1
|
Olthof A, Schwoerer C, Girardini K, Weber A, Doggett K, Mieruszynski S, Heath J, Moore T, Biran J, Kanadia R. Taxonomy of introns and the evolution of minor introns. Nucleic Acids Res 2024; 52:9247-9266. [PMID: 38943346 PMCID: PMC11347168 DOI: 10.1093/nar/gkae550] [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: 11/30/2023] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 07/01/2024] Open
Abstract
Classification of introns, which is crucial to understanding their evolution and splicing, has historically been binary and has resulted in the naming of major and minor introns that are spliced by their namesake spliceosome. However, a broad range of intron consensus sequences exist, leading us to here reclassify introns as minor, minor-like, hybrid, major-like, major and non-canonical introns in 263 species across six eukaryotic supergroups. Through intron orthology analysis, we discovered that minor-like introns are a transitory node for intron conversion across evolution. Despite close resemblance of their consensus sequences to minor introns, these introns possess an AG dinucleotide at the -1 and -2 position of the 5' splice site, a salient feature of major introns. Through combined analysis of CoLa-seq, CLIP-seq for major and minor spliceosome components, and RNAseq from samples in which the minor spliceosome is inhibited we found that minor-like introns are also an intermediate class from a splicing mechanism perspective. Importantly, this analysis has provided insight into the sequence elements that have evolved to make minor-like introns amenable to recognition by both minor and major spliceosome components. We hope that this revised intron classification provides a new framework to study intron evolution and splicing.
Collapse
Affiliation(s)
- Anouk M Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
| | - Charles F Schwoerer
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
| | - Kaitlin N Girardini
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
| | - Audrey L Weber
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
| | - Karen Doggett
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Stephen Mieruszynski
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Joan K Heath
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Timothy E Moore
- Statistical Consulting Services, Center for Open Research Resources & Equipment, University of Connecticut, Storrs, CT, USA
| | - Jakob Biran
- Department of Poultry and Aquaculture, Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon, Israel
| | - Rahul N Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| |
Collapse
|
2
|
Chen X, Li G, Zhang J, Hu L, Zhao G, Wu B, Wei F, Xiong F. The temporal protein signature analyses of developing human deciduous molar tooth germ. Proteomics 2024:e2300396. [PMID: 38522031 DOI: 10.1002/pmic.202300396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/31/2024] [Accepted: 03/05/2024] [Indexed: 03/25/2024]
Abstract
The tooth serves as an exemplary model for developmental studies, encompassing epithelial-mesenchymal transition and cell differentiation. The essential factors and pathways identified in tooth development will help understand the natural development process and the malformations of mineralized tissues such as skeleton. The time-dependent proteomic changes were investigated through the proteomics of healthy human molars during embryonic stages, ranging from the cap-to-early bell stage. A comprehensive analysis revealed 713 differentially expressed proteins (DEPs) exhibiting five distinct temporal expression patterns. Through the application of weighted gene co-expression network analysis (WGCNA), 24 potential driver proteins of tooth development were screened, including CHID1, RAP1GDS1, HAPLN3, AKAP12, WLS, GSS, DDAH1, CLSTN1, AFM, RBP1, AGO1, SET, HMGB2, HMGB1, ANP32A, SPON1, FREM1, C8B, PRPS2, FCHO2, PPP1R12A, GPALPP1, U2AF2, and RCC2. Then, the proteomics and transcriptomics expression patterns of these proteins were further compared, complemented by single-cell RNA-sequencing (scRNA-seq). In summary, this study not only offers a wealth of information regarding the molecular intricacies of human embryonic epithelial and mesenchymal cell differentiation but also serves as an invaluable resource for future mechanistic inquiries into tooth development.
Collapse
Affiliation(s)
- Xiaohang Chen
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, China
- Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Gaochi Li
- Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Jian Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Liang Hu
- Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Guoqiang Zhao
- Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Buling Wu
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, China
| | - Fengxiang Wei
- Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Fu Xiong
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| |
Collapse
|
3
|
Larue GE, Roy SW. Where the minor things are: a pan-eukaryotic survey suggests neutral processes may explain much of minor intron evolution. Nucleic Acids Res 2023; 51:10884-10908. [PMID: 37819006 PMCID: PMC10639083 DOI: 10.1093/nar/gkad797] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Spliceosomal introns are gene segments removed from RNA transcripts by ribonucleoprotein machineries called spliceosomes. In some eukaryotes a second 'minor' spliceosome is responsible for processing a tiny minority of introns. Despite its seemingly modest role, minor splicing has persisted for roughly 1.5 billion years of eukaryotic evolution. Identifying minor introns in over 3000 eukaryotic genomes, we report diverse evolutionary histories including surprisingly high numbers in some fungi and green algae, repeated loss, as well as general biases in their positional and genic distributions. We estimate that ancestral minor intron densities were comparable to those of vertebrates, suggesting a trend of long-term stasis. Finally, three findings suggest a major role for neutral processes in minor intron evolution. First, highly similar patterns of minor and major intron evolution contrast with both functionalist and deleterious model predictions. Second, observed functional biases among minor intron-containing genes are largely explained by these genes' greater ages. Third, no association of intron splicing with cell proliferation in a minor intron-rich fungus suggests that regulatory roles are lineage-specific and thus cannot offer a general explanation for minor splicing's persistence. These data constitute the most comprehensive view of minor introns and their evolutionary history to date, and provide a foundation for future studies of these remarkable genetic elements.
Collapse
Affiliation(s)
- Graham E Larue
- Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA 95343, USA
| | - Scott W Roy
- Department of Molecular and Cell Biology, University of California Merced, Merced, CA 95343, USA
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
| |
Collapse
|
4
|
Siebert AE, Corll J, Paige Gronevelt J, Levine L, Hobbs LM, Kenney C, Powell CLE, Battistuzzi FU, Davenport R, Mark Settles A, Brad Barbazuk W, Westrick RJ, Madlambayan GJ, Lal S. Genetic analysis of human RNA binding motif protein 48 (RBM48) reveals an essential role in U12-type intron splicing. Genetics 2022; 222:iyac129. [PMID: 36040194 PMCID: PMC9526058 DOI: 10.1093/genetics/iyac129] [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: 05/13/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
U12-type or minor introns are found in most multicellular eukaryotes and constitute ∼0.5% of all introns in species with a minor spliceosome. Although the biological significance for the evolutionary conservation of U12-type introns is debated, mutations disrupting U12 splicing cause developmental defects in both plants and animals. In human hematopoietic stem cells, U12 splicing defects disrupt proper differentiation of myeloid lineages and are associated with myelodysplastic syndrome, predisposing individuals to acute myeloid leukemia. Mutants in the maize ortholog of RNA binding motif protein 48 (RBM48) have aberrant U12-type intron splicing. Human RBM48 was recently purified biochemically as part of the minor spliceosome and shown to recognize the 5' end of the U6atac snRNA. In this report, we use CRISPR/Cas9-mediated ablation of RBM48 in human K-562 cells to show the genetic function of RBM48. RNA-seq analysis comparing wild-type and mutant K-562 genotypes found that 48% of minor intron-containing genes have significant U12-type intron retention in RBM48 mutants. Comparing these results to maize rbm48 mutants defined a subset of minor intron-containing genes disrupted in both species. Mutations in the majority of these orthologous minor intron-containing genes have been reported to cause developmental defects in both plants and animals. Our results provide genetic evidence that the primary defect of human RBM48 mutants is aberrant U12-type intron splicing, while a comparison of human and maize RNA-seq data identifies candidate genes likely to mediate mutant phenotypes of U12-type splicing defects.
