebec, Canada; Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Cindy Baldwin
- Institut de recherches cliniques de Montreal (IRCM), Montreal, Quebec, Canada
| | - Annie Dumouchel
- Institut de recherches cliniques de Montreal (IRCM), Montreal, Quebec, Canada
| | - Jorge C Correia
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Paulo R Jannig
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Jonathan Boulais
- Institut de recherches cliniques de Montreal (IRCM), Montreal, Quebec, Canada
| | - Jorge L Ruas
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Jennifer L Estall
- Institut de recherches cliniques de Montreal (IRCM), Montreal, Quebec, Canada; Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada; Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada.
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Zhou W, Chen Z, Wang Y, Li X, Lu A, Sun X, Liu Z. Systems Pharmacology-Based Method to Assess the Mechanism of Action of Weight-Loss Herbal Intervention Therapy for Obesity. Front Pharmacol 2019; 10:1165. [PMID: 31680953 PMCID: PMC6802489 DOI: 10.3389/fphar.2019.01165] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 09/10/2019] [Indexed: 12/13/2022] Open
Abstract
Obesity is a multi-factorial chronic disease that has become a serious, prevalent, and refractory public health challenge globally because of high rates of various complications. Traditional Chinese medicines (TCMs) as a functional food are considered to be a valuable and readily available resource for treating obesity because of their better therapeutic effects and reduced side effects. However, their "multi-compound" and "multi-target" features make it extremely difficult to interpret the potential mechanism underlying the anti-obesity effects of TCMs from a holistic perspective. An innovative systems-pharmacology approach was employed, which combined absorption, distribution, metabolism, and excretion screening and multiple target fishing, gene ontology enrichment analysis, network pharmacology, and pathway analysis to explore the potential therapeutic mechanism of weight-loss herbal intervention therapy in obesity and related diseases. The current study provides a promising approach to facilitate the development and discovery of new botanical drugs.
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Affiliation(s)
- Wei Zhou
- Department of Respirology and Allergy, The Third Affiliated Hospital of ShenZhen University, Shenzhen, China
- School of Basic Medical Sciences, Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Ziyi Chen
- Department of Respirology and Allergy, The Third Affiliated Hospital of ShenZhen University, Shenzhen, China
| | - Yonghua Wang
- College of Life Sciences, Northwest University, Xi’an, China
| | - Xiumin Li
- Department of Respirology and Allergy, The Third Affiliated Hospital of ShenZhen University, Shenzhen, China
- School of Basic Medical Sciences, Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Aiping Lu
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Xizhuo Sun
- Department of Respirology and Allergy, The Third Affiliated Hospital of ShenZhen University, Shenzhen, China
| | - Zhigang Liu
- Department of Respirology and Allergy, The Third Affiliated Hospital of ShenZhen University, Shenzhen, China
- School of Basic Medical Sciences, Henan University of Traditional Chinese Medicine, Zhengzhou, China
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Temporal Splicing Switches in Elements of the TNF-Pathway Identified by Computational Analysis of Transcriptome Data for Human Cell Lines. Int J Mol Sci 2019; 20:ijms20051182. [PMID: 30857150 PMCID: PMC6429354 DOI: 10.3390/ijms20051182] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 12/22/2022] Open
Abstract
Alternative splicing plays an important role in numerous cellular processes and aberrant splice decisions are associated with cancer. Although some studies point to a regulation of alternative splicing and its effector mechanisms in a time-dependent manner, the extent and consequences of such a regulation remains poorly understood. In the present work, we investigated the time-dependent production of isoforms in two Hodgkin lymphoma cell lines of different progression stages (HD-MY-Z, stage IIIb and L-1236, stage IV) compared to a B lymphoblastoid cell line (LCL-HO) with a focus on tumour necrosis factor (TNF) pathway-related elements. For this, we used newly generated time-course RNA-sequencing data from the mentioned cell lines and applied a computational pipeline to identify genes with isoform-switching behaviour in time. We analysed the temporal profiles of the identified events and evaluated in detail the potential functional implications of alterations in isoform expression for the selected top-switching genes. Our data indicate that elements within the TNF pathway undergo a time-dependent variation in isoform production with a putative impact on cell migration, proliferation and apoptosis. These include the genes TRAF1, TNFRSF12A and NFKB2. Our results point to a role of temporal alternative splicing in isoform production, which may alter the outcome of the TNF pathway and impact on tumorigenesis.
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