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Jiang Y, Yue Y, Lu C, Latif MZ, Liu H, Wang Z, Yin Z, Li Y, Ding X. AtSNU13 modulates pre-mRNA splicing of RBOHD and ALD1 to regulate plant immunity. BMC Biol 2024; 22:153. [PMID: 38982460 PMCID: PMC11234627 DOI: 10.1186/s12915-024-01951-9] [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: 03/12/2024] [Accepted: 07/05/2024] [Indexed: 07/11/2024] Open
Abstract
Pre-mRNA splicing is a significant step for post-transcriptional modifications and functions in a wide range of physiological processes in plants. Human NHP2L binds to U4 snRNA during spliceosome assembly; it is involved in RNA splicing and mediates the development of human tumors. However, no ortholog has yet been identified in plants. Therefore, we report At4g12600 encoding the ortholog NHP2L protein, and AtSNU13 associates with the component of the spliceosome complex; the atsnu13 mutant showed compromised resistance in disease resistance, indicating that AtSNU13 is a positive regulator of plant immunity. Compared to wild-type plants, the atsnu13 mutation resulted in altered splicing patterns for defense-related genes and decreased expression of defense-related genes, such as RBOHD and ALD1. Further investigation shows that AtSNU13 promotes the interaction between U4/U6.U5 tri-snRNP-specific 27 K and the motif in target mRNAs to regulate the RNA splicing. Our study highlights the role of AtSNU13 in regulating plant immunity by affecting the pre-mRNA splicing of defense-related genes.
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Affiliation(s)
- Yanke Jiang
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai an, Shandong, 271018, China
| | - Yingzhe Yue
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai an, Shandong, 271018, China
| | - Chongchong Lu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai an, Shandong, 271018, China
| | - Muhammad Zunair Latif
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai an, Shandong, 271018, China
| | - Haifeng Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Zhaoxu Wang
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai an, Shandong, 271018, China
| | - Ziyi Yin
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai an, Shandong, 271018, China
| | - Yang Li
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai an, Shandong, 271018, China
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai an, Shandong, 271018, China.
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Wu X, Du X, Pian H, Yu D. Effect of Curcumin on Hepatic mRNA and lncRNA Co-Expression in Heat-Stressed Laying Hens. Int J Mol Sci 2024; 25:5393. [PMID: 38791430 PMCID: PMC11121607 DOI: 10.3390/ijms25105393] [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: 04/18/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Heat stress is an important factor affecting poultry production; birds have a range of inflammatory reactions under high-temperature environments. Curcumin has anti-inflammatory and antioxidant effects. The purpose of this experiment was to investigate the effect of dietary curcumin supplementation on the liver transcriptome of laying hens under heat stress conditions. In the animal experiment, a total of 240 Hy-Line brown hens aged 280 days were divided randomly into four different experimental diets with four replicates, and each replicate consisted of 15 hens during a 42-D experiment. The ambient temperature was adjusted to 34 ± 2 °C for 8 h per day, transiting to a range of 22 °C to 28 °C for the remaining 16 h. In the previous study of our lab, it was found that supplemental 150 mg/kg curcumin can improve production performance, antioxidant enzyme activity, and immune function in laying hens under heat stress. To further investigate the regulatory mechanism of curcumin on heat stress-related genes, in total, six samples of three liver tissues from each of 0 mg/kg and 150 mg/kg curcumin test groups were collected for RNA-seq analysis. In the transcriptome analysis, we reported for the first time that the genes related to heat stress of mRNA, such as HSPA8, HSPH1, HSPA2, and DNAJA4, were co-expressed with lncRNA such as XLOC010450, XLOC037987, XLOC053511, XLOC061207, and XLOC100318, and all of these genes are shown to be down-regulated. These findings provide a scientific basis for the possible benefits of dietary curcumin addition in heat-stressed laying hens.
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Affiliation(s)
- Xinyue Wu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (X.W.); (H.P.)
| | - Xubin Du
- Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing 210095, China;
| | - Huifang Pian
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (X.W.); (H.P.)
| | - Debing Yu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (X.W.); (H.P.)