Collapse
Affiliation(s)
- Amy E Siebert
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Jacob Corll
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - J Paige Gronevelt
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Laurel Levine
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Linzi M Hobbs
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Catalina Kenney
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Christopher L E Powell
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Fabia U Battistuzzi
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Ruth Davenport
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - A Mark Settles
- Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA
| | - W Brad Barbazuk
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Randal J Westrick
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Gerard J Madlambayan
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Shailesh Lal
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| |
Collapse
|
5
|
Weinstein R, Bishop K, Broadbridge E, Yu K, Carrington B, Elkahloun A, Zhen T, Pei W, Burgess SM, Liu P, Bresciani E, Sood R. Zrsr2 Is Essential for the Embryonic Development and Splicing of Minor Introns in RNA and Protein Processing Genes in Zebrafish. Int J Mol Sci 2022; 23:10668. [PMID: 36142581 PMCID: PMC9501576 DOI: 10.3390/ijms231810668] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022] Open
Abstract
ZRSR2 (zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2) is an essential splicing factor involved in 3' splice-site recognition as a component of both the major and minor spliceosomes that mediate the splicing of U2-type (major) and U12-type (minor) introns, respectively. Studies of ZRSR2-depleted cell lines and ZRSR2-mutated patient samples revealed its essential role in the U12-dependent minor spliceosome. However, the role of ZRSR2 during embryonic development is not clear, as its function is compensated for by Zrsr1 in mice. Here, we utilized the zebrafish model to investigate the role of zrsr2 during embryonic development. Using CRISPR/Cas9 technology, we generated a zrsr2-knockout zebrafish line, termed zrsr2hg129/hg129 (p.Trp167Argfs*9) and examined embryo development in the homozygous mutant embryos. zrsr2hg129/hg129 embryos displayed multiple developmental defects starting at 4 days post fertilization (dpf) and died after 8 dpf, suggesting that proper Zrsr2 function is required during embryonic development. The global transcriptome analysis of 3 dpf zrsr2hg129/hg129 embryos revealed that the loss of Zrsr2 results in the downregulation of essential metabolic pathways and the aberrant retention of minor introns in about one-third of all minor intron-containing genes in zebrafish. Overall, our study has demonstrated that the role of Zrsr2 as a component of the minor spliceosome is conserved and critical for proper embryonic development in zebrafish.
Collapse
Affiliation(s)
- Rachel Weinstein
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin Bishop
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elizabeth Broadbridge
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kai Yu
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Blake Carrington
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Abdel Elkahloun
- Microarray Core, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tao Zhen
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wuhong Pei
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shawn M. Burgess
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Liu
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erica Bresciani
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raman Sood
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
6
|
Lan W, Qiu Y, Xu Y, Liu Y, Miao Y. Ubiquitination and Ubiquitin-Like Modifications as Mediators of Alternative Pre-mRNA Splicing in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:869870. [PMID: 35646014 PMCID: PMC9134077 DOI: 10.3389/fpls.2022.869870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
Alternative splicing (AS) is a common post-transcriptional regulatory process in eukaryotes. AS has an irreplaceable role during plant development and in response to environmental stress as it evokes differential expression of downstream genes or splicing factors (e.g., serine/arginine-rich proteins). Numerous studies have reported that loss of AS capacity leads to defects in plant growth and development, and induction of stress-sensitive phenotypes. A role for post-translational modification (PTM) of AS components has emerged in recent years. These modifications are capable of regulating the activity, stability, localization, interaction, and folding of spliceosomal proteins in human cells and yeast, indicating that PTMs represent another layer of AS regulation. In this review, we summarize the recent reports concerning ubiquitin and ubiquitin-like modification of spliceosome components and analyze the relationship between spliceosome and the ubiquitin/26S proteasome pathway in plants. Based on the totality of the evidence presented, we further speculate on the roles of protein ubiquitination mediated AS in plant development and environmental response.
Collapse
|
7
|
Gómez-Redondo I, Pericuesta E, Navarrete-Lopez P, Ramos-Ibeas P, Planells B, Fonseca-Balvís N, Vaquero-Rey A, Fernández-González R, Laguna-Barraza R, Horiuchi K, Gutiérrez-Adán A. Zrsr2 and functional U12-dependent spliceosome are necessary for follicular development. iScience 2022; 25:103860. [PMID: 35198906 PMCID: PMC8850803 DOI: 10.1016/j.isci.2022.103860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/26/2021] [Accepted: 01/27/2022] [Indexed: 12/13/2022] Open
Abstract
ZRSR2 is a splicing factor involved in recognition of 3'-intron splice sites that is frequently mutated in myeloid malignancies and several tumors; however, the role of mutations of Zrsr2 in other tissues has not been analyzed. To explore the biological role of ZRSR2, we generated three Zrsr2 mutant mouse lines. All Zrsr2 mutant lines exhibited blood cell anomalies, and in two lines, oogenesis was blocked at the secondary follicle stage. RNA-seq of Zrsr2 mu secondary follicles showed aberrations in gene expression and showed altered alternative splicing (AS) events involving enrichment of U12-type intron retention (IR), supporting the functional Zrsr2 action in minor spliceosomes. IR events were preferentially associated with centriole replication, protein phosphorylation, and DNA damage checkpoint. Notably, we found alterations in AS events of 50 meiotic genes. These results indicate that ZRSR2 mutations alter splicing mainly in U12-type introns, which may affect peripheral blood cells, and impede oogenesis and female fertility.
Collapse
Affiliation(s)
- Isabel Gómez-Redondo
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Eva Pericuesta
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Paula Navarrete-Lopez
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Priscila Ramos-Ibeas
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Benjamín Planells
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Noelia Fonseca-Balvís
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Aida Vaquero-Rey
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Raúl Fernández-González
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Ricardo Laguna-Barraza
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Keiko Horiuchi
- Department of Protein-Protein Interaction Research, Institute for Advanced Medical Sciences, Nippon Medical School, 1-396 Kosugi-cho, Nakahara-ku, Kawasaki, Kanagawa 211-8533, Japan
| | - Alfonso Gutiérrez-Adán
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| |
Collapse
|
8
|
Yan X, Bai D, Song H, Lin K, Pang E. Alternative splicing during fruit development among fleshy fruits. BMC Genomics 2021; 22:762. [PMID: 34702184 PMCID: PMC8547070 DOI: 10.1186/s12864-021-08111-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/20/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Alternative splicing (AS) is an important mechanism of posttranscriptional modification and dynamically regulates multiple physiological processes in plants, including fruit ripening. However, little is known about alternative splicing during fruit development in fleshy fruits. RESULTS We studied the alternative splicing at the immature and ripe stages during fruit development in cucumber, melon, papaya and peach. We found that 14.96-17.48% of multiexon genes exhibited alternative splicing. Intron retention was not always the most frequent event, indicating that the alternative splicing pattern during different developmental process differs. Alternative splicing was significantly more prevalent at the ripe stage than at the immature stage in cucumber and melon, while the opposite trend was shown in papaya and peach, implying that developmental stages adopt different alternative splicing strategies for their specific functions. Some genes involved in fruit ripening underwent stage-specific alternative splicing, indicating that alternative splicing regulates fruits ripening. Conserved alternative splicing events did not appear to be stage-specific. Clustering fruit developmental stages across the four species based on alternative splicing profiles resulted in species-specific clustering, suggesting that diversification of alternative splicing contributes to lineage-specific evolution in fleshy fruits. CONCLUSIONS We obtained high quality transcriptomes and alternative splicing events during fruit development across the four species. Dynamics and nonconserved alternative splicing were discovered. The candidate stage-specific AS genes involved in fruit ripening will provide valuable insight into the roles of alternative splicing during the developmental processes of fleshy fruits.
