Skip to main content

Alternative Splicing and Alternative Polyadenylation in Moso Bamboo

  • Chapter
  • First Online:
The Moso Bamboo Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

The processes of gene expression can happen at diverse levels and utilizes multiple molecular mechanisms. Alternative polyadenylation (APA) and alternative splicing (AS) account for two important regulatory events for generating distinct alternatively spliced isoforms or mRNA transcripts with different 3’ termini at post-transcription level. Therefore, AS and APA increase diversity and complexity of transcriptome and proteome. Moso bamboo is non-timber forest species which present unique fast growing and late flowering characteristic. AS and APA are prevalent in bamboo to regulate development. Therefore, understanding the post-transcriptional mechanisms involving unique characteristic in moso bamboo will provide key insights into gene regulation on development. We review here the profile of AS and APA from latest research progresses which will help to understand underlying role of AS and APA during the diverse processes in moso bamboo.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abdel-Ghany SE, Hamilton M, Jacobi JL et al (2016) A survey of the sorghum transcriptome using single-molecule long reads. Nat Commun 7:11706

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Barbazuk WB, Fu Y, McGinnis KM (2008) Genome-wide analyses of alternative splicing in plants: opportunities and challenges. Genome Res 18:1381–1392

    Article  CAS  PubMed  Google Scholar 

  • Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297

    Article  CAS  Google Scholar 

  • Bhasi A, Pandey RV, Utharasamy SP, Senapathy P (2007) EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes. Bioinformatics 23:1815–1823

    Article  CAS  PubMed  Google Scholar 

  • Blaustein M, Quadrana L, Risso G et al (2009) SF2/ASF regulates proteomic diversity by affecting the balance between translation initiation mechanisms. J Cell Biochem 107:826–833

    Article  CAS  PubMed  Google Scholar 

  • Blekhman R, Marioni JC, Zumbo P et al (2009) Sex-specific and lineage-specific alternative splicing in primates. Genome Res 20:180-189.

    Google Scholar 

  • Blencowe BJ (2000) Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases. Trends Biochem Sci 25:106–110

    Article  CAS  PubMed  Google Scholar 

  • Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen et al (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science 320:1185–1190

    Google Scholar 

  • Cartegni L, Chew SL, Krainer AR (2002) Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet 3:285–298

    Article  CAS  PubMed  Google Scholar 

  • Chang YF, Imam JS, Wilkinson MF (2007) The nonsense-mediated decay RNA surveillance pathway. Annu Rev Biochem 76:51–74

    Article  CAS  PubMed  Google Scholar 

  • Chen FC, Wang SS, Chaw SM et al (2007) Plant gene and alternatively spliced variant annotator. a plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species. Plant Physiol 143:1086–1095

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen L, Zhang P, Fan Y et al (2018) Circular RNAs mediated by transposons are associated with transcriptomic and phenotypic variation in maize. New Phytol 217:1292–1306

    Article  CAS  PubMed  Google Scholar 

  • Chen S, Huang V, Xu X et al (2019) Widespread and functional RNA circularization in localized prostate cancer. Cell 176:831–843

    Google Scholar 

  • Chico JM, Chini A, Fonseca S et al (2008) JAZ repressors set the rhythm in jasmonate signaling. Curr Opin Plant Biol 11:486–494

    Google Scholar 

  • Chung HS, Howe GA (2009) A critical role for the TIFY motif in repression of jasmonate signaling by a stabilized splice variant of the JASMONATE ZIM-domain protein JAZ10 in arabidopsis. Plant Cell 21:131–145

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • de la Grange P, Dutertre M, Correa M et al (2007) A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants. BMC Bioinform 8:180

    Article  Google Scholar 

  • Filichkin SA, Priest HD, Givan SA et al (2010) Genome-wide mapping of alternative splicing in arabidopsis thaliana. Genome Res 20:45-58

    Google Scholar 

  • Fu H, Yang D, Su W et al (2016) Genome-wide dynamics of alternative polyadenylation in rice. Genome Res 26:1753–1760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gao Y, Wang H, Zhang H et al (2018) PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq. Bioinformatics 34:1580–1582

    Article  CAS  PubMed  Google Scholar 

  • Gao ZM, Li CL, Peng ZH (2011) Generation and analysis of expressed sequence tags from a normalized cDNA library of young leaf from Ma bamboo (Dendrocalamus latiflorus Munro). Plant Cell Rep 30:2045–2057