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Hadar S, Meller A, Saida N, Shalgi R. Stress-induced transcriptional readthrough into neighboring genes is linked to intron retention. iScience 2022; 25:105543. [PMID: 36505935 PMCID: PMC9732411 DOI: 10.1016/j.isci.2022.105543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/10/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Exposure to certain stresses leads to readthrough transcription. Using polyA-selected RNA-seq in mouse fibroblasts subjected to heat shock, oxidative, or osmotic stress, we found that readthrough transcription can proceed into proximal downstream genes, in a phenomenon previously termed "read-in." We found that read-in genes share distinctive genomic characteristics; they are GC-rich and extremely short , with genomic features conserved in human. Using ribosome profiling, we found that read-in genes show significantly reduced translation. Strikingly, read-in genes demonstrate marked intron retention, mostly in their first introns, which could not be explained solely by their short introns and GC-richness, features often associated with intron retention. Finally, we revealed H3K36me3 enrichment upstream to read-in genes. Moreover, demarcation of exon-intron junctions by H3K36me3 was absent in read-in first introns. Our data portray a relationship between read-in and intron retention, suggesting they may have co-evolved to facilitate reduced translation of read-in genes during stress.
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Affiliation(s)
- Shani Hadar
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa 31096, Israel
| | - Anatoly Meller
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa 31096, Israel
| | - Naseeb Saida
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa 31096, Israel
| | - Reut Shalgi
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa 31096, Israel,Corresponding author
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4
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A Quality Control Mechanism of Splice Site Selection Abrogated under Stress and in Cancer. Cancers (Basel) 2022; 14:cancers14071750. [PMID: 35406522 PMCID: PMC8996931 DOI: 10.3390/cancers14071750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/14/2022] [Accepted: 03/28/2022] [Indexed: 12/26/2022] Open
Abstract
Simple Summary Splicing and alternative splicing play a major role in regulating gene expression, and mis-regulation of splicing can lead to several diseases, including cancer. The aim of this review is to summarize the current knowledge of a quality control mechanism of splice site selection termed Suppression of Splicing (SOS), proposed to protect cells from splicing at the numerous intronic unused 5′ splice sites, and emphasize its relevance to cancer. This relevance stems from the finding that SOS is abrogated under stress and in cancer resulting in the expression of thousands of aberrant nonsense mRNAs that may be toxic to cells. These findings highlight the unexplored potential of such aberrant isoforms as novel targets for cancer diagnosis and therapies. Abstract Latent 5’ splice sites, highly abundant in human introns, are not normally used. This led to the proposal of a quality control mechanism, Suppression of Splicing (SOS), which protects cells from splicing at the numerous intronic latent sites, and whose activation can generate nonsense mRNAs. SOS was shown to be independent of Nonsense-Mediated mRNA Decay (NMD). Efforts to decipher the SOS mechanism revealed a pivotal role for initiator-tRNA, independent of protein translation. Recently, nucleolin (a multifunctional protein) was found to directly and specifically bind the initiator-tRNA in the nucleus and was shown to be a protein component of SOS, enabling an updated model of the SOS mechanism. Importantly, SOS is abrogated under stress and in cancer (e.g., in breast cancer cells and gliomas), generating thousands of nonsense mRNAs due to activation of latent splicing. The resulting affected human genes cover a variety of functional groups, including genes involved in cell proliferation and differentiation. Furthermore, in oligodendroglioma, the extent of activation of latent splicing increases with the severity of the cancer. Interesting examples are genes expressing aberrant nonsense mRNAs in both breast cancer and glioma, due to latent splicing activation. These findings highlight the unexplored potential of such aberrant isoforms as novel targets for cancer diagnosis and therapies.
