Skip to main content
SpringerLink
Log in

Long Noncoding RNAs in Plants

  • Chapter
  • First Online:
Long Non Coding RNA Biology

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1008))

Abstract

The eukaryotic genomes are pervasively transcribed. In addition to protein-coding RNAs, thousands of long noncoding RNAs (lncRNAs) modulate key molecular and biological processes. Most lncRNAs are found in the nucleus and associate with chromatin, but lncRNAs can function in both nuclear and cytoplasmic compartments. Emerging work has found that many lncRNAs regulate gene expression and can affect genome stability and nuclear domain organization both in plant and in the animal kingdom. Here, we describe the major plant lncRNAs and how they act, with a focus on research in Arabidopsis thaliana and our emerging understanding of lncRNA functions in serving as molecular sponges and decoys, functioning in regulation of transcription and silencing, particularly in RNA-directed DNA methylation, and in epigenetic regulation of flowering time.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
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

  1. Chekanova JA, Gregory BD, Reverdatto SV, Chen H, Kumar R, Hooker T, Yazaki J, Li P, Skiba N, Peng Q, Alonso J, Brukhin V, Grossniklaus U, Ecker JR, Belostotsky DA (2007) Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell 131(7):1340–1353. doi:10.1016/j.cell.2007.10.056

    Article  CAS  PubMed  Google Scholar 

  2. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316(5830):1484–1488. doi:10.1126/science.1138341

    Article  CAS  PubMed  Google Scholar 

  3. Jin J, Liu J, Wang H, Wong L, Chua N-H (2013) PLncDB: plant long non-coding RNA database. Bioinformatics 29(8):1068–1071. doi:10.1093/bioinformatics/btt107

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Wang H, Chung PJ, Liu J, Jang I-C, Kean MJ, Xu J, Chua N-H (2014) Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis. Genome Res 24(3):444–453. doi:10.1101/gr.165555.113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Zhang Y-C, Liao J-Y, Li Z-Y, Yu Y, Zhang J-P, Li Q-F, Qu L-H, Shu W-S, Chen Y-Q (2014) Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. Genome Biol 15(12):512. doi:10.1186/s13059-014-0512-1

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  6. Wierzbicki AT, Haag JR, Pikaard CS (2008) Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 135(4):635–648. doi:10.1016/j.cell.2008.09.035

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Li L, Eichten SR, Shimizu R, Petsch K, Yeh C-T, Wu W, Chettoor AM, Givan SA, Cole RA, Fowler JE, Evans MM, Scanlon MJ, Yu J, Schnable PS, Timmermans MC, Springer NM, Muehlbauer GJ (2014) Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biol 15(2):R40. doi:10.1186/gb-2014-15-2-r40

    Article  PubMed  PubMed Central  Google Scholar 

  8. Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, FANTOM C, Forrest ARR, Carninci P, Rehli M, Sandelin A (2014) An atlas of active enhancers across human cell types and tissues. Nature 507(7493):455–461. doi:10.1038/nature12787

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Heo JB, Sung S (2011) Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331(6013):76–79. doi:10.1126/science.1197349

    Article  CAS  PubMed  Google Scholar 

  10. Shin J-H, Chekanova JA (2014) Arabidopsis RRP6L1 and RRP6L2 function in FLOWERING LOCUS C silencing via regulation of antisense RNA synthesis. PLoS Genet 10(9):e1004612. doi:10.1371/journal.pgen.1004612

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  11. Kim D-H, Sung S (2017) Vernalization-triggered intragenic chromatin loop formation by long noncoding RNAs. Dev Cell 40(3):302–312.e4. doi:10.1016/j.devcel.2016.12.021

    Article  CAS  PubMed  Google Scholar 

  12. Di C, Yuan J, Wu Y, Li J, Lin H, Hu L, Zhang T, Qi Y, Gerstein MB, Guo Y, Lu ZJ (2014) Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features. Plant J 80(5):848–861. doi:10.1111/tpj.12679

    Article  CAS  PubMed  Google Scholar 

  13. Yuan J, Zhang Y, Dong J, Sun Y, Lim BL, Liu D, Lu ZJ (2016) Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana. BMC Genomics 17(1):655. doi:10.1186/s12864-016-2929-2