    Article  CAS  PubMed  Google Scholar 

  • Gilbert W (1978) Why genes in pieces? Nature 271:501

    Article  CAS  PubMed  Google Scholar 

  • Graveley BR (2000) Sorting out the complexity of SR protein functions. RNA 6:1197–1211

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gregory BD, O’Malley RC, Lister R et al (2008) A link between RNA metabolism and silencing affecting arabidopsis development. Dev Cell 14:854–866

    Article  CAS  PubMed  Google Scholar 

  • Guo H, Ingolia NT, Weissman JS et al (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466:835–840

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guo ZH, Ma PF, Yang GQ et al (2019) Genome sequences provide insights into the reticulate origin and unique traits of woody bamboos. Mol Plant 12:1353–1365

    Article  CAS  PubMed  Google Scholar 

  • Haas BJ, Delcher AL, Mount SM et al (2003) Improving the arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 31:5654–5666

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Han MH, Goud S, Song L et al (2004) The arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc Natl Acad Sci U S A 101:1093–1098

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Henderson IR, Jacobsen SE (2008) Sequencing sliced ends reveals microRNA targets. Nat Biotechnol 26:881–882

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Holste D, Huo G, Tung V et al (2006) HOLLYWOOD: a comparative relational database of alternative splicing. Nucleic Acids Res 34:D56-62

    Article  CAS  PubMed  Google Scholar 

  • Hong L, Ye C, Lin J et al (2018) Alternative polyadenylation is involved in auxin-based plant growth and development. Plant J 93:246–258

    Article  CAS  PubMed  Google Scholar 

  • Hsu M-T, Coca-Prados M (1979) Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells. Nature 280:339–340

    Article  CAS  PubMed  Google Scholar 

  • Hung LH, Heiner M, Hui J et al (2008) Diverse roles of hnRNP L in mammalian mRNA processing: a combined microarray and RNAi analysis. RNA 14:284–296

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Iida K, Seki M, Sakurai T et al (2004) Genome-wide analysis of alternative pre-mRNA splicing in arabidopsis thaliana based on full-length cDNA sequences. Nucleic Acids Res 32:5096–5103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ip JY, Schmidt D, Pan Q et al (2011) Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Res 21:390–401

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jeck WR, Sorrentino JA, Wang K et al (2013) Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 19:141–157

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Johnson JM, Castle J, Garrett-Engele P et al (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302:2141–2144

    Article  CAS  PubMed  Google Scholar 

  • Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14:787–799

    Article  CAS  PubMed  Google Scholar 

  • Ke S, Alemu EA, Mertens C et al (2015) A majority of m6A residues are in the last exons, allowing the potential for 3’ UTR regulation. Genes Dev 29:2037–2053

    Google Scholar 

  • Kim N, Alekseyenko AV, Roy M et al (2007) The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species. Nucleic Acids Res 35:D93-98

    Article  CAS  PubMed  Google Scholar 

  • Kim P, Kim N, Lee Y et al (2005) ECgene: genome annotation for alternative splicing. Nucleic Acids Res 33:D75-79

    Article  CAS  PubMed  Google Scholar 

  • Kim S, Yang JY, Xu J et al (2008) Two cap-binding proteins CBP20 and CBP80 are involved in processing primary MicroRNAs. Plant Cell Physiol 49:1634–1644

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kitagawa N, Washio T, Kosugi S et al (2005) Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). Bioinformatics 21:1758–1763

    Article  CAS  PubMed  Google Scholar 

  • Kriventseva EV, Koch I, Apweiler R et al (2003) Increase of functional diversity by alternative splicing. Trends Genet 19:124–128

    Article  CAS  PubMed  Google Scholar 

  • Kwan T, Benovoy D, Dias C et al (2008) Genome-wide analysis of transcript isoform variation in humans. Nat Genet 40:225–231

    Article  CAS  PubMed  Google Scholar 

  • Lam BJ, Hertel KJ (2002) A general role for splicing enhancers in exon definition. RNA 8:1233–1241

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Laubinger S, Sachsenberg T, Zeller G et al (2008) Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in arabidopsis thaliana. Proc Natl Acad Sci USA 105:8795–8800

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li L, Shi Q, Hou D et al (2018) Transcriptome analysis of alternative splicing in different moso bamboo tissues. Acta Physiol Plant 40:89