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Huang S, Dou J, Li Z, Hu L, Yu Y, Wang Y. Analysis of Genomic Alternative Splicing Patterns in Rat under Heat Stress Based on RNA-Seq Data. Genes (Basel) 2022; 13:genes13020358. [PMID: 35205403 PMCID: PMC8871965 DOI: 10.3390/genes13020358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/13/2022] [Accepted: 02/15/2022] [Indexed: 12/14/2022] Open
Abstract
Heat stress is one of the most severe challenges faced in livestock production in summer. Alternative splicing as an important post-transcriptional regulation is rarely studied in heat-stressed animals. Here, we performed and analyzed RNA-sequencing assays on the liver of Sprague-Dawley rats in control (22 °C, n = 5) and heat stress (4 °C for 120 min, H120; n = 5) groups, resulting in the identification of 636 differentially expressed genes. Identification analysis of the alternative splicing events revealed that heat stress-induced alternative splicing events increased by 20.18%. Compared with other types of alternative splicing events, the alternative start increased the most (43.40%) after heat stress. Twenty-eight genes were differentially alternatively spliced (DAS) between the control and H120 groups, among which Acly, Hnrnpd and mir3064 were also differentially expressed. For DAS genes, Srebf1, Shc1, Srsf5 and Ensa were associated with insulin, while Cast, Srebf1, Tmem33, Tor1aip2, Slc39a7 and Sqstm1 were enriched in the composition of the endoplasmic reticulum. In summary, our study conducts a comprehensive profile of alternative splicing in heat-stressed rats, indicating that alternative splicing is one of the molecular mechanisms of heat stress response in mammals and providing reference data for research on heat tolerance in mammalian livestock.
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Affiliation(s)
- Shangzhen Huang
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.H.); (L.H.); (Y.Y.)
| | - Jinhuan Dou
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 100193, China
- Correspondence: (J.D.); (Y.W.)
| | - Zhongshu Li
- Agricultural College, Yanbian University, Yanji 133002, China;
| | - Lirong Hu
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.H.); (L.H.); (Y.Y.)
| | - Ying Yu
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.H.); (L.H.); (Y.Y.)
| | - Yachun Wang
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.H.); (L.H.); (Y.Y.)
- Correspondence: (J.D.); (Y.W.)
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Shefer K, Boulos A, Gotea V, Arafat M, Ben Chaim Y, Muharram A, Isaac S, Eden A, Sperling J, Elnitski L, Sperling R. A novel role for nucleolin in splice site selection. RNA Biol 2021; 19:333-352. [PMID: 35220879 PMCID: PMC8890436 DOI: 10.1080/15476286.2021.2020455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 12/10/2021] [Indexed: 01/12/2023] Open
Abstract
Latent 5' splice sites, not normally used, are highly abundant in human introns, but are activated under stress and in cancer, generating thousands of nonsense mRNAs. A previously proposed mechanism to suppress latent splicing was shown to be independent of NMD, with a pivotal role for initiator-tRNA independent of protein translation. To further elucidate this mechanism, we searched for nuclear proteins directly bound to initiator-tRNA. Starting with UV-crosslinking, we identified nucleolin (NCL) interacting directly and specifically with initiator-tRNA in the nucleus, but not in the cytoplasm. Next, we show the association of ini-tRNA and NCL with pre-mRNA. We further show that recovery of suppression of latent splicing by initiator-tRNA complementation is NCL dependent. Finally, upon nucleolin knockdown we show activation of latent splicing in hundreds of coding transcripts having important cellular functions. We thus propose nucleolin, a component of the endogenous spliceosome, through its direct binding to initiator-tRNA and its effect on latent splicing, as the first protein of a nuclear quality control mechanism regulating splice site selection to protect cells from latent splicing that can generate defective mRNAs.