    Article  PubMed  PubMed Central  Google Scholar 

  14. Li S, Yamada M, Han X, Ohler U, Benfey PN (2016) High-resolution expression map of the Arabidopsis root reveals alternative splicing and lincRNA regulation. Dev Cell 39(4):508–522. doi:10.1016/j.devcel.2016.10.012

    Article  CAS  PubMed  Google Scholar 

  15. Mattick JS, Rinn JL (2015) Discovery and annotation of long noncoding RNAs. Nat Struct Mol Biol 22(1):5–7. doi:10.1038/nsmb.2942

    Article  CAS  PubMed  Google Scholar 

  16. Xu Z, Wei W, Gagneur J, Perocchi F, Keller C, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM (2009) Bidirectional promoters generate pervasive transcription in yeast. Nature 457(7232):1033–1037. doi:10.1038/nature07728

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. van Dijk EL, Chen CL, d’Aubenton-Carafa Y, Gourvennec S, Kwapisz M, Roche V, Bertrand C, Silvain M, Legoix-Né P, Loeillet S, Nicolas A, Thermes C, Morillon A (2011) XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast. Nature 475(7354):114–117. doi:10.1038/nature10118

    Article  PubMed  CAS  Google Scholar 

  18. Schulz D, Schwalb B, Kiesel A, Baejen C, Torkler P, Gagneur J, Soeding J, Cramer P (2013) Transcriptome surveillance by selective termination of noncoding RNA synthesis. Cell 155(5):1075–1087. doi:10.1016/j.cell.2013.10.024

    Article  CAS  PubMed  Google Scholar 

  19. Fox MJ, Gao H, Smith-Kinnaman WR, Liu Y, Mosley AL (2015) The exosome component Rrp6 is required for RNA polymerase II termination at specific targets of the Nrd1-Nab3 pathway. PLoS Genet 11(2):e1004999. doi:10.1371/journal.pgen.1004999

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  20. Flynn RA, Almada AE, Zamudio JR, Sharp PA (2011) Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome. Proc Natl Acad Sci 108(26):10460–10465. doi:10.1073/pnas.1106630108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Hetzel J, Duttke SH, Benner C, Chory J (2016) Nascent RNA sequencing reveals distinct features in plant transcription. Proc Natl Acad Sci 113(43):12316–12321. doi:10.1073/pnas.1603217113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Zhu B, Zhang W, Zhang T, Liu B, Jiang J (2015) Genome-wide prediction and validation of intergenic enhancers in Arabidopsis using open chromatin signatures. Plant Cell 27(9):2415–2426. doi:10.1105/tpc.15.00537

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40(Database issue):D1202–D1210. doi:10.1093/nar/gkr1090

    Article  CAS  PubMed  Google Scholar 

  24. Cheng C-Y, Krishnakumar V, Chan AP, Thibaud-Nissen F, Schobel S, Town CD (2017) Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. Plant J 89(4):789–804. doi:10.1111/tpj.13415

    Article  CAS  PubMed  Google Scholar 

  25. Paytuví Gallart A, Hermoso Pulido A, Anzar Martínez de Lagrán I, Sanseverino W, Aiese Cigliano R (2015) GREENC: a Wiki-based database of plant lncRNAs. Nucleic Acids Res. doi:10.1093/nar/gkv1215. gkv1215

  26. Zhao Y, Li H, Fang S, Kang Y, Wu W, Hao Y, Li Z, Bu D, Sun N, Zhang MQ, Chen R (2016) NONCODE 2016: an informative and valuable data source of long non-coding RNAs. Nucleic Acids Res 44(D1):D203–D208. doi:10.1093/nar/gkv1252

    Article  CAS  PubMed  Google Scholar 

  27. Szcześniak MW, Rosikiewicz W, Makałowska I (2016) CANTATAdb: a collection of plant long non-coding RNAs. Plant Cell Physiol 57(1):e8–e8. doi:10.1093/pcp/pcv201

    Article  PubMed  CAS  Google Scholar 

  28. Yi X, Zhang Z, Ling Y, Xu W, Su Z (2015) PNRD: a plant non-coding RNA database. Nucleic Acids Res 43(Database issue):D982–D989. doi:10.1093/nar/gku1162

    Article  CAS  PubMed  Google Scholar 

  29. Chen D, Yuan C, Zhang J, Zhang Z, Bai L, Meng Y, Chen L-L, Chen M (2012) PlantNATsDB: a comprehensive database of plant natural antisense transcripts. Nucleic Acids Res 40(Database issue):D1187–D1193. doi:10.1093/nar/gkr823