    Article  Google Scholar 

  • Licatalosi DD, Mele A, Fak JJ et al (2008) HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 456:464–469

    Google Scholar 

  • Lin XC, Chow TY, Chen HH et al (2010) Understanding bamboo flowering based on large-scale analysis of expressed sequence tags. Genet Mol Res 9:1085–1093

    Article  CAS  PubMed  Google Scholar 

  • Loraine AE, Helt GA, Cline MS et al (2003) Exploring alternative transcript structure in the human genome using blocks and InterPro. J Bioinform Comput Biol 1:289–306

    Article  CAS  PubMed  Google Scholar 

  • Lu T, Cui L, Zhou Y et al (2015) Transcriptome-wide investigation of circular RNAs in rice. RNA 21:2076–2087

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Matranga C, Zamore PD (2007) Small silencing RNAs. Curr Biol 17:R789-793

    Article  CAS  PubMed  Google Scholar 

  • Memczak S, Jens M, Elefsinioti A et al (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495:333–338

    Article  CAS  PubMed  Google Scholar 

  • Molinie B, Wang J, Lim KS et al (2016) m(6)A-LAIC-seq reveals the census and complexity of the m(6)A epitranscriptome. Nat Methods 13:692–698

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moore MJ, Silver PA (2008) Global analysis of mRNA splicing. RNA 14:197–203

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nagasaki H, Arita M, Nishizawa T et al (2006) Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns. Bioinformatics 22:1211–1216

    Article  CAS  PubMed  Google Scholar 

  • Ner-Gaon H, Halachmi R, Savaldi-Goldstein S et al (2004) Intron retention is a major phenomenon in alternative splicing in arabidopsis. Plant J 39:877–885

    Article  CAS  PubMed  Google Scholar 

  • Nodine MD, Bartel DP (2010) MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis. Genes Dev 24:2678–2692

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pan Q, Shai O, Lee LJ et al (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40:1413–1415

    Article  CAS  PubMed  Google Scholar 

  • Pearson JL, Robinson TJ, Munoz MJ et al (2008) Identification of the cellular targets of the transcription factor TCERG1 reveals a prevalent role in mRNA processing. J Biol Chem 283:7949–7961

    Article  CAS  PubMed  Google Scholar 

  • Peng Z, Lu T, Li L et al (2010) Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences. BMC Plant Biol 10:116

    Article  PubMed  PubMed Central  Google Scholar 

  • Peng Z, Lu Y, Li L et al (2013) The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). Nat Genet 45:456–461

    Google Scholar 

  • Qiao G, Yang H, Zhang L et al (2014) Enhanced cold stress tolerance of transgenic Dendrocalamus latiflorus Munro (Ma bamboo) plants expressing a bacterial CodA gene. In Vitro Cellular & Developmental Biology-Plant 50:385–391

    Google Scholar 

  • Raczynska KD, Simpson CG, Ciesiolka A et al (2010) Involvement of the nuclear cap-binding protein complex in alternative splicing in arabidopsis thaliana. Nucleic Acids Res 38:265-278

    Google Scholar 

  • Rambaldi D, Felice B, Praz V et al (2007) Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data. BMC Bioinform 8(Suppl 1):S17

    Article  Google Scholar 

  • Reddy AS (2007) Alternative splicing of pre-messenger RNAs in plants in the genomic era. Annu Rev Plant Biol 58:267–294

    Article  CAS  PubMed  Google Scholar 

  • Resch A, Xing Y, Modrek B et al (2004) Assessing the impact of alternative splicing on domain interactions in the human proteome. J Proteome Res 3:76–83

    Google Scholar 

  • Rossbach O, Hung LH, Schreiner S, Grishina I, Heiner M, Hui J, Bindereif A (2009) Auto- and cross-regulation of the hnRNP L proteins by alternative splicing. Mol Cell Biol 29:1442–1451

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Routh A (2019) DPAC: a tool for differential poly(A)-cluster usage from poly(A)-targeted RNAseq data. G3: Genes, Genomes, Genetics 9:1825–1830

    Google Scholar 

  • Ryan MC, Zeeberg BR, Caplen NJ, Cleland JA, Kahn AB, Liu H, Weinstein JN (2008) SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies. BMC Bioinform 9:313

