Global Co-transcriptional Splicing in Arabidopsis and the Correlation with Splicing Regulation in Mature RNAs

Molecular Plant - Tập 13 - Trang 266-277 - 2020
Shaofang Li1,2, Yuan Wang3,4,5, Yonghui Zhao3,6, Xinjie Zhao2, Xuemei Chen3, Zhizhong Gong2
1State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
2Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
3Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
4Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
5Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
6Plant Phenomics Research Center, Nanjing Agricultural University, Nanjing 210018, China

Tài liệu tham khảo

Bauren, 1994, Splicing of Balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription, Cell, 76, 183, 10.1016/0092-8674(94)90182-1 Bentley, 2014, Coupling mRNA processing with transcription in time and space, Nat. Rev. Genet., 15, 163, 10.1038/nrg3662 Beyer, 1988, Splice site selection, rate of splicing, and alternative splicing on nascent transcripts, Genes Dev., 2, 754, 10.1101/gad.2.6.754 Bezzi, 2013, Regulation of constitutive and alternative splicing by PRMT5 reveals a role for Mdm4 pre-mRNA in sensing defects in the spliceosomal machinery, Genes Dev., 27, 1903, 10.1101/gad.219899.113 Bhatt, 2012, Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions, Cell, 150, 279, 10.1016/j.cell.2012.05.043 Brugiolo, 2013, Counting on co-transcriptional splicing, F1000Prime Rep., 5, 9 Carlson, 2017, RBM25 is a global splicing factor promoting inclusion of alternatively spliced exons and is itself regulated by lysine mono-methylation, J. Biol. Chem., 292, 13381, 10.1074/jbc.M117.784371 Carrillo Oesterreich, 2010, Global analysis of nascent RNA reveals transcriptional pausing in terminal exons, Mol. Cell, 40, 571, 10.1016/j.molcel.2010.11.004 Deng, 2010, Arginine methylation mediated by the Arabidopsis homolog of PRMT5 is essential for proper pre-mRNA splicing, Proc. Natl. Acad. Sci. U S A, 107, 19114, 10.1073/pnas.1009669107 Dobin, 2013, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, 29, 15, 10.1093/bioinformatics/bts635 Drechsel, 2013, Nonsense-mediated decay of alternative precursor mRNA splicing variants is a major determinant of the Arabidopsis steady state transcriptome, Plant Cell, 25, 3726, 10.1105/tpc.113.115485 Feng, 2015, SKIP confers osmotic tolerance during salt stress by controlling alternative gene splicing in Arabidopsis, Mol. Plant, 8, 1038, 10.1016/j.molp.2015.01.011 Gaidatzis, 2015, Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation, Nat. Biotechnol., 33, 722, 10.1038/nbt.3269 Girard, 2012, Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion, Nat. Commun., 3, 994, 10.1038/ncomms1998 Griebel, 2012, Modelling and simulating generic RNA-Seq experiments with the flux simulator, Nucleic Acids Res., 40, 10073, 10.1093/nar/gks666 Guo, 2014, BS69/ZMYND11 reads and connects histone H3.3 lysine 36 trimethylation-decorated chromatin to regulated pre-mRNA processing, Mol. Cell, 56, 298, 10.1016/j.molcel.2014.08.022 Hernando, 2015, Genome wide comparative analysis of the effects of PRMT5 and PRMT4/CARM1 arginine methyltransferases on the Arabidopsis thaliana transcriptome, BMC Genomics, 16, 192, 10.1186/s12864-015-1399-2 Herzel, 2017, Splicing and transcription touch base: co-transcriptional spliceosome assembly and function, Nat. Rev. Mol. Cell Biol., 18, 637, 10.1038/nrm.2017.63 Hetzel, 2016, Nascent RNA sequencing reveals distinct features in plant transcription, Proc. Natl. Acad. Sci. U S A, 113, 12316, 10.1073/pnas.1603217113 Hogg, 2010, The function of the NineTeen Complex (NTC) in regulating spliceosome conformations and fidelity during pre-mRNA splicing, Biochem. Soc. Trans., 38, 1110, 10.1042/BST0381110 Jaganathan, 2019, Predicting splicing from primary sequence with deep learning, Cell, 176, 535, 10.1016/j.cell.2018.12.015 