    Article  CAS  PubMed  Google Scholar 

  30. Liu J, Jung C, Xu J, Wang H, Deng S, Bernad L, Arenas-Huertero C, Chua N-H (2012) Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 24(11):4333–4345. doi:10.1105/tpc.112.102855

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Wang Y, Wang X, Deng W, Fan X, Liu T-T, He G, Chen R, Terzaghi W, Zhu D, Deng XW (2014) Genomic features and regulatory roles of intermediate-sized non-coding RNAs in Arabidopsis. Mol Plant 7(3):514–527. doi:10.1093/mp/sst177

    Article  CAS  PubMed  Google Scholar 

  32. Liu T-T, Zhu D, Chen W, Deng W, He H, He G, Bai B, Qi Y, Chen R, Deng XW (2013) A global identification and analysis of small nucleolar RNAs and possible intermediate-sized non-coding RNAs in Oryza sativa. Mol Plant 6(3):830–846. doi:10.1093/mp/sss087

    Article  CAS  PubMed  Google Scholar 

  33. van Werven FJ, Neuert G, Hendrick N, Lardenois A, Buratowski S, van Oudenaarden A, Primig M, Amon A (2012) Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast. Cell 150:1170–1181. doi:10.1016/j.cell.2012.06.049

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  34. Zofall M, Yamanaka S, Reyes-Turcu FE, Zhang K, Rubin C, Grewal SIS (2012) RNA elimination machinery targeting meiotic mRNAs promotes facultative heterochromatin formation. Science 335(6064):96–100. doi:10.1126/science.1211651

    Article  CAS  PubMed  Google Scholar 

  35. Flynn RA, Chang HY (2014) Long noncoding RNAs in cell-fate programming and reprogramming. Cell Stem Cell 14(6):752–761. doi:10.1016/j.stem.2014.05.014

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Berry S, Dean C (2015) Environmental perception and epigenetic memory: mechanistic insight through FLC. Plant J 83(1):133–148. doi:10.1111/tpj.12869

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Matzke MA, Mosher RA (2014) RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat Rev Genet 15(6):394–408. doi:10.1038/nrg3683

    Article  CAS  PubMed  Google Scholar 

  38. Bardou F, Ariel F, Simpson CG, Romero-Barrios N, Laporte P, Balzergue S, Brown JWS, Crespi M (2014) Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Dev Cell 30(2):166–176. doi:10.1016/j.devcel.2014.06.017

    Article  CAS  PubMed  Google Scholar 

  39. Wang Y, Fan X, Lin F, He G, Terzaghi W, Zhu D, Deng XW (2014) Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light. Proc Natl Acad Sci 111(28):10359–10364. doi:10.1073/pnas.1409457111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Wang D, Qu Z, Yang L, Zhang Q, Liu Z-H, Do T, Adelson DL, Wang Z-Y, Searle I, Zhu J-K (2017) Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in plants. Plant J. doi:10.1111/tpj.13481

  41. Pefanis E, Wang J, Rothschild G, Lim J, Kazadi D, Sun J, Federation A, Chao J, Elliott O, Liu Z-P, Economides AN, Bradner JE, Rabadan R, Basu U (2015) RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity. Cell 161(4):774–789. doi:10.1016/j.cell.2015.04.034

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Zilberman D, Cao X, Jacobsen SE (2003) ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299(5607):716–719. doi:10.1126/science.1079695

    Article  CAS  PubMed  Google Scholar 

  43. Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2(5):E104. doi:10.1371/journal.pbio.0020104.sg002

    Article  PubMed  PubMed Central  Google Scholar 

  44. Zheng X, Zhu J, Kapoor A, Zhu J-K (2007) Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing. EMBO J 26(6):1691–1701

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Gao Z, Liu H-L, Daxinger L, Pontes O, He X, Qian W, Lin H, Xie M, Lorkovic ZJ, Zhang S, Miki D, Zhan X, Pontier D, Lagrange T, Jin H, Matzke AJM, Matzke M, Pikaard CS, Zhu J-K (2010) An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature 465(7294):106–109. doi:10.1038/nature09025