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Affiliation(s)
- Kinneret Shefer
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Ayub Boulos
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Valer Gotea
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MDUSA
| | - Maram Arafat
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Yair Ben Chaim
- Department of Natural Sciences, The Open University, RaananaIsrael
| | - Aya Muharram
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Sara Isaac
- Department of Cell and Developmental Biology, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Amir Eden
- Department of Cell and Developmental Biology, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Joseph Sperling
- Department of Organic Chemistry, The Weizmann Institute of Science, RehovotIsrael
| | - Laura Elnitski
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MDUSA
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
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7
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Shepard A, Kissil JL. The use of non-traditional models in the study of cancer resistance-the case of the naked mole rat. Oncogene 2020; 39:5083-5097. [PMID: 32535616 DOI: 10.1038/s41388-020-1355-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/15/2020] [Accepted: 06/03/2020] [Indexed: 12/16/2022]
Abstract
Non-traditional model organisms are typically defined as any model the deviates from the typical laboratory animals, such as mouse, rat, and worm. These models are becoming increasingly important in human disease research, such as cancer, as they often display unusual biological features. Naked mole rats (NMRs) are currently one of the most popular non-traditional model, particularly in the longevity and cancer research fields. NMRs display an exceptionally long lifespan (~30 years), yet have been observed to display a low incidence of cancer, making them excellent candidates for understanding endogenous cancer resistance mechanisms. Over the past decade, many potential resistance mechanisms have been characterized. These include unique biological mechanisms involved in genome stability, protein stability, oxidative metabolism, and other cellular mechanisms such as cell cycle regulation and senescence. This review aims to summarize the many identified cancer resistance mechanisms to understand some of the main hypotheses that have thus far been generated. Many of these proposed mechanisms remain to be fully characterized or confirmed in vivo, giving the field a direction to grow and further understand the complex biology displayed by the NMR.
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Affiliation(s)
- Alyssa Shepard
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Joseph L Kissil
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA.
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8
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Lee BP, Smith M, Buffenstein R, Harries LW. Negligible senescence in naked mole rats may be a consequence of well-maintained splicing regulation. GeroScience 2020; 42:633-651. [PMID: 31927681 PMCID: PMC7205774 DOI: 10.1007/s11357-019-00150-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 12/27/2019] [Indexed: 02/07/2023] Open
Abstract
Naked mole-rats (NMRs) have amongst the longest lifespans relative to body size of any known, non-volant mammalian species. They also display an enhanced stress resistance phenotype, negligible senescence and very rarely are they burdened with chronic age-related diseases. Alternative splicing (AS) dysregulation is emerging as a potential driver of senescence and ageing. We hypothesised that the expression of splicing factors, important regulators of patterns of AS, may differ in NMRs when compared to other species with relatively shorter lifespans. We designed assays specific to NMR splicing regulatory factors and also to a panel of pre-selected brain-expressed genes known to demonstrate senescence-related alterations in AS in other species, and measured age-related changes in the transcript expression levels of these using embryonic and neonatal developmental stages through to extreme old age in NMR brain samples. We also compared splicing factor expression in both young mouse and NMR spleen and brain samples. Both NMR tissues showed approximately double the expression levels observed in tissues from similarly sized mice. Furthermore, contrary to observations in other species, following a brief period of labile expression in early life stages, adult NMR splicing factors and patterns of AS for functionally relevant brain genes remained remarkably stable for at least two decades. These findings are consistent with a model whereby the conservation of splicing regulation and stable patterns of AS may contribute to better molecular stress responses and the avoidance of senescence in NMRs, contributing to their exceptional lifespan and prolonged healthspan.
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Affiliation(s)
- B P Lee
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK
| | - M Smith
- Calico Life Sciences LLC, 1170 Veterans Blvd., South San Francisco, CA, 94080, USA
| | - R Buffenstein
- Calico Life Sciences LLC, 1170 Veterans Blvd., South San Francisco, CA, 94080, USA.
| | - L W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK.