Ji, 2015, PRL1 modulates root stem cell niche activity and meristem size through WOX5 and PLTs in Arabidopsis, Plant J., 81, 399, 10.1111/tpj.12733 Jia, 2017, The Arabidopsis MOS4-associated complex promotes MicroRNA biogenesis and precursor messenger RNA splicing, Plant Cell, 29, 2626, 10.1105/tpc.17.00370 Keren, 2010, Alternative splicing and evolution: diversification, exon definition and function, Nat. Rev. Genet., 11, 345, 10.1038/nrg2776 Khodor, 2012, Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse, RNA, 18, 2174, 10.1261/rna.034090.112 Khodor, 2011, Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila, Genes Dev., 25, 2502, 10.1101/gad.178962.111 Li, 2015, Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis, Genome Res., 25, 235, 10.1101/gr.182238.114 Luco, 2011, Epigenetics in alternative pre-mRNA splicing, Cell, 144, 16, 10.1016/j.cell.2010.11.056 Luco, 2010, Regulation of alternative splicing by histone modifications, Science, 327, 996, 10.1126/science.1184208 Meyer, 2017, Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7, Genome Biol., 18, 204, 10.1186/s13059-017-1332-x Monaghan, 2009, Two Prp19-like U-box proteins in the MOS4-associated complex play redundant roles in plant innate immunity, PLoS Pathog., 5, e1000526, 10.1371/journal.ppat.1000526 Pandya-Jones, 2009, Co-transcriptional splicing of constitutive and alternative exons, RNA, 15, 1896, 10.1261/rna.1714509 Reddy, 2007, Alternative splicing of pre-messenger RNAs in plants in the genomic era, Annu. Rev. Plant Biol., 58, 267, 10.1146/annurev.arplant.58.032806.103754 Reddy, 2012, Localization and dynamics of nuclear speckles in plants, Plant Physiol., 158, 67, 10.1104/pp.111.186700 Ruhl, 2012, Polypyrimidine tract binding protein homologs from Arabidopsis are key regulators of alternative splicing with implications in fundamental developmental processes, Plant Cell, 24, 4360, 10.1105/tpc.112.103622 Saxena, 2011, Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs, Bioessays, 33, 830, 10.1002/bies.201100084 Schwartz, 2009, Chromatin organization marks exon-intron structure, Nat. Struct. Mol. Biol., 16, 990, 10.1038/nsmb.1659 Spies, 2009, Biased chromatin signatures around polyadenylation sites and exons, Mol. Cell, 36, 245, 10.1016/j.molcel.2009.10.008 Tilgner, 2012, Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs, Genome Res., 22, 1616, 10.1101/gr.134445.111 Trapnell, 2013, Differential analysis of gene regulation at transcript resolution with RNA-seq, Nat. Biotechnol., 31, 46, 10.1038/nbt.2450 Wang, 2011, An importin beta protein negatively regulates MicroRNA activity in Arabidopsis, Plant Cell, 23, 3565, 10.1105/tpc.111.091058 Wang, 2012, SKIP is a component of the spliceosome linking alternative splicing and the circadian clock in Arabidopsis, Plant Cell, 24, 3278, 10.1105/tpc.112.100081 Wang, 2019, The protein Phosphatase4 complex promotes transcription and processing of primary microRNAs in Arabidopsis, Plant Cell, 31, 486, 10.1105/tpc.18.00556 Will, 2011, Spliceosome structure and function, Cold Spring Harb. Perspect. Biol., 3, 10.1101/cshperspect.a003707 Xiong, 2014, The human splicing code reveals new insights into the genetic determinants of disease, Science, 347, 1254806, 10.1126/science.1254806 Yeo, 2004, Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals, J. Comput. Biol., 11, 377, 10.1089/1066527041410418 Zaffagnini, 2013, Plant cytoplasmic GAPDH: redox post-translational modifications and moonlighting properties, Front. Plant Sci., 4, 450, 10.3389/fpls.2013.00450 Zhan, 2015, An Arabidopsis PWI and RRM motif-containing protein is critical for pre-mRNA splicing and ABA responses, Nat. Commun., 6, 8139, 10.1038/ncomms9139 Zhang, 2011, GC content around splice sites affects splicing through pre-mRNA secondary structures, BMC Genomics, 12, 90, 10.1186/1471-2164-12-90