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Matzke M, Kanno T, Daxinger L, Huettel B, Matzke AJ (2009) RNA-mediated chromatin-based silencing in plants. Curr Opin Cell Biol 21(3):367–376. doi:10.1016/j.ceb.2009.01.025

    Article  CAS  PubMed  Google Scholar 

  47. Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, Rubio-Somoza I, Leyva A, Weigel D, García JA, Paz-Ares J (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 39(8):1033–1037. doi:10.1038/ng2079

    Article  CAS  PubMed  Google Scholar 

  48. Wang P, Xue Y, Han Y, Lin L, Wu C, Xu S, Jiang Z, Xu J, Liu Q, Cao X (2014) The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation. Science 344(6181):310–313. doi:10.1126/science.1251456

    Article  CAS  PubMed  Google Scholar 

  49. Bonasio R, Shiekhattar R (2014) Regulation of transcription by long noncoding RNAs. Annu Rev Genet 48:433–455. doi:10.1146/annurev-genet-120213-092323

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA, Chang HY (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472(7341):120–124. doi:10.1038/nature09819

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY (2010) Long noncoding RNA as modular scaffold of histone modification complexes. Science 329(5992):689–693. doi:10.1126/science.1192002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Li W, Notani D, Rosenfeld MG (2016) Enhancers as non-coding RNA transcription units: recent insights and future perspectives. Nat Rev Genet 17(4):207–223. doi:10.1038/nrg.2016.4

    Article  CAS  PubMed  Google Scholar 

  53. Lai F, Orom UA, Cesaroni M, Beringer M, Taatjes DJ, Blobel GA, Shiekhattar R (2013) Activating RNAs associate with mediator to enhance chromatin architecture and transcription. Nature 494(7438):497–501. doi:10.1038/nature11884

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Skourti-Stathaki K, Proudfoot NJ (2014) A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression. Genes Dev 28(13):1384–1396. doi:10.1101/gad.242990.114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Swiezewski S, Liu F, Magusin A, Dean C (2009) Cold-induced silencing by long antisense transcripts of an Arabidopsis polycomb target. Nature 462(7274):799–802. doi:10.1038/nature08618

    Article  CAS  PubMed  Google Scholar 

  56. Ariel F, Jegu T, Latrasse D, Romero-Barrios N, Christ A, Benhamed M, Crespi M (2014) Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop. Mol Cell 55(3):383–396. doi:10.1016/j.molcel.2014.06.011

    Article  CAS  PubMed  Google Scholar 

  57. Li S, Vandivier LE, Tu B, Gao L, Won SY, Li S, Zheng B, Gregory BD, Chen X (2015) Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis. Genome Res 25(2):235–245. doi:10.1101/gr.182238.114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Blevins T, Podicheti R, Mishra V, Marasco M, Wang J, Rusch D, Tang H, Pikaard CS (2015) Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis. eLife 4:e09591. doi:10.7554/eLife.09591

    Article  PubMed  PubMed Central  Google Scholar 

  59. Zhai J, Bischof S, Wang H, Feng S, Lee T-F, Teng C, Chen X, Park SY, Liu L, Gallego-Bartolome J, Liu W, Henderson IR, Meyers BC, Ausin I, Jacobsen SE (2015) A one precursor one siRNA model for Pol IV-dependent siRNA biogenesis. Cell 163(2):445–455. doi:10.1016/j.cell.2015.09.032

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Böhmdorfer G, Sethuraman S, Rowley MJ, Krzyszton M, Rothi MH, Bouzit L, Wierzbicki AT (2016) Long non-coding RNA produced by RNA polymerase V determines boundaries of heterochromatin. eLife 5:1325. doi:10.7554/eLife.19092

    Article  Google Scholar 

  61. Campalans A, Kondorosi A, Crespi M (2004) Enod40, a short open reading frame-containing mRNA, induces cytoplasmic localization of a nuclear RNA binding protein in Medicago truncatula. Plant Cell 16(4):1047–1059. doi:10.1105/tpc.019406

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Ding J, Lu Q, Ouyang Y, Mao H, Zhang P, Yao J, Xu C, Li X, Xiao J, Zhang Q (2012) A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proc Natl Acad Sci 109(7):2654–2659. doi:10.1073/pnas.1121374109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Wu H-J, Wang Z-M, Wang M, Wang X-J (2013) Widespread long noncoding RNAs as endogenous target mimics for microRNAs in plants. Plant Physiol 161(4):1875–1884. doi:10.1104/pp.113.215962