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Sperling R. Small non-coding RNA within the endogenous spliceosome and alternative splicing regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194406. [PMID: 31323432 DOI: 10.1016/j.bbagrm.2019.07.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
Abstract
Splicing and alternative splicing (AS), which occur in the endogenous spliceosome, play major roles in regulating gene expression, and defects in them are involved in numerous human diseases including cancer. Although the mechanism of the splicing reaction is well understood, the regulation of AS remains to be elucidated. A group of essential regulatory factors in gene expression are small non-coding RNAs (sncRNA): e.g. microRNA, mainly known for their inhibitory role in translation in the cytoplasm; and small nucleolar RNA, known for their role in methylating non-coding RNA in the nucleolus. Here I highlight a new aspect of sncRNAs found within the endogenous spliceosome. Assembled in non-canonical complexes and through different base pairing than their canonical ones, spliceosomal sncRNAs can potentially target different RNAs. Examples of spliceosomal sncRNAs regulating AS, regulating gene expression, and acting in a quality control of AS are reviewed, suggesting novel functions for spliceosomal sncRNAs. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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Sperling J, Sperling R. Structural studies of the endogenous spliceosome - The supraspliceosome. Methods 2017; 125:70-83. [PMID: 28412289 PMCID: PMC5546952 DOI: 10.1016/j.ymeth.2017.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 04/01/2017] [Accepted: 04/10/2017] [Indexed: 12/17/2022] Open
Abstract
Pre-mRNA splicing is executed in mammalian cell nuclei within a huge (21MDa) and highly dynamic molecular machine - the supraspliceosome - that individually package pre-mRNA transcripts of different sizes and number of introns into complexes of a unique structure, indicating their universal nature. Detailed structural analysis of this huge and complex structure requires a stepwise approach using hybrid methods. Structural studies of the supraspliceosome by room temperature electron tomography, cryo-electron tomography, and scanning transmission electron microscope mass measurements revealed that it is composed of four native spliceosomes, each resembling an in vitro assembled spliceosome, which are connected by the pre-mRNA. It also elucidated the arrangement of the native spliceosomes within the intact supraspliceosome. Native spliceosomes and supraspliceosomes contain all five spliceosomal U snRNPs together with other splicing factors, and are active in splicing. The structure of the native spliceosome, at a resolution of 20Å, was determined by cryo-electron microscopy, and a unique spatial arrangement of the spliceosomal U snRNPs within the native spliceosome emerged from in silico studies. The supraspliceosome also harbor components for all pre-mRNA processing activities. Thus the supraspliceosome - the endogenous spliceosome - is a stand-alone complete macromolecular machine capable of performing splicing, alternative splicing, and encompass all nuclear pre-mRNA processing activities that the pre-mRNA has to undergo before it can exit from the nucleus to the cytoplasm to encode for protein. Further high-resolution cryo-electron microscopy studies of the endogenous spliceosome are required to decipher the regulation of alternative splicing, and elucidate the network of processing activities within it.
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Affiliation(s)
- Joseph Sperling
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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11
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Menotta M, Biagiotti S, Spapperi C, Orazi S, Rossi L, Chessa L, Leuzzi V, D'Agnano D, Soresina A, Micheli R, Magnani M. ATM splicing variants as biomarkers for low dose dexamethasone treatment of A-T. Orphanet J Rare Dis 2017; 12:126. [PMID: 28679388 PMCID: PMC5498894 DOI: 10.1186/s13023-017-0669-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/12/2017] [Indexed: 12/31/2022] Open
Abstract
Background Ataxia Telangiectasia (AT) is a rare incurable genetic disease, caused by biallelic mutations in the Ataxia Telangiectasia-Mutated (ATM) gene. Treatment with glucocorticoid analogues has been shown to improve the neurological symptoms that characterize this syndrome. Nevertheless, the molecular mechanism underlying the glucocorticoid action in AT patients is not yet understood. Recently, we have demonstrated that Dexamethasone treatment may partly restore ATM activity in AT lymphoblastoid cells by a new ATM transcript, namely ATMdexa1. Results In the present study, the new ATMdexa1 transcript was also identified in vivo, specifically in the PMBCs of AT patients treated with intra-erythrocyte Dexamethasone (EryDex). In these patients it was also possible to isolate new “ATMdexa1 variants” originating from canonical and non-canonical splicing, each containing the coding sequence for the ATM kinase domain. The expression of the ATMdexa1 transcript family was directly related to treatment and higher expression levels of the transcript in patients’ blood correlated with a positive response to Dexamethasone therapy. Neither untreated AT patients nor untreated healthy volunteers possessed detectable levels of the transcripts. ATMdexa1 transcript expression was found to be elevated 8 days after the drug infusion, while it decreased 21 days after treatment. Conclusions For the first time, the expression of ATM splicing variants, similar to those previously observed in vitro, has been found in the PBMCs of patients treated with EryDex. These findings show a correlation between the expression of ATMdexa1 transcripts and the clinical response to low dose dexamethasone administration. Electronic supplementary material The online version of this article (doi:10.1186/s13023-017-0669-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michele Menotta
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", 61029, Urbino, PU, Italy.