Collapse
Affiliation(s)
- Xiaomin Yan
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875, China
| | - Dan Bai
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875, China
| | - Hongtao Song
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875, China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875, China
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875, China.
| |
Collapse
|
9
|
Tognacca RS, Botto JF. Post-transcriptional regulation of seed dormancy and germination: Current understanding and future directions. PLANT COMMUNICATIONS 2021; 2:100169. [PMID: 34327318 PMCID: PMC8299061 DOI: 10.1016/j.xplc.2021.100169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/26/2021] [Accepted: 02/13/2021] [Indexed: 05/06/2023]
Abstract
Seed dormancy is a developmental checkpoint that prevents mature seeds from germinating under conditions that are otherwise favorable for germination. Temperature and light are the most relevant environmental factors that regulate seed dormancy and germination. These environmental cues can trigger molecular and physiological responses including hormone signaling, particularly that of abscisic acid and gibberellin. The balance between the content and sensitivity of these hormones is the key to the regulation of seed dormancy. Temperature and light tightly regulate the transcription of thousands of genes, as well as other aspects of gene expression such as mRNA splicing, translation, and stability. Chromatin remodeling determines specific transcriptional outputs, and alternative splicing leads to different outcomes and produces transcripts that encode proteins with altered or lost functions. Proper regulation of chromatin remodeling and alternative splicing may be highly relevant to seed germination. Moreover, microRNAs are also critical for the control of gene expression in seeds. This review aims to discuss recent updates on post-transcriptional regulation during seed maturation, dormancy, germination, and post-germination events. We propose future prospects for understanding how different post-transcriptional processes in crop seeds can contribute to the design of genotypes with better performance and higher productivity.
Collapse
Affiliation(s)
- Rocío Soledad Tognacca
- Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CP1428 Buenos Aires, Argentina
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, CP1417 Buenos Aires, Argentina
| | - Javier Francisco Botto
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, CP1417 Buenos Aires, Argentina
| |
Collapse
|
10
|
Guo Y, Ren G, Zhang K, Li Z, Miao Y, Guo H. Leaf senescence: progression, regulation, and application. MOLECULAR HORTICULTURE 2021; 1:5. [PMID: 37789484 PMCID: PMC10509828 DOI: 10.1186/s43897-021-00006-9] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/11/2021] [Indexed: 05/24/2023]
Abstract
Leaf senescence, the last stage of leaf development, is a type of postmitotic senescence and is characterized by the functional transition from nutrient assimilation to nutrient remobilization which is essential for plants' fitness. The initiation and progression of leaf senescence are regulated by a variety of internal and external factors such as age, phytohormones, and environmental stresses. Significant breakthroughs in dissecting the molecular mechanisms underpinning leaf senescence have benefited from the identification of senescence-altered mutants through forward genetic screening and functional assessment of hundreds of senescence-associated genes (SAGs) via reverse genetic research in model plant Arabidopsis thaliana as well as in crop plants. Leaf senescence involves highly complex genetic programs that are tightly tuned by multiple layers of regulation, including chromatin and transcription regulation, post-transcriptional, translational and post-translational regulation. Due to the significant impact of leaf senescence on photosynthesis, nutrient remobilization, stress responses, and productivity, much effort has been made in devising strategies based on known senescence regulatory mechanisms to manipulate the initiation and progression of leaf senescence, aiming for higher yield, better quality, or improved horticultural performance in crop plants. This review aims to provide an overview of leaf senescence and discuss recent advances in multi-dimensional regulation of leaf senescence from genetic and molecular network perspectives. We also put forward the key issues that need to be addressed, including the nature of leaf age, functional stay-green trait, coordination between different regulatory pathways, source-sink relationship and nutrient remobilization, as well as translational researches on leaf senescence.
Collapse
Affiliation(s)
- Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 Shandong China
| | - Guodong Ren
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Kewei Zhang
- Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004 Zhejiang China
| | - Zhonghai Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083 China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Hongwei Guo
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, 518055 Guangdong China
| |
Collapse
|
11
|
Reynolds KA, Rosa-Molinar E, Ward RE, Zhang H, Urbanowicz BR, Settles AM. Accelerating biological insight for understudied genes. Integr Comp Biol 2021; 61:2233-2243. [PMID: 33970251 DOI: 10.1093/icb/icab029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The rapid expansion of genome sequence data is increasing the discovery of protein-coding genes across all domains of life. Annotating these genes with reliable functional information is necessary to understand evolution, to define the full biochemical space accessed by nature, and to identify target genes for biotechnology improvements. The vast majority of proteins are annotated based on sequence conservation with no specific biological, biochemical, genetic, or cellular function identified. Recent technical advances throughout the biological sciences enable experimental research on these understudied protein-coding genes in a broader collection of species. However, scientists have incentives and biases to continue focusing on well documented genes within their preferred model organism. This perspective suggests a research model that seeks to break historic silos of research bias by enabling interdisciplinary teams to accelerate biological functional annotation. We propose an initiative to develop coordinated projects of collaborating evolutionary biologists, cell biologists, geneticists, and biochemists that will focus on subsets of target genes in multiple model organisms. Concurrent analysis in multiple organisms takes advantage of evolutionary divergence and selection, which causes individual species to be better suited as experimental models for specific genes. Most importantly, multisystem approaches would encourage transdisciplinary critical thinking and hypothesis testing that is inherently slow in current biological research.