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Bühler M, Haas W, Gygi SP, Moazed D (2007) RNAi-dependent and -independent RNA turnover mechanisms contribute to heterochromatic gene silencing. Cell 129(4):707–721. doi:10.1016/j.cell.2007.03.038

    Article  PubMed  CAS  Google Scholar 

  65. Bühler M, Spies N, Bartel DP, Moazed D (2008) TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway. Nat Struct Mol Biol 15(10):1015–1023. doi:10.1038/nsmb.1481

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  66. Reyes-Turcu FE, Zhang K, Zofall M, Chen E, Grewal SIS (2011) Defects in RNA quality control factors reveal RNAi-independent nucleation of heterochromatin. Nat Struct Mol Biol 18(10):1132–1138. doi:10.1038/nsmb.2122

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Holoch D, Moazed D (2015) RNA-mediated epigenetic regulation of gene expression. Nat Rev Genet 16(2):71–84. doi:10.1038/nrg3863

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Zheng B, Wang Z, Li S, Yu B, Liu JY, Chen X (2009) Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes Dev 23(24):2850–2860. doi:10.1101/gad.1868009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Zhang X, Henderson IR, Lu C, Green PJ, Jacobsen SE (2007) Role of RNA polymerase IV in plant small RNA metabolism. Proc Natl Acad Sci 104(11):4536–4541. doi:10.1073/pnas.0611456104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Lee T-F, Gurazada SGR, Zhai J, Li S, Simon SA, Matzke MA, Chen X, Meyers BC (2012) RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats. Epigenetics 7(7):781–795. doi:10.4161/epi.20290

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. You W, Lorkovic ZJ, Matzke AJM, Matzke M (2013) Interplay among RNA polymerases II, IV and V in RNA-directed DNA methylation at a low copy transgene locus in Arabidopsis thaliana. Plant Mol Biol 82(1–2):85–96. doi:10.1007/s11103-013-0041-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Sasaki T, Lee T-F, Liao W-W, Naumann U, Liao J-L, Eun C, Huang Y-Y, Fu JL, Chen P-Y, Meyers BC, Matzke AJM, Matzke M (2014) Distinct and concurrent pathways of Pol II- and Pol IV-dependent siRNA biogenesis at a repetitive trans-silencer locus in Arabidopsis thaliana. Plant J 79(1):127–138. doi:10.1111/tpj.12545

    Article  CAS  PubMed  Google Scholar 

  73. Law JA, Du J, Hale CJ, Feng S, Krajewski K, Palanca AMS, Strahl BD, Patel DJ, Jacobsen SE (2013) Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Nature 498(7454):385–389. doi:10.1038/nature12178

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Liu Z-W, Shao C-R, Zhang C-J, Zhou J-X, Zhang S-W, Li L, Chen S, Huang H-W, Cai T, He X-J (2014) The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy at RNA-directed DNA methylation loci. PLoS Genet 10(1):e1003948. doi:10.1371/journal.pgen.1003948

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  75. Zhong X, Hale CJ, Law JA, Johnson LM, Feng S, Tu A, Jacobsen SE (2012) DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons. Nat Struct Mol Biol 19(9):870–875. doi:10.1038/nsmb.2354

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Zhu Y, Rowley MJ, Böhmdorfer G, Wierzbicki AT (2013) A SWI/SNF chromatin-remodeling complex acts in noncoding RNA-mediated transcriptional silencing. Mol Cell 49(2):298–309. doi:10.1016/j.molcel.2012.11.011

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Wierzbicki AT, Cocklin R, Mayampurath A, Lister R, Rowley MJ, Gregory BD, Ecker JR, Tang H, Pikaard CS (2012) Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome. Genes Dev 26(16):1825–1836. doi:10.1101/gad.197772.112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Wierzbicki AT, Ream TS, Haag JR, Pikaard CS (2009) RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat Genet 41(5):630–634. doi:10.1038/ng.365

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Zheng Q, Rowley MJ, Böhmdorfer G, Sandhu D, Gregory BD, Wierzbicki AT (2012) RNA polymerase V targets transcriptional silencing components to promoters of protein-coding genes. Plant J. doi:10.1111/tpj.12034