| | - Sara Biagiotti
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", 61029, Urbino, PU, Italy
| | - Chiara Spapperi
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", 61029, Urbino, PU, Italy
| | - Sara Orazi
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", 61029, Urbino, PU, Italy
| | - Luigia Rossi
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", 61029, Urbino, PU, Italy
| | - Luciana Chessa
- Department of Clinical and Molecular Medicine, University "La Sapienza", 00198, Rome, Italy
| | - Vincenzo Leuzzi
- Department of Pediatrics and Child Neurology and Psychiatry, University "La Sapienza", Rome, Italy
| | - Daniela D'Agnano
- Department of Pediatrics and Child Neurology and Psychiatry, University "La Sapienza", Rome, Italy
| | - Annarosa Soresina
- Department of Clinical and Experimental Sciences, Pediatrics Clinic and Institute of Molecular Medicine "A. Nocivelli", Unit of Child Neurology and Psychiatry Spedali Civili and University of Brescia, Brescia, Italy
| | - Roberto Micheli
- Department of Clinical and Experimental Sciences, Pediatrics Clinic and Institute of Molecular Medicine "A. Nocivelli", Unit of Child Neurology and Psychiatry Spedali Civili and University of Brescia, Brescia, Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", 61029, Urbino, PU, Italy
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12
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Yamamoto K, Furukawa MT, Fukumura K, Kawamura A, Yamada T, Suzuki H, Hirose T, Sakamoto H, Inoue K. Control of the heat stress-induced alternative splicing of a subset of genes by hnRNP K. Genes Cells 2016; 21:1006-14. [DOI: 10.1111/gtc.12400] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 07/06/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Koichi Yamamoto
- Bio Process Research and Development Laboratories; Kyowa Hakko Kirin Co. Ltd; 100-1 Hagiwara-machi Takasaki Gunma 370-0013 Japan
- Department of Biology; Graduate School of Science; Kobe University; Kobe 657-8501 Japan
| | - Mari T. Furukawa
- Department of Biology; Graduate School of Science; Kobe University; Kobe 657-8501 Japan
| | - Kazuhiro Fukumura
- Department of Biology; Graduate School of Science; Kobe University; Kobe 657-8501 Japan
- Institute for Comprehensive Medical Science (ICMS); Fujita Health University; Toyoake Aichi 470-1192 Japan
| | - Arisa Kawamura
- Department of Biology; Graduate School of Science; Kobe University; Kobe 657-8501 Japan
| | - Tomoko Yamada
- Department of Biology; Graduate School of Science; Kobe University; Kobe 657-8501 Japan
| | - Hitoshi Suzuki
- Japan Advanced Institute of Science and Technology; Nomi Ishikawa 923-1292 Japan
| | - Tetsuro Hirose
- Institute for Genetic Medicine; Hokkaido University; Sapporo 060-0815 Japan
| | - Hiroshi Sakamoto
- Department of Biology; Graduate School of Science; Kobe University; Kobe 657-8501 Japan
| | - Kunio Inoue
- Department of Biology; Graduate School of Science; Kobe University; Kobe 657-8501 Japan
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13
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Lin L, Swerdel MR, Lazaropoulos MP, Hoffman GS, Toro-Ramos AJ, Wright J, Lederman H, Chen J, Moore JC, Hart RP. Spontaneous ATM Gene Reversion in A-T iPSC to Produce an Isogenic Cell Line. Stem Cell Reports 2015; 5:1097-1108. [PMID: 26677768 PMCID: PMC4682125 DOI: 10.1016/j.stemcr.2015.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 10/16/2015] [Accepted: 10/19/2015] [Indexed: 12/21/2022] Open
Abstract