Collapse
Affiliation(s)
- Kimberly A Reynolds
- The Green Center for Systems Biology and the Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eduardo Rosa-Molinar
- Department of Pharmacology & Toxicology, The University of Kansas, Lawrence, KS 66047, USA
| | - Robert E Ward
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Hongbin Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Breeanna R Urbanowicz
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - A Mark Settles
- Bioengineering Branch, NASA Ames Research Center, Moffett Field, CA USA
| |
Collapse
|
12
|
Inoue D, Polaski JT, Taylor J, Castel P, Chen S, Kobayashi S, Hogg SJ, Hayashi Y, Pineda JMB, El Marabti E, Erickson C, Knorr K, Fukumoto M, Yamazaki H, Tanaka A, Fukui C, Lu SX, Durham BH, Liu B, Wang E, Mehta S, Zakheim D, Garippa R, Penson A, Chew GL, McCormick F, Bradley RK, Abdel-Wahab O. Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition. Nat Genet 2021; 53:707-718. [PMID: 33846634 PMCID: PMC8177065 DOI: 10.1038/s41588-021-00828-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 02/24/2021] [Indexed: 12/13/2022]
Abstract
Most eukaryotes harbor two distinct pre-mRNA splicing machineries: the major spliceosome, which removes >99% of introns, and the minor spliceosome, which removes rare, evolutionarily conserved introns. Although hypothesized to serve important regulatory functions, physiologic roles of the minor spliceosome are not well understood. For example, the minor spliceosome component ZRSR2 is subject to recurrent, leukemia-associated mutations, yet functional connections among minor introns, hematopoiesis and cancers are unclear. Here, we identify that impaired minor intron excision via ZRSR2 loss enhances hematopoietic stem cell self-renewal. CRISPR screens mimicking nonsense-mediated decay of minor intron-containing mRNA species converged on LZTR1, a regulator of RAS-related GTPases. LZTR1 minor intron retention was also discovered in the RASopathy Noonan syndrome, due to intronic mutations disrupting splicing and diverse solid tumors. These data uncover minor intron recognition as a regulator of hematopoiesis, noncoding mutations within minor introns as potential cancer drivers and links among ZRSR2 mutations, LZTR1 regulation and leukemias.
Collapse
Affiliation(s)
- Daichi Inoue
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Jacob T Polaski
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Justin Taylor
- Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Pau Castel
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Sisi Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Susumu Kobayashi
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
- Division of Cellular Therapy, The Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Simon J Hogg
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Yasutaka Hayashi
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
| | - Jose Mario Bello Pineda
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Ettaib El Marabti
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Caroline Erickson
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Katherine Knorr
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Miki Fukumoto
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
| | - Hiromi Yamazaki
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
| | - Atsushi Tanaka
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
- Department of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
| | - Chie Fukui
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
| | - Sydney X Lu
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Benjamin H Durham
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Bo Liu
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Eric Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Sanjoy Mehta
- Gene Editing & Screening Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Zakheim
- Gene Editing & Screening Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ralph Garippa
- Gene Editing & Screening Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alex Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Guo-Liang Chew
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Robert K Bradley
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA.
| |
Collapse
|
13
|
Dai D, Ma Z, Song R. Maize kernel development. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:2. [PMID: 37309525 PMCID: PMC10231577 DOI: 10.1007/s11032-020-01195-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/03/2020] [Indexed: 06/14/2023]
Abstract
Maize (Zea mays) is a leading cereal crop in the world. The maize kernel is the storage organ and the harvest portion of this crop and is closely related to its yield and quality. The development of maize kernel is initiated by the double fertilization event, leading to the formation of a diploid embryo and a triploid endosperm. The embryo and endosperm are then undergone independent developmental programs, resulting in a mature maize kernel which is comprised of a persistent endosperm, a large embryo, and a maternal pericarp. Due to the well-characterized morphogenesis and powerful genetics, maize kernel has long been an excellent model for the study of cereal kernel development. In recent years, with the release of the maize reference genome and the development of new genomic technologies, there has been an explosive expansion of new knowledge for maize kernel development. In this review, we overviewed recent progress in the study of maize kernel development, with an emphasis on genetic mapping of kernel traits, transcriptome analysis during kernel development, functional gene cloning of kernel mutants, and genetic engineering of kernel traits.
Collapse
Affiliation(s)
- Dawei Dai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444 China
| | - Zeyang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Rentao Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| |
Collapse
|
14
|
Ribeiro C, Hennen-Bierwagen TA, Myers AM, Cline K, Settles AM. Engineering 6-phosphogluconate dehydrogenase improves grain yield in heat-stressed maize. Proc Natl Acad Sci U S A 2020; 117:33177-33185. [PMID: 33323483 DOI: 10.1101/2020.05.21.108985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023] Open
Abstract
Endosperm starch synthesis is a primary determinant of grain yield and is sensitive to high-temperature stress. The maize chloroplast-localized 6-phosphogluconate dehydrogenase (6PGDH), PGD3, is critical for endosperm starch accumulation. Maize also has two cytosolic isozymes, PGD1 and PGD2, that are not required for kernel development. We found that cytosolic PGD1 and PGD2 isozymes have heat-stable activity, while amyloplast-localized PGD3 activity is labile under heat stress conditions. We targeted heat-stable 6PGDH to endosperm amyloplasts by fusing the Waxy1 chloroplast targeting the peptide coding sequence to the Pgd1 and Pgd2 open reading frames (ORFs). These WPGD1 and WPGD2 fusion proteins import into isolated chloroplasts, demonstrating a functional targeting sequence. Transgenic maize plants expressing WPGD1 and WPGD2 with an endosperm-specific promoter increased 6PGDH activity with enhanced heat stability in vitro. WPGD1 and WPGD2 transgenes complement the pgd3-defective kernel phenotype, indicating the fusion proteins are targeted to the amyloplast. In the field, the WPGD1 and WPGD2 transgenes can mitigate grain yield losses in high-nighttime-temperature conditions by increasing kernel number. These results provide insight into the subcellular distribution of metabolic activities in the endosperm and suggest the amyloplast pentose phosphate pathway is a heat-sensitive step in maize kernel metabolism that contributes to yield loss during heat stress.
Collapse
Affiliation(s)
- Camila Ribeiro
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611
| | - Tracie A Hennen-Bierwagen
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011
| | - Alan M Myers
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011
| | - Kenneth Cline
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611
| | - A Mark Settles
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611
| |
Collapse
|
15
|
Engineering 6-phosphogluconate dehydrogenase improves grain yield in heat-stressed maize. Proc Natl Acad Sci U S A 2020; 117:33177-33185. [PMID: 33323483 DOI: 10.1073/pnas.2010179117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Endosperm starch synthesis is a primary determinant of grain yield and is sensitive to high-temperature stress. The maize chloroplast-localized 6-phosphogluconate dehydrogenase (6PGDH), PGD3, is critical for endosperm starch accumulation. Maize also has two cytosolic isozymes, PGD1 and PGD2, that are not required for kernel development. We found that cytosolic PGD1 and PGD2 isozymes have heat-stable activity, while amyloplast-localized PGD3 activity is labile under heat stress conditions. We targeted heat-stable 6PGDH to endosperm amyloplasts by fusing the Waxy1 chloroplast targeting the peptide coding sequence to the Pgd1 and Pgd2 open reading frames (ORFs). These WPGD1 and WPGD2 fusion proteins import into isolated chloroplasts, demonstrating a functional targeting sequence. Transgenic maize plants expressing WPGD1 and WPGD2 with an endosperm-specific promoter increased 6PGDH activity with enhanced heat stability in vitro. WPGD1 and WPGD2 transgenes complement the pgd3-defective kernel phenotype, indicating the fusion proteins are targeted to the amyloplast. In the field, the WPGD1 and WPGD2 transgenes can mitigate grain yield losses in high-nighttime-temperature conditions by increasing kernel number. These results provide insight into the subcellular distribution of metabolic activities in the endosperm and suggest the amyloplast pentose phosphate pathway is a heat-sensitive step in maize kernel metabolism that contributes to yield loss during heat stress.