  80. Böhmdorfer G, Rowley MJ, Kuciński J, Zhu Y, Amies I, Wierzbicki AT (2014) RNA-directed DNA methylation requires stepwise binding of silencing factors to long non-coding RNA. Plant J 79(2):181–191. doi:10.1111/tpj.12563

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  81. Shin J-H, Wang H-LV, Lee J, Dinwiddie BL, Belostotsky DA, Chekanova JA (2013) The role of the Arabidopsis exosome in siRNA-independent silencing of heterochromatic loci. PLoS Genet 9(3):e1003411. doi:10.1371/journal.pgen.1003411.s007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Zhang H, Tang K, Qian W, Duan C-G, Wang B, Zhang H, Wang P, Zhu X, Lang Z, Yang Y, Zhu J-K (2014) An Rrp6-like protein positively regulates noncoding RNA levels and DNA methylation in Arabidopsis. Mol Cell 54(3):418–430. doi:10.1016/j.molcel.2014.03.019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Amasino RM, Michaels SD (2010) The timing of flowering. Plant Physiol 154(2):516–520. doi:10.1104/pp.110.161653

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Liu F, Marquardt S, Lister C, Swiezewski S, Dean C (2009) Targeted 3′ processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing. Science 327(5961):94–97. doi:10.1126/science.1180278

    Article  PubMed  CAS  Google Scholar 

  85. Davidovich C, Wang X, Cifuentes-Rojas C, Goodrich KJ, Gooding AR, Lee JT, Cech TR (2015) Toward a consensus on the binding specificity and promiscuity of PRC2 for RNA. Mol Cell 57(3):552–558. doi:10.1016/j.molcel.2014.12.017

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Helliwell CA, Robertson M, Finnegan EJ, Buzas DM, Dennis ES (2011) Vernalization-repression of Arabidopsis FLC requires promoter sequences but not antisense transcripts. PLoS One 6(6):e21513. doi:10.1371/journal.pone.0021513

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Csorba T, Questa JI, Sun Q, Dean C (2014) Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization. Proc Natl Acad Sci 111(45):16160–16165. doi:10.1073/pnas.1419030111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Hornyik C, Terzi LC, Simpson GG (2010) The Spen family protein FPA controls alternative cleavage and polyadenylation of RNA. Dev Cell 18(2):203–213. doi:10.1016/j.devcel.2009.12.009

    Article  CAS  PubMed  Google Scholar 

  89. Marquardt S, Raitskin O, Wu Z, Liu F, Sun Q, Dean C (2014) Functional consequences of splicing of the antisense transcript COOLAIR on FLC transcription. Mol Cell 54(1):156–165. doi:10.1016/j.molcel.2014.03.026

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Liu F, Quesada V, Crevillen P, Bäurle I, Swiezewski S, Dean C (2007) The Arabidopsis RNA-binding protein FCA requires a lysine-specific demethylase 1 homolog to downregulate FLC. Mol Cell 28(3):398–407. doi:10.1016/j.molcel.2007.10.018

    Article  PubMed  CAS  Google Scholar 

  91. Hawkes EJ, Hennelly SP, Novikova IV, Irwin JA, Dean C, Sanbonmatsu KY (2016) COOLAIR antisense RNAs form evolutionarily conserved elaborate secondary structures. Cell Rep 16(12):3087–3096. doi:10.1016/j.celrep.2016.08.045

    Article  CAS  PubMed  Google Scholar 

  92. Callahan KP, Butler JS (2008) Evidence for core exosome independent function of the nuclear exoribonuclease Rrp6p. Nucleic Acids Res 36(21):6645–6655. doi:10.1093/nar/gkn743

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Kiss DL, Andrulis ED (2010) Genome-wide analysis reveals distinct substrate specificities of Rrp6, Dis3, and core exosome subunits. RNA 16(4):781–791. doi:10.1261/rna.1906710

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Ciaudo C, Bourdet A, Cohen-Tannoudji M, Dietz HC, Rougeulle C, Avner P (2006) Nuclear mRNA degradation pathway(s) are implicated in Xist regulation and X chromosome inactivation. PLoS Genet 2(6):e94. doi:10.1371/journal.pgen.0020094

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  95. Sun Q, Csorba T, Skourti-Stathaki K, Proudfoot NJ, Dean C (2013) R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus. Science 340(6132):619–621. doi:10.1126/science.1234848

