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