Collapse
|
16
|
Dionnet E, Defour A, Da Silva N, Salvi A, Lévy N, Krahn M, Bartoli M, Puppo F, Gorokhova S. Splicing impact of deep exonic missense variants in CAPN3 explored systematically by minigene functional assay. Hum Mutat 2020; 41:1797-1810. [PMID: 32668095 DOI: 10.1002/humu.24083] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 07/01/2020] [Accepted: 07/09/2020] [Indexed: 01/10/2023]
Abstract
Improving the accuracy of variant interpretation during diagnostic sequencing is a major goal for genomic medicine. To explore an often-overlooked splicing effect of missense variants, we developed the functional assay ("minigene") for the majority of exons of CAPN3, the gene responsible for limb girdle muscular dystrophy. By systematically screening 21 missense variants distributed along the gene, we found that eight clinically relevant missense variants located at a certain distance from the exon-intron borders (deep exonic missense variants) disrupted normal splicing of CAPN3 exons. Several recent machine learning-based computational tools failed to predict splicing impact for the majority of these deep exonic missense variants, highlighting the importance of including variants of this type in the training sets during the future algorithm development. Overall, 24 variants in CAPN3 gene were explored, leading to the change in the American College of Medical Genetics and Genomics classification of seven of them when results of the "minigene" functional assay were considered. Our findings reveal previously unknown splicing impact of several clinically important variants in CAPN3 and draw attention to the existence of deep exonic variants with a disruptive effect on gene splicing that could be overlooked by the current approaches in clinical genetics.
Collapse
Affiliation(s)
- Eugénie Dionnet
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Aurélia Defour
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Nathalie Da Silva
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Alexandra Salvi
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Nicolas Lévy
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France.,Service de génétique Médicale, Hôpital de la Timone, APHM, Marseille, France.,GIPTIS (Genetics Institute for Patients, Therapies Innovation and Science), Marseille, France
| | - Martin Krahn
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France.,Service de génétique Médicale, Hôpital de la Timone, APHM, Marseille, France
| | - Marc Bartoli
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Francesca Puppo
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Svetlana Gorokhova
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France.,Service de génétique Médicale, Hôpital de la Timone, APHM, Marseille, France
| |
Collapse
|
17
|
Gómez-Redondo I, Ramos-Ibeas P, Pericuesta E, Fernández-González R, Laguna-Barraza R, Gutiérrez-Adán A. Minor Splicing Factors Zrsr1 and Zrsr2 Are Essential for Early Embryo Development and 2-Cell-Like Conversion. Int J Mol Sci 2020; 21:E4115. [PMID: 32527007 PMCID: PMC7312986 DOI: 10.3390/ijms21114115] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/04/2020] [Accepted: 06/04/2020] [Indexed: 12/18/2022] Open
Abstract
Minor splicing plays an important role in vertebrate development. Zrsr1 and Zrsr2 paralog genes have essential roles in alternative splicing, mainly participating in the recognition of minor (U12) introns. To further explore their roles during early embryo development, we produced Zrsr1mu and Zrsr2mu mutant mice, containing truncating mutations within the second zinc finger domain. Both homozygous mutant mice were viable with a normal lifespan. When we crossed a homozygous Zrsr2mu/mu female with Zrsr1mu/mu male, the double heterozygotes were non-viable, giving rise to embryos that stopped developing mainly between the 2- and 4-cell stages, just after zygotic gene activation. RNA-seq analysis of Zrsr1/2mu 2-cell embryos showed altered gene and isoform expression of thousands of genes enriched in gene ontology terms and biological pathways related to ribosome, RNA transport, spliceosome, and essential zygotic gene activation steps. Alternative splicing was analyzed, showing a significant increase in intron retention in both U2 and U12 intron-containing genes related to cell cycle and mitotic nuclear division. Remarkably, both Zrsr1 and Zrsr2 were required for the conversion of mouse-induced pluripotent stem cells into 2C-like cells. According to our results, Zrsr1 or Zrsr2 are necessary for ZGA and both are indispensable for the conversion of induced pluripotent stem cells into 2C-like cells.
Collapse
Affiliation(s)
| | | | | | | | | | - Alfonso Gutiérrez-Adán
- Departamento de Reproducción Animal, INIA, Avda. Puerta de Hierro n° 12. Local 10, 28040 Madrid, Spain; (I.G.-R.); (P.R.-I.); (E.P.); (R.F.-G.); (R.L.-B.)
| |
Collapse
|
18
|
Baumgartner M, Drake K, Kanadia RN. An Integrated Model of Minor Intron Emergence and Conservation. Front Genet 2019; 10:1113. [PMID: 31798628 PMCID: PMC6865273 DOI: 10.3389/fgene.2019.01113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 10/16/2019] [Indexed: 12/12/2022] Open
Abstract
Minor introns constitute <0.5% of the introns in the human genome and have remained an enigma since their discovery. These introns are removed by a distinct splicing complex, the minor spliceosome. Both are ancient, tracing back to the last eukaryotic common ancestor (LECA), which is reflected by minor intron enrichment in specific gene families, such as the mitogen activated-protein kinase kinases, voltage-gated sodium and calcium ion channels, and E2F transcription factors. Most minor introns occur as single introns in genes with predominantly major introns. Due to this organization, minor intron-containing gene (MIG) expression requires the coordinated action of two spliceosomes, which increases the probability of missplicing. Thus, one would expect loss of minor introns via purifying selection. This has resulted in complete minor intron loss in at least nine eukaryotic lineages. However, minor introns are highly conserved in land plants and metazoans, where their importance is underscored by embryonic lethality when the minor spliceosome is inactivated. Conditional inactivation of the minor spliceosome has shown that rapidly dividing progenitor cells are highly sensitive to minor spliceosome loss. Indeed, we found that MIGs were significantly enriched in a screen for genes essential for survival in 341 cycling cell lines. Here, we propose that minor introns inserted randomly into genes in LECA or earlier and were subsequently conserved in genes crucial for cycling cell survival. We hypothesize that the essentiality of MIGs allowed minor introns to endure through the unicellularity of early eukaryotic evolution. Moreover, we identified 59 MIGs that emerged after LECA, and that many of these are essential for cycling cell survival, reinforcing our essentiality model for MIG conservation. This suggests that minor intron emergence is dynamic across eukaryotic evolution, and that minor introns should not be viewed as molecular fossils. We also posit that minor intron splicing was co-opted in multicellular evolution as a regulatory switch for en masse control of MIG expression and the biological processes they regulate. Specifically, this mode of regulation could control cell proliferation and thus body size, an idea supported by domestication syndrome, wherein MIGs are enriched in common candidate animal domestication genes.
