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Jones A, Kraus WL. Multiomics analysis of the NAD +-PARP1 axis reveals a role for site-specific ADP-ribosylation in splicing in embryonic stem cells. Genes Dev 2022; 36:601-617. [PMID: 35654456 DOI: 10.1101/gad.349335.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/16/2022] [Indexed: 11/25/2022]
Abstract
The differentiation of embryonic stem cells (ESCs) into a lineage-committed state is a dynamic process involving changes in cellular metabolism, epigenetic modifications, post-translational modifications, gene expression, and RNA processing. Here we integrated data from metabolomic, proteomic, and transcriptomic assays to characterize how alterations in NAD+ metabolism during the differentiation of mouse ESCs lead to alteration of the PARP1-mediated ADP-ribosylated (ADPRylated) proteome and mRNA isoform specialization. Our metabolomic analyses indicate that mESCs use distinct NAD+ biosynthetic pathways in different cell states: the de novo pathway in the pluripotent state, and the salvage and Preiss-Handler pathways as differentiation progresses. We observed a dramatic induction of PARP1 catalytic activity driven by enhanced nuclear NAD+ biosynthesis during the early stages of mESC differentiation (e.g., within 12 h of LIF removal). PARP1-modified proteins in mESCs are enriched for biological processes related to stem cell maintenance, transcriptional regulation, and RNA processing. The PARP1 substrates include core spliceosome components, such as U2AF35 and U2AF65, whose splicing functions are modulated by PARP1-mediated site-specific ADP-ribosylation. Finally, we observed that splicing is dysregulated genome-wide in Parp1 knockout mESCs. Together, these results demonstrate a role for the NAD+-PARP1 axis in the maintenance of mESC state, specifically in the splicing program during differentiation.
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Affiliation(s)
- Aarin Jones
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - W Lee Kraus
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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Gachet-Castro C, Freitas-Castro F, Gonzáles-Córdova RA, da Fonseca CK, Gomes MD, Ishikawa-Ankerhold HC, Baqui MMA. Modulation of the Host Nuclear Compartment by Trypanosoma cruzi Uncovers Effects on Host Transcription and Splicing Machinery. Front Cell Infect Microbiol 2021; 11:718028. [PMID: 34737973 PMCID: PMC8560699 DOI: 10.3389/fcimb.2021.718028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/24/2021] [Indexed: 11/22/2022] Open
Abstract
Host manipulation is a common strategy for invading pathogens. Trypanosoma cruzi, the causative agent of Chagas Disease, lives intracellularly within host cells. During infection, parasite-associated modifications occur to the host cell metabolism and morphology. However, little is known about the effect of T. cruzi infection on the host cell nucleus and nuclear functionality. Here, we show that T. cruzi can modulate host transcription and splicing machinery in non-professional phagocytic cells during infection. We found that T. cruzi regulates host RNA polymerase II (RNAPII) in a time-dependent manner, resulting in a drastic decrease in RNAPII activity. Furthermore, host cell ribonucleoproteins associated with mRNA transcription (hnRNPA1 and AB2) are downregulated concurrently. We reasoned that T. cruzi may hijack the host U2AF35 auxiliary factor, a key regulator for RNA processing, as a strategy to affect the splicing machinery activities directly. In support of our hypothesis, we carried out in vivo splicing assays using an adenovirus E1A pre-mRNA splicing reporter, showing that intracellular T. cruzi directly modulates the host cells by appropriating U2AF35. For the first time, our results provide evidence of a complex and intimate molecular relationship between T. cruzi and the host cell nucleus during infection.