    Article  Google Scholar 

  • Sanford JR, Wang X, Mort M, et al (2008) Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res 19:381-394

    Google Scholar 

  • Schoning JC, Streitner C, Meyer IM, Gao Y, Staiger D (2008) Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in arabidopsis. Nucleic Acids Res 36:6977–6987

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shen H, Green MR (2004) A pathway of sequential arginine-serine-rich domain-splicing signal interactions during mammalian spliceosome assembly. Mol Cell 16:363–373

    Article  CAS  PubMed  Google Scholar 

  • Shen H, Kan JL, Green MR (2004) Arginine-serine-rich domains bound at splicing enhancers contact the branchpoint to promote prespliceosome assembly. Mol Cell 13:367–376

    Article  CAS  PubMed  Google Scholar 

  • Shen S, Park JW, Lu ZX, Lin L, Henry MD, Wu YN, Zhou Q, Xing Y (2014) rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc Natl Acad Sci USA 111:E5593-5601

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shen S, Warzecha C, Carstens R, Xing Y (2010) MADS+: discovery of differential splicing events from Affymetrix exon junction array data. Bioinformatics 26:268-269

    Google Scholar 

  • Shen Y, Venu RC, Nobuta K, Wu X, Notibala V, Demirci C, Meyers BC, Wang GL, Ji G, Li QQ (2011) Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing. Genome Res 21:1478–1486

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Spellman R, Llorian M, Smith CW (2007) Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1. Mol Cell 27:420–434

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stamm S, Riethoven JJ, Le Texier V et al (2006) ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Res 34:D46-55

    Article  CAS  PubMed  Google Scholar 

  • Staswick PE (2008) JAZing up jasmonate signaling. Trends Plant Sci 13:66–71

    Article  CAS  PubMed  Google Scholar 

  • Sultan M, Schulz MH, Richard H et al (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321:956–960

    Article  CAS  PubMed  Google Scholar 

  • Szabo L, Salzman J (2016) Detecting circular RNAs: bioinformatic and experimental challenges. Nat Rev Genet 17:679–692

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thierry-Mieg D, Thierry-Mieg J (2006) AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol 7:1–14

    Google Scholar 

  • Tian B, Manley JL (2017) Alternative polyadenylation of mRNA precursors. Nat Rev Mol Cell Biol 18:18–30

    Article  CAS  PubMed  Google Scholar 

  • Todesco M, Rubio-Somoza I, Paz-Ares J et al (2010) A collection of target mimics for comprehensive analysis of microRNA function in arabidopsis thaliana. PLoS Genet 6:e1001031

    Google Scholar 

  • Tress ML, Martelli PL, Frankish A et al (2007) The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci USA 104:5495–5500

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vaucheret H (2008) Plant ARGONAUTES. Trends Plant Sci 13:350–358

    Article  CAS  PubMed  Google Scholar 

  • Vazquez F, Gasciolli V, Crete P et al (2004) The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr Biol 14:346–351

    Article  CAS  PubMed  Google Scholar 

  • Vo JN, Cieslik M, Zhang Y et al (2019) The landscape of circular RNA in cancer. Cell 176:869–881

    Google Scholar 

  • Wang BB, Brendel V (2006) Genomewide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci USA 103:7175–7180

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang BB, O’Toole M, Brendel V et al (2008) Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes. BMC Plant Biol 8:17

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang ET, Sandberg R, Luo S et al (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456:470–476

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang H, Wang H, Zhang H, Liu S et al (2019) The interplay between microRNA and alternative splicing of linear and circular RNAs in eleven plant species. Bioinformatics 35:3119–3126

    Article  CAS  PubMed  Google Scholar 

  • Wang PL, Bao Y, Yee M-C et al (2014) Circular RNA is expressed across the eukaryotic tree of life. PloS One 9:e90859

    Google Scholar 

  • Wang T, Wang H, Cai D et al (2017) Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis). Plant J 91:684–699

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Gao Y, Zhang H et al (2019) Genome-wide profiling of circular RNAs in the rapidly growing shoots of moso bamboo (Phyllostachys edulis). Plant Cell Physiol 60:1354–1373

    Article  CAS  PubMed  Google Scholar 

  • Wu X, Liu M, Downie B et al (2011) Genome-wide landscape of polyadenylation in arabidopsis provides evidence for extensive alternative polyadenylation. Proc Natl Acad Sci USA 108:12533–12538