A spontaneously reverted iPSC line was identified from an A-T subject with heterozygous ATM truncation mutations. The reverted iPSC line expressed ATM protein and was capable of radiation-induced phosphorylation of CHK2 and H2A.X. Genome-wide SNP analysis confirmed a match to source T cells and also to a distinct, non-reverted iPSC line from the same subject. Rearranged T cell receptor sequences predict that the iPSC culture originated as several independently reprogrammed cells that resolved into a single major clone, suggesting that gene correction likely occurred early in the reprogramming process. Gene expression analysis comparing ATM(-/-) iPSC lines to unrelated ATM(+/-) cells identifies a large number of differences, but comparing only the isogenic pair of A-T iPSC lines reveals that the primary pathway affected by loss of ATM is a diminished expression of p53-related mRNAs. Gene reversion in culture, although likely a rare event, provided a novel, reverted cell line for studying ATM function.
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Affiliation(s)
- Lucy Lin
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Mavis R Swerdel
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Michael P Lazaropoulos
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Gary S Hoffman
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Alana J Toro-Ramos
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Jennifer Wright
- A-T Clinic, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Howard Lederman
- A-T Clinic, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jianmin Chen
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Jennifer C Moore
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA; Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA; Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA; Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA.
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14
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Nevo Y, Sperling J, Sperling R. Heat shock activates splicing at latent alternative 5' splice sites in nematodes. Nucleus 2015; 6:225-35. [PMID: 25634319 DOI: 10.1080/19491034.2015.1010956] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Pre-mRNA splicing is essential for the regulation of gene expression in eukaryotes and is fundamental in development and cancer, and involves the selection of a consensus sequence that defines the 5' splice site (5'SS). Human introns harbor multiple sequences that conform to the 5'SS consensus, which are not used under normal growth conditions. Under heat shock conditions, splicing at such intronic latent 5'SSs occurred in thousands of human transcripts, resulting in pre-maturely terminated aberrant proteins. Here we performed a survey of the C. elegans genome, showing that worm's introns contain latent 5'SSs, whose use for splicing would have resulted in pre-maturely terminated mRNAs. Splicing at these latent 5'SSs could not be detected under normal growth conditions, while heat shock activated latent splicing in a number of tested C. elegans transcripts. Two scenarios could account for the lack of latent splicing under normal growth conditions (i) Splicing at latent 5'SSs do occur, but the nonsense mRNAs thus formed are rapidly and efficiently degraded (e.g. by NMD); and (ii) Splicing events at intronic latent 5'SSs are suppressed. Here we support the second scenario, because, nematode smg mutants that are devoid of NMD-essential factors, did not show latent splicing under normal growth conditions. Hence, these experiments together with our previous experiments in mammalian cells, indicate the existence of a nuclear quality control mechanism, termed Suppression Of Splicing (SOS), which discriminates between latent and authentic 5'SSs in an open reading frame dependent manner, and allows splicing only at the latter. Our results show that SOS is an evolutionary conserved mechanism, probably shared by most eukaryotes.