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Affiliation(s)
- Camila Gachet-Castro
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Felipe Freitas-Castro
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Raul Alexander Gonzáles-Córdova
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Carol Kobori da Fonseca
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Marcelo Damário Gomes
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Munira Muhammad Abdel Baqui
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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Kováčová T, Souček P, Hujová P, Freiberger T, Grodecká L. Splicing Enhancers at Intron-Exon Borders Participate in Acceptor Splice Sites Recognition. Int J Mol Sci 2020; 21:ijms21186553. [PMID: 32911621 PMCID: PMC7554774 DOI: 10.3390/ijms21186553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/05/2020] [Accepted: 09/06/2020] [Indexed: 02/07/2023] Open
Abstract
Acceptor splice site recognition (3′ splice site: 3′ss) is a fundamental step in precursor messenger RNA (pre-mRNA) splicing. Generally, the U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) heterodimer recognizes the 3′ss, of which U2AF35 has a dual function: (i) It binds to the intron–exon border of some 3′ss and (ii) mediates enhancer-binding splicing activators’ interactions with the spliceosome. Alternative mechanisms for 3′ss recognition have been suggested, yet they are still not thoroughly understood. Here, we analyzed 3′ss recognition where the intron–exon border is bound by a ubiquitous splicing regulator SRSF1. Using the minigene analysis of two model exons and their mutants, BRCA2 exon 12 and VARS2 exon 17, we showed that the exon inclusion correlated much better with the predicted SRSF1 affinity than 3′ss quality, which were assessed using the Catalog of Inferred Sequence Binding Preferences of RNA binding proteins (CISBP-RNA) database and maximum entropy algorithm (MaxEnt) predictor and the U2AF35 consensus matrix, respectively. RNA affinity purification proved SRSF1 binding to the model 3′ss. On the other hand, knockdown experiments revealed that U2AF35 also plays a role in these exons’ inclusion. Most probably, both factors stochastically bind the 3′ss, supporting exon recognition, more apparently in VARS2 exon 17. Identifying splicing activators as 3′ss recognition factors is crucial for both a basic understanding of splicing regulation and human genetic diagnostics when assessing variants’ effects on splicing.
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Affiliation(s)
- Tatiana Kováčová
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic; (T.K.); (P.S.); (P.H.); (T.F.)
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Přemysl Souček
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic; (T.K.); (P.S.); (P.H.); (T.F.)
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Pavla Hujová
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic; (T.K.); (P.S.); (P.H.); (T.F.)
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Tomáš Freiberger
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic; (T.K.); (P.S.); (P.H.); (T.F.)
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Lucie Grodecká
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic; (T.K.); (P.S.); (P.H.); (T.F.)
- Correspondence:
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Park HY, Lee KC, Jang YH, Kim SK, Thu MP, Lee JH, Kim JK. The Arabidopsis splicing factors, AtU2AF65, At U2AF35, and AtSF1 shuttle between nuclei and cytoplasms. Plant Cell Rep 2017; 36:1113-1123. [PMID: 28432478 DOI: 10.1007/s00299-017-2142-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/12/2017] [Indexed: 05/07/2023]
Abstract
The Arabidopsis splicing factors, AtU2AF65, AtU2AF35, and AtSF1 shuttle between nuclei and cytoplasms. These proteins also move rapidly and continuously in the nuclei, and their movements are affected by ATP depletion. The U2AF65 proteins are splicing factors that interact with SF1 and U2AF35 proteins to promote U2snRNP for the recognition of the pre-mRNA 3' splice site during early spliceosome assembly. We have determined the subcellular localization and movement of these proteins' Arabidopsis homologs. It was found that Arabidopsis U2AF65 homologs, AtU2AF65a, and AtU2AF65b proteins interact with AtU2AF35a and AtU2AF35b, which are Arabidopsis U2AF35 homologs. We have examined the mobility of these proteins including AtSF1 using fluorescence recovery after photobleaching and fluorescence loss in photobleaching analyses. These proteins displayed dynamic movements in nuclei and their movements were affected by ATP depletion. We have also demonstrated that these proteins shuttle between nuclei and cytoplasms, suggesting that they may also function in cytoplasm. These results indicate that such splicing factors show very similar characteristics to their human counterparts, suggesting evolutionary conservation.
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Affiliation(s)
- Hyo-Young Park
- Department of Life Sciences, Korea University, Anam-dong 5 ga, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Keh Chien Lee
- Department of Life Sciences, Korea University, Anam-dong 5 ga, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Yun Hee Jang
- Department of Life Sciences, Korea University, Anam-dong 5 ga, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Soon-Kap Kim
- Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - May Phyo Thu
- Department of Life Sciences, Korea University, Anam-dong 5 ga, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Jeong Hwan Lee
- Department of Life Sciences, Chonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-Si, Jeollabuk-do, 54896, Republic of Korea.
| | - Jeong-Kook Kim
- Department of Life Sciences, Korea University, Anam-dong 5 ga, Seongbuk-gu, Seoul, 02841, Republic of Korea.
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