Collapse
Affiliation(s)
- Marybeth Baumgartner
- Department of Physiology and Neurobiology, University of Connecticut, Mansfield, CT, United States.,Institute of Brain and Cognitive Sciences, University of Connecticut, Mansfield, CT, United States
| | - Kyle Drake
- Department of Physiology and Neurobiology, University of Connecticut, Mansfield, CT, United States
| | - Rahul N Kanadia
- Department of Physiology and Neurobiology, University of Connecticut, Mansfield, CT, United States.,Institute of Systems Genomics, University of Connecticut, Mansfield, CT, United States
| |
Collapse
|
19
|
Cologne A, Benoit-Pilven C, Besson A, Putoux A, Campan-Fournier A, Bober MB, De Die-Smulders CEM, Paulussen ADC, Pinson L, Toutain A, Roifman CM, Leutenegger AL, Mazoyer S, Edery P, Lacroix V. New insights into minor splicing-a transcriptomic analysis of cells derived from TALS patients. RNA (NEW YORK, N.Y.) 2019; 25:1130-1149. [PMID: 31175170 PMCID: PMC6800510 DOI: 10.1261/rna.071423.119] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
Minor intron splicing plays a central role in human embryonic development and survival. Indeed, biallelic mutations in RNU4ATAC, transcribed into the minor spliceosomal U4atac snRNA, are responsible for three rare autosomal recessive multimalformation disorders named Taybi-Linder (TALS/MOPD1), Roifman (RFMN), and Lowry-Wood (LWS) syndromes, which associate numerous overlapping signs of varying severity. Although RNA-seq experiments have been conducted on a few RFMN patient cells, none have been performed in TALS, and more generally no in-depth transcriptomic analysis of the ∼700 human genes containing a minor (U12-type) intron had been published as yet. We thus sequenced RNA from cells derived from five skin, three amniotic fluid, and one blood biosamples obtained from seven unrelated TALS cases and from age- and sex-matched controls. This allowed us to describe for the first time the mRNA expression and splicing profile of genes containing U12-type introns, in the context of a functional minor spliceosome. Concerning RNU4ATAC-mutated patients, we show that as expected, they display distinct U12-type intron splicing profiles compared to controls, but that rather unexpectedly mRNA expression levels are mostly unchanged. Furthermore, although U12-type intron missplicing concerns most of the expressed U12 genes, the level of U12-type intron retention is surprisingly low in fibroblasts and amniocytes, and much more pronounced in blood cells. Interestingly, we found several occurrences of introns that can be spliced using either U2, U12, or a combination of both types of splice site consensus sequences, with a shift towards splicing using preferentially U2 sites in TALS patients' cells compared to controls.
Collapse
Affiliation(s)
- Audric Cologne
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, F-69622 Villeurbanne, France
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
| | - Clara Benoit-Pilven
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, F-69622 Villeurbanne, France
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
| | - Alicia Besson
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
| | - Audrey Putoux
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
- Clinical Genetics Unit, Department of Genetics, Hospices Civils de Lyon, F-69500 Bron, France
| | - Amandine Campan-Fournier
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, F-69622 Villeurbanne, France
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
| | - Michael B Bober
- Division of Medical Genetics, Nemours/Alfred I. du Pont Hospital for Children, Wilmington, Delaware 19803, USA
| | - Christine E M De Die-Smulders
- Department of Clinical Genetics, Maastricht University Medical Center, 6202 AZ Maastricht, The Netherlands
- School for Oncology and Developmental Biology, GROW, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Aimee D C Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center, 6202 AZ Maastricht, The Netherlands
- School for Oncology and Developmental Biology, GROW, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Lucile Pinson
- Genetic Department for Rare Diseases and Personalized Medicine, Clinical Division, CHU Montpellier, F-34000 Montpellier, France
| | - Annick Toutain
- Department of Genetics, Tours University Hospital, F-37000 Tours, France
- UMR 1253, iBrain, Tours University, Inserm, F-37000 Tours, France
| | - Chaim M Roifman
- Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
- Division for Immunology and Allergy, Canadian Center for Primary Immunodeficiency, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | | | - Sylvie Mazoyer
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
| | - Patrick Edery
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
- Clinical Genetics Unit, Department of Genetics, Hospices Civils de Lyon, F-69500 Bron, France
| | - Vincent Lacroix
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, F-69622 Villeurbanne, France
| |
Collapse
|
20
|
Olthof AM, Hyatt KC, Kanadia RN. Minor intron splicing revisited: identification of new minor intron-containing genes and tissue-dependent retention and alternative splicing of minor introns. BMC Genomics 2019; 20:686. [PMID: 31470809 PMCID: PMC6717393 DOI: 10.1186/s12864-019-6046-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 08/19/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Mutations in minor spliceosome components such as U12 snRNA (cerebellar ataxia) and U4atac snRNA (microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1)) result in tissue-specific symptoms. Given that the minor spliceosome is ubiquitously expressed, we hypothesized that these restricted phenotypes might be caused by the tissue-specific regulation of the minor spliceosome targets, i.e. minor intron-containing genes (MIGs). The current model of inefficient splicing is thought to apply to the regulation of the ~ 500 MIGs identified in the U12DB. However this database was created more than 10 years ago. Therefore, we first wanted to revisit the classification of minor introns in light of the most recent reference genome. We then sought to address specificity of MIG expression, minor intron retention, and alternative splicing (AS) across mouse and human tissues. RESULTS We employed position-weight matrices to obtain a comprehensive updated list of minor introns, consisting of 722 mouse and 770 human minor introns. These can be found in the Minor Intron DataBase (MIDB). Besides identification of 99% of the minor introns found in the U12DB, we also discovered ~ 150 new MIGs. We then analyzed the RNAseq data from eleven different mouse tissues, which revealed tissue-specific MIG expression and minor intron retention. Additionally, many minor introns were efficiently spliced compared to their flanking major introns. Finally, we identified several novel AS events across minor introns in both mouse and human, which were also tissue-dependent. Bioinformatics analysis revealed that several of the AS events could result in the production of novel tissue-specific proteins. Moreover, like the major introns, we found that these AS events were more prevalent in long minor introns, while retention was favoured in shorter introns. CONCLUSION Here we show that minor intron splicing and AS across minor introns is a highly organised process that might be regulated in coordination with the major spliceosome in a tissue-specific manner. We have provided a framework to further study the impact of the minor spliceosome and the regulation of MIG expression. These findings may shed light on the mechanism underlying tissue-specific phenotypes in diseases associated with minor spliceosome inactivation. MIDB can be accessed at https://midb.pnb.uconn.edu .
Collapse
Affiliation(s)
- Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269 USA
| | - Katery C. Hyatt
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269 USA
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269 USA
- Institute of Systems Genomics, University of Connecticut, Storrs, CT 06269 USA
| |
Collapse
|
21
|
Sex-Dimorphic Behavioral Alterations and Altered Neurogenesis in U12 Intron Splicing-Defective Zrsr1 Mutant Mice. Int J Mol Sci 2019; 20:ijms20143543. [PMID: 31331069 PMCID: PMC6678158 DOI: 10.3390/ijms20143543] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/15/2019] [Accepted: 07/17/2019] [Indexed: 01/10/2023] Open
Abstract
Mutant mice with respect to the splicing factor Zrsr1 present altered spermatogenesis and infertility. To investigate whether Zrsr1 is involved in the homeostatic control that the hypothalamus exerts over reproductive functions, we first analyzed both differential gene and isoform expression and alternative splicing alterations in Zrsr1 mutant (Zrsr1mu) hypothalamus; second, we analyzed the spontaneous and social behavior of Zrsr1mu mice; and third, we analyzed adult cell proliferation and survival in the Zrsr1mu hypothalamus. The Zrsr1mu hypothalamus showed altered expression of genes and isoforms related to the glutathione metabolic process, synaptonemal complex assembly, mRNA transport, and altered splicing events involving the enrichment of U12-type intron retention (IR). Furthermore, increased IR in U12-containing genes related with the prolactin, progesterone, and gonadotropin-releasing hormone (GnRH) reproductive signaling pathway was observed. This was associated with a hyperactive phenotype in both males and females, with an anxious phenotype in females, and with increased social interaction in males, instead of the classical aggressive behavior. In addition, Zrsr1mu females but not males exhibited reduced cell proliferation in both the hypothalamus and the subventricular zone. Overall, these results suggest that Zrsr1 expression and function are relevant to organization of the hypothalamic cell network controlling behavior.