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Affiliation(s)
- Yuval Nevo
- a Department of Genetics; The Hebrew University of Jerusalem ; Jerusalem , Israel
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15
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Shefer K, Sperling J, Sperling R. The Supraspliceosome - A Multi-Task Machine for Regulated Pre-mRNA Processing in the Cell Nucleus. Comput Struct Biotechnol J 2014; 11:113-22. [PMID: 25408845 PMCID: PMC4232567 DOI: 10.1016/j.csbj.2014.09.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 01/23/2023] Open
Abstract
Pre-mRNA splicing of Pol II transcripts is executed in the mammalian cell nucleus within a huge (21 MDa) and highly dynamic RNP machine — the supraspliceosome. It is composed of four splicing active native spliceosomes, each resembling an in vitro assembled spliceosome, which are connected by the pre-mRNA. Supraspliceosomes harbor protein splicing factors and all the five-spliceosomal U snRNPs. Recent analysis of specific supraspliceosomes at defined splicing stages revealed that they harbor all five spliceosomal U snRNAs at all splicing stages. Supraspliceosomes harbor additional pre-mRNA processing components, such as the 5′-end and 3′-end processing components, and the RNA editing enzymes ADAR1 and ADAR2. The structure of the native spliceosome, at a resolution of 20 Å, was determined by cryo-EM. A unique spatial arrangement of the spliceosomal U snRNPs within the native spliceosome emerged from in-silico studies, localizing the five U snRNPs mostly within its large subunit, and sheltering the active core components deep within the spliceosomal cavity. The supraspliceosome provides a platform for coordinating the numerous processing steps that the pre-mRNA undergoes: 5′ and 3′-end processing activities, RNA editing, constitutive and alternative splicing, and processing of intronic microRNAs. It also harbors a quality control mechanism termed suppression of splicing (SOS) that, under normal growth conditions, suppresses splicing at abundant intronic latent 5′ splice sites in a reading frame-dependent fashion. Notably, changes in these regulatory processing activities are associated with human disease and cancer. These findings emphasize the supraspliceosome as a multi-task master regulator of pre-mRNA processing in the cell nucleus.
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Affiliation(s)
- Kinneret Shefer
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Joseph Sperling
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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16
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Thomas MP, Lieberman J. Live or let die: posttranscriptional gene regulation in cell stress and cell death. Immunol Rev 2013; 253:237-52. [PMID: 23550650 DOI: 10.1111/imr.12052] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Studies of the regulation of gene expression historically focused on transcription. However, during stress and apoptosis, profound gene expression changes occur more rapidly and globally than is possible by regulating transcription. Posttranscriptional changes in mRNA processing and translation in response to diverse stresses shut down most protein translation to conserve energy and lead to rapid remodeling of the proteome to promote repair. Pre-mRNA splicing and mRNA stability are fundamentally altered under some stress conditions. Stress pathways coordinate a cytoprotective repair response, while simultaneously initiating signaling that can ultimately trigger cell death. How the cell mediates the decision between repair and apoptosis is largely not understood. In some stresses, microRNAs may tip the balance. Here, we review what is known about posttranscriptional gene regulation during stress, focusing on what is still unknown and how new technologies might be used to understand what changes are most physiologically important in different forms of stress and death.
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Affiliation(s)
- Marshall P Thomas
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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17
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Karam R, Wengrod J, Gardner LB, Wilkinson MF. Regulation of nonsense-mediated mRNA decay: implications for physiology and disease. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:624-33. [PMID: 23500037 DOI: 10.1016/j.bbagrm.2013.03.002] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 03/02/2013] [Accepted: 03/04/2013] [Indexed: 01/24/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is an mRNA quality control mechanism that destabilizes aberrant mRNAs harboring premature termination (nonsense) codons (PTCs). Recent studies have shown that NMD also targets mRNAs transcribed from a large subset of wild-type genes. This raises the possibility that NMD itself is under regulatory control. Indeed, several recent studies have shown that NMD activity is modulated in specific cell types and that key components of the NMD pathway are regulated by several pathways, including microRNA circuits and NMD itself. Cellular stress also modulates the magnitude of NMD by mechanisms that are beginning to be understood. Here, we review the evidence that NMD is regulated and discuss the physiological role for this regulation. We propose that the efficiency of NMD is altered in some cellular contexts to regulate normal biological events. In disease states-such as in cancer-NMD is disturbed by intrinsic and extrinsic factors, resulting in altered levels of crucial NMD-targeted mRNAs that lead to downstream pathological consequences. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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Affiliation(s)
- Rachid Karam
- Department of Reproductive Medicine, University of California, San Diego, CA 92093-0864, USA
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