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Skourti-Stathaki K, Kamieniarz-Gdula K, Proudfoot NJ (2014) R-loops induce repressive chromatin marks over mammalian gene terminators. Nature 516(7531):436–439. doi:10.1038/nature13787

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR, Morse M, Engreitz J, Lander ES, Guttman M, Lodish HF, Flavell R, Raj A, Rinn JL (2014) Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol 21(2):198–206. doi:10.1038/nsmb.2764

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C, Kadri S, Xing J, Goren A, Lander ES, Plath K, Guttman M (2013) The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 341(6147):1237973. doi:10.1126/science.1237973

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  99. Quinodoz S, Guttman M (2014) Long noncoding RNAs: an emerging link between gene regulation and nuclear organization. Trends Cell Biol 24(11):651–663. doi:10.1016/j.tcb.2014.08.009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Feng S, Cokus SJ, Schubert V, Zhai J, Pellegrini M, Jacobsen SE (2014) Genome-wide Hi-C analyses in wild-type and mutants reveal high-resolution chromatin interactions in Arabidopsis. Mol Cell 55(5):694–707. doi:10.1016/j.molcel.2014.07.008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Grob S, Schmid MW, Grossniklaus U (2014) Hi-C analysis in Arabidopsis identifies the knot, a structure with similarities to the flamenco locus of Drosophila. Mol Cell 55(5):678–693. doi:10.1016/j.molcel.2014.07.009

    Article  CAS  PubMed  Google Scholar 

  102. Wang C, Liu C, Roqueiro D, Grimm D, Schwab R, Becker C, Lanz C, Weigel D (2015) Genome-wide analysis of local chromatin packing in Arabidopsis thaliana. Genome Res 25(2):246–256. doi:10.1101/gr.170332.113

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  103. Liu C, Weigel D (2015) Chromatin in 3D: progress and prospects for plants. Genome Biol 16(1):170. doi:10.1186/s13059-015-0738-6

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  104. Liu C, Wang C, Wang G, Becker C, Zaidem M, Weigel D (2016) Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution. Genome Res. doi:10.1101/gr204032.116. gr204032116

  105. Moissiard G, Cokus SJ, Cary J, Feng S, Billi AC, Stroud H, Husmann D, Zhan Y, Lajoie BR, McCord RP, Hale CJ, Feng W, Michaels SD, Frand AR, Matteo P, Dekker J, Kim JK, Jacobsen SE (2012) MORC family ATPases required for heterochromatin condensation and gene silencing. Science 336(6087):1448–1451. doi:10.1126/science.1221472

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Crevillen P, Sonmez C, Wu Z, Dean C (2013) A gene loop containing the floral repressor FLC is disrupted in the early phase of vernalization. EMBO J 32(1):140–148. doi:10.1038/emboj.2012.324

    Article  CAS  PubMed  Google Scholar 

  107. Jegu T, Latrasse D, Delarue M, Hirt H, Domenichini S, Ariel F, Crespi M, Bergounioux C, Raynaud C, Benhamed M (2014) The BAF60 subunit of the SWI/SNF chromatin-remodeling complex directly controls the formation of a gene loop at FLOWERING LOCUS C in Arabidopsis. Plant Cell 26(2):538–551. doi:10.1105/tpc.113.114454

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Rosa S, De Lucia F, Mylne JS, Zhu D, Ohmido N, Pendle A, Kato N, Shaw P, Dean C (2013) Physical clustering of FLC alleles during polycomb-mediated epigenetic silencing in vernalization. Genes Dev 27(17):1845–1850. doi:10.1101/gad.221713.113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO, 64110, USA

    Hsiao-Lin V. Wang & Julia A. Chekanova

Authors
  1. Hsiao-Lin V. Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Julia A. Chekanova
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Julia A. Chekanova .

Editor information

Editors and Affiliations

  1. Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India

    M.R.S. Rao

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Nature Singapore Pte Ltd.

About this chapter

Cite this chapter

Wang, HL.V., Chekanova, J.A. (2017). Long Noncoding RNAs in Plants. In: Rao, M. (eds) Long Non Coding RNA Biology. Advances in Experimental Medicine and Biology, vol 1008. Springer, Singapore. https://doi.org/10.1007/978-981-10-5203-3_5

Download citation

Publish with us

Policies and ethics

Search

Navigation