Collapse
|
22
|
Zuo Y, Feng F, Qi W, Song R. Dek42 encodes an RNA-binding protein that affects alternative pre-mRNA splicing and maize kernel development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:728-748. [PMID: 30839161 DOI: 10.1111/jipb.12798] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/28/2019] [Indexed: 05/22/2023]
Abstract
RNA-binding proteins (RBPs) play an important role in post-transcriptional gene regulation. However, the functions of RBPs in plants remain poorly understood. Maize kernel mutant dek42 has small defective kernels and lethal seedlings. Dek42 was cloned by Mutator tag isolation and further confirmed by an independent mutant allele and clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 materials. Dek42 encodes an RRM_RBM48 type RNA-binding protein that localizes to the nucleus. Dek42 is constitutively expressed in various maize tissues. The dek42 mutation caused a significant reduction in the accumulation of DEK42 protein in mutant kernels. RNA-seq analysis showed that the dek42 mutation significantly disturbed the expression of thousands of genes during maize kernel development. Sequence analysis also showed that the dek42 mutation significantly changed alternative splicing in expressed genes, which were especially enriched for the U12-type intron-retained type. Yeast two-hybrid screening identified SF3a1 as a DEK42-interacting protein. DEK42 also interacts with the spliceosome component U1-70K. These results suggested that DEK42 participates in the regulation of pre-messenger RNA splicing through its interaction with other spliceosome components. This study showed the function of a newly identified RBP and provided insights into alternative splicing regulation during maize kernel development.
Collapse
Affiliation(s)
- Yi Zuo
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Fan Feng
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Weiwei Qi
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Rentao Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
23
|
Bai F, Corll J, Shodja DN, Davenport R, Feng G, Mudunkothge J, Brigolin CJ, Martin F, Spielbauer G, Tseung CW, Siebert AE, Barbazuk WB, Lal S, Settles AM. RNA Binding Motif Protein 48 Is Required for U12 Splicing and Maize Endosperm Differentiation. THE PLANT CELL 2019; 31:715-733. [PMID: 30760564 PMCID: PMC6482629 DOI: 10.1105/tpc.18.00754] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/11/2019] [Accepted: 02/13/2019] [Indexed: 05/19/2023]
Abstract
The last eukaryotic common ancestor had two classes of introns that are still found in most eukaryotic lineages. Common U2-type and rare U12-type introns are spliced by the major and minor spliceosomes, respectively. Relatively few splicing factors have been shown to be specific to the minor spliceosome. We found that the maize (Zea mays) RNA binding motif protein 48 (RBM48) is a U12 splicing factor that functions to promote cell differentiation and repress cell proliferation. RBM48 is coselected with the U12 splicing factor, zinc finger CCCH-type, RNA binding motif, and Ser/Arg rich 2/Rough endosperm 3 (RGH3). Protein-protein interactions between RBM48, RGH3, and U2 Auxiliary Factor (U2AF) subunits suggest major and minor spliceosome factors required for intron recognition form complexes with RBM48. Human RBM48 interacts with armadillo repeat containing 7 (ARMC7). Maize RBM48 and ARMC7 have a conserved protein-protein interaction. These data predict that RBM48 is likely to function in U12 splicing throughout eukaryotes and that U12 splicing promotes endosperm cell differentiation in maize.
Collapse
Affiliation(s)
- Fang Bai
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Jacob Corll
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - Donya N Shodja
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - Ruth Davenport
- Department of Biology and Genetics Institute, University of Florida, Gainesville, Florida 32611
| | - Guanqiao Feng
- Department of Biology and Genetics Institute, University of Florida, Gainesville, Florida 32611
| | - Janaki Mudunkothge
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Christian J Brigolin
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - Federico Martin
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Gertraud Spielbauer
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Chi-Wah Tseung
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Amy E Siebert
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - W Brad Barbazuk
- Department of Biology and Genetics Institute, University of Florida, Gainesville, Florida 32611
| | - Shailesh Lal
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - A Mark Settles
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| |
Collapse
|
24
|
Oghabian A, Greco D, Frilander MJ. IntEREst: intron-exon retention estimator. BMC Bioinformatics 2018; 19:130. [PMID: 29642843 PMCID: PMC5896110 DOI: 10.1186/s12859-018-2122-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 03/21/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND In-depth study of the intron retention levels of transcripts provide insights on the mechanisms regulating pre-mRNA splicing efficiency. Additionally, detailed analysis of retained introns can link these introns to post-transcriptional regulation or identify aberrant splicing events in human diseases. RESULTS We present IntEREst, Intron-Exon Retention Estimator, an R package that supports rigorous analysis of non-annotated intron retention events (in addition to the ones annotated by RefSeq or similar databases), and support intra-sample in addition to inter-sample comparisons. It accepts binary sequence alignment/map (.bam) files as input and determines genome-wide estimates of intron retention or exon-exon junction levels. Moreover, it includes functions for comparing subsets of user-defined introns (e.g. U12-type vs U2-type) and its plotting functions allow visualization of the distribution of the retention levels of the introns. Statistical methods are adapted from the DESeq2, edgeR and DEXSeq R packages to extract the significantly more or less retained introns. Analyses can be performed either sequentially (on single core) or in parallel (on multiple cores). We used IntEREst to investigate the U12- and U2-type intron retention in human and plant RNAseq dataset with defects in the U12-dependent spliceosome due to mutations in the ZRSR2 component of this spliceosome. Additionally, we compared the retained introns discovered by IntEREst with that of other methods and studies. CONCLUSION IntEREst is an R package for Intron retention and exon-exon junction levels analysis of RNA-seq data. Both the human and plant analyses show that the U12-type introns are retained at higher level compared to the U2-type introns already in the control samples, but the retention is exacerbated in patient or plant samples carrying a mutated ZRSR2 gene. Intron retention events caused by ZRSR2 mutation that we discovered using IntEREst (DESeq2 based function) show considerable overlap with the retained introns discovered by other methods (e.g. IRFinder and edgeR based function of IntEREst). Our results indicate that increase in both the number of biological replicates and the depth of sequencing library promote the discovery of retained introns, but the effect of library size gradually decreases with more than 35 million reads mapped to the introns.