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu X, Zhang Y, Li QQ (2016) PlantAPA: a portal for visualization and analysis of alternative polyadenylation in plants. Front Plant Sci 7:889

    Article  PubMed  PubMed Central  Google Scholar 

  • Xing Y, Stoilov P, Kapur K et al (2008) MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA 14:1470–1479

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang L, Liu Z, Lu F et al (2006) SERRATE is a novel nuclear regulator in primary microRNA processing in arabidopsis. Plant J 47:841–850

    Article  CAS  PubMed  Google Scholar 

  • Ye CY, Chen L, Liu C et al (2015) Widespread noncoding circular RNAs in plants. New Phytol 208:88–95

    Article  CAS  PubMed  Google Scholar 

  • Ye S, Cai C, Ren H et al (2017) An efficient plant regeneration and transformation system of Ma Bamboo (Dendrocalamus latiflorus Munro) started from young shoot as explant. Front Plant Sci 8:1298

    Google Scholar 

  • Ye S, Chen G, Kohnen MV et al (2020) Robust CRISPR/Cas9 mediated genome editing and its application in manipulating plant height in the first generation of hexaploid Ma bamboo (Dendrocalamus latiflorus Munro). Plant Biotechnol. J 18:1501

    Google Scholar 

  • Yu X, Wang Y, Kohnen MV et al. (2019) Large scale profiling of protein isoforms using label-free quantitative proteomics revealed the regulation of nonsense-mediated decay in moso bamboo (Phyllostachys edulis). Cells 8:744

    Google Scholar 

  • Yuan Y, Chung JD, Fu X et al (2009) Alternative splicing and gene duplication differentially shaped the regulation of isochorismate synthase in Populus and arabidopsis. Proc Natl Acad Sci USA 106:22020-22025

    Google Scholar 

  • Yue Y, Liu J, Cui X et al (2018) VIRMA mediates preferential m(6)A mRNA methylation in 3’UTR and near stop codon and associates with alternative polyadenylation. Cell Discov 4:10

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang G, Guo G, Hu X et al (2010) Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res 20:646–654

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang H, Wang H, Zhu Q et al (2018) Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications. BMC Plant Biol 18:125

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang P, Fan Y, Sun X et al (2019) A large-scale circular RNA profiling reveals universal molecular mechanisms responsive to drought stress in maize and arabidopsis. Plant J 98:697-713

    Google Scholar 

  • Zhang XN, Mount SM (2009) Two Alternatively spliced Isoforms of the arabidopsis SR45 protein have distinct roles during normal plant development. Plant Physiol 150:1450–1458

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang XO, Dong R, Zhang Y et al (2016) Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res 26:1277–1287

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Y, Gu L, Hou Y et al (2015) Integrative genome-wide analysis reveals HLP1, a novel RNA-binding protein, regulates plant flowering by targeting alternative polyadenylation. Cell Res 25:864–876

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Z, Lotti F, Dittmar K et al (2008) SMN deficiency causes tissue-specific perturbations in the repertoire of snRNAs and widespread defects in splicing. Cell 133:585–600

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhao H, Gao Z, Wang L et al (2018) Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis). Gigascience 7:giy115

    Google Scholar 

  • Zhao H, Peng Z, Fei B et al (2014) BambooGDB: a bamboo genome database with functional annotation and an analysis platform. Database 2014: bau006

    Google Scholar 

  • Zhao L, Zhang H, Kohnen MV et al (2019) Analysis of transcriptome and epitranscriptome in plants using PacBio Iso-Seq and nanopore-based direct RNA sequencing. Front Genet 10:253

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhao T, Wang L, Li S et al (2017) Characterization of conserved circular RNA in polyploid Gossypium species and their ancestors. FEBS Lett 591:3660–3669

    Article  CAS  PubMed  Google Scholar 

  • Zuo J, Wang Q, Zhu B et al (2016) Deciphering the roles of circRNAs on chilling injury in tomato. Biochem Biophys Res Commun 479:132–138

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Lianfeng Gu .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Gu, L., Zhang, H., Gao, J. (2021). Alternative Splicing and Alternative Polyadenylation in Moso Bamboo. In: Gao, J. (eds) The Moso Bamboo Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-80836-5_7

Download citation

Publish with us

Policies and ethics