Collapse
Affiliation(s)
- Ali Oghabian
- Institute of Biotechnology, University of Helsinki, P.O. Box 56 (Viikinkaari 5), FI-00014, Helsinki, Finland
| | - Dario Greco
- Institute of Biotechnology, University of Helsinki, P.O. Box 56 (Viikinkaari 5), FI-00014, Helsinki, Finland.,Faculty of Medicine and Life Sciences, Tampere, Finland.,Institute of Biosciences and Medical Technologies (BioMediTech), Arvo Ylpön Katu 34, FI-33014 University of Tampere, Tampere, Finland
| | - Mikko J Frilander
- Institute of Biotechnology, University of Helsinki, P.O. Box 56 (Viikinkaari 5), FI-00014, Helsinki, Finland.
| |
Collapse
|
25
|
Jutzi D, Akinyi MV, Mechtersheimer J, Frilander MJ, Ruepp MD. The emerging role of minor intron splicing in neurological disorders. Cell Stress 2018; 2:40-54. [PMID: 31225466 PMCID: PMC6558932 DOI: 10.15698/cst2018.03.126] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pre-mRNA splicing is an essential step in eukaryotic gene expression. Mutations in cis-acting sequence elements within pre-mRNA molecules or trans-acting factors involved in pre-mRNA processing have both been linked to splicing dysfunction that give rise to a large number of human diseases. These mutations typically affect the major splicing pathway, which excises more than 99% of all introns in humans. However, approximately 700-800 human introns feature divergent intron consensus sequences at their 5' and 3' ends and are recognized by a separate pre-mRNA processing machinery denoted as the minor spliceosome. This spliceosome has been studied less than its major counterpart, but has received increasing attention during the last few years as a novel pathomechanistic player on the stage in neurodevelopmental and neurodegenerative diseases. Here, we review the current knowledge on minor spliceosome function and discuss its potential pathomechanistic role and impact in neurodegeneration.
Collapse
Affiliation(s)
- Daniel Jutzi
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Maureen V Akinyi
- Institute of Biotechnology, University of Helsinki, FI-00014, Finland
| | - Jonas Mechtersheimer
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Mikko J Frilander
- Institute of Biotechnology, University of Helsinki, FI-00014, Finland
| | - Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.,United Kingdom Dementia Research Institute Centre, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE5 9NU London, UK
| |
Collapse
|
26
|
Minor spliceosome and disease. Semin Cell Dev Biol 2017; 79:103-112. [PMID: 28965864 DOI: 10.1016/j.semcdb.2017.09.036] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/21/2017] [Accepted: 09/27/2017] [Indexed: 01/09/2023]
Abstract
The U12-dependent (minor) spliceosome excises a rare group of introns that are characterized by a highly conserved 5' splice site and branch point sequence. Several new congenital or somatic diseases have recently been associated with mutations in components of the minor spliceosome. A common theme in these diseases is the detection of elevated levels of transcripts containing U12-type introns, of which a subset is associated with other splicing defects. Here we review the present understanding of minor spliceosome diseases, particularly those associated with the specific components of the minor spliceosome. We also present a model for interpreting the molecular-level consequences of the different diseases.
Collapse
|
27
|
Isobaric tags for relative and absolute quantification-based proteomic analysis of testis biopsies in rhesus monkeys treated with transient scrotal hyperthermia. Oncotarget 2017; 8:85909-85925. [PMID: 29156766 PMCID: PMC5689656 DOI: 10.18632/oncotarget.20719] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/29/2017] [Indexed: 11/25/2022] Open
Abstract
This study aimed to examine the cellular and molecular events that occur in rhesus monkey testes after scrotal hyperthermia. Eight male adult rhesus monkeys were subjected to scrotal hyperthermia at 43°C for 30 min daily for 6 consecutive days. Sperm concentration, reproductive hormones, and testis histology were examined before hyperthermia (day 0), and at 8, 15, 30, 45, 60, 75, and 90 days after the initiation of hyperthermia. iTRAQ-based proteomic analysis was conducted on testicular tissues collected on days 0, 8, and 60 to identify differentially expressed proteins at the early and recovery stages of testicular damage. The sperm concentration was significantly decreased at days 30 and 45 after treatment (p < 0.01) and recovered to baseline at day 60. When compared with day 0, 101 and 24 differentially expressed proteins were identified at days 8 and 60 after heat treatment, respectively. The molecular functions of the differentially expressed proteins at day 8 were mainly nucleic acid binding, unfolded protein binding, nucleotide binding, and nucleoside phosphate binding. Spliceosome was enriched as the most significant pathway at day 8. CIRBP, PSIP1, Sam68, and Decorin were validated and found to be consistent with the proteomic data, indicating the reliability of the proteomic profiles identified in this study. In summary, we suggest that the proteins identified in this study may play important roles in heat-induced spermatogenic impairment. Some of these proteins, such as CIRBP, PSIP1, Sam68, and Decorin, may be early molecular targets responsible for spermatogenesis suppression induced by heat treatment.
Collapse
|
28
|
Mei W, Liu S, Schnable JC, Yeh CT, Springer NM, Schnable PS, Barbazuk WB. A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize. FRONTIERS IN PLANT SCIENCE 2017; 8:694. [PMID: 28539927 PMCID: PMC5423905 DOI: 10.3389/fpls.2017.00694] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/18/2017] [Indexed: 05/19/2023]
Abstract
Identifying and characterizing alternative splicing (AS) enables our understanding of the biological role of transcript isoform diversity. This study describes the use of publicly available RNA-Seq data to identify and characterize the global diversity of AS isoforms in maize using the inbred lines B73 and Mo17, and a related species, sorghum. Identification and characterization of AS within maize tissues revealed that genes expressed in seed exhibit the largest differential AS relative to other tissues examined. Additionally, differences in AS between the two genotypes B73 and Mo17 are greatest within genes expressed in seed. We demonstrate that changes in the level of alternatively spliced transcripts (intron retention and exon skipping) do not solely reflect differences in total transcript abundance, and we present evidence that intron retention may act to fine-tune gene expression across seed development stages. Furthermore, we have identified temperature sensitive AS in maize and demonstrate that drought-induced changes in AS involve distinct sets of genes in reproductive and vegetative tissues. Examining our identified AS isoforms within B73 × Mo17 recombinant inbred lines (RILs) identified splicing QTL (sQTL). The 43.3% of cis-sQTL regulated junctions are actually identified as alternatively spliced junctions in our analysis, while 10 Mb windows on each side of 48.2% of trans-sQTLs overlap with splicing related genes. Using sorghum as an out-group enabled direct examination of loss or conservation of AS between homeologous genes representing the two subgenomes of maize. We identify several instances where AS isoforms that are conserved between one maize homeolog and its sorghum ortholog are absent from the second maize homeolog, suggesting that these AS isoforms may have been lost after the maize whole genome duplication event. This comprehensive analysis provides new insights into the complexity of AS in maize.
Collapse
Affiliation(s)
- Wenbin Mei
- Department of Biology, University of Florida, GainesvilleFL, USA
| | - Sanzhen Liu
- Department of Agronomy, Iowa State University, AmesIA, USA
- Department of Plant Pathology, Kansas State University, ManhattanKS, USA
| | - James C. Schnable
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, LincolnNE, USA
| | - Cheng-Ting Yeh
- Department of Agronomy, Iowa State University, AmesIA, USA
| | - Nathan M. Springer
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint PaulMN, USA
| | - Patrick S. Schnable
- Department of Agronomy, Iowa State University, AmesIA, USA
- Center for Plant Genomics, Iowa State University, AmesIA, USA
| | - William B. Barbazuk
- Department of Biology, University of Florida, GainesvilleFL, USA
- Genetics Institute, University of Florida, GainesvilleFL, USA
- *Correspondence: William B. Barbazuk,
| |
Collapse
|