Seed Dormancy in Arabidopsis Is Controlled by Alternative Polyadenylation of DOG1

Overview

Journal Plant Physiol

Specialty Physiology

Date 2015 Dec 2

PMID 26620523

Citations 45

Authors

Malgorzata Cyrek

Halina Fedak

Arkadiusz Ciesielski

Yanwu Guo

Aleksandra Sliwa

Lien Brzezniak

Katarzyna Krzyczmonik

Zbigniew Pietras

Szymon Kaczanowski

Fuquan Liu

Szymon Swiezewski

Affiliations

Soon will be listed here.

Abstract

DOG1 (Delay of Germination 1) is a key regulator of seed dormancy in Arabidopsis (Arabidopsis thaliana) and other plants. Interestingly, the C terminus of DOG1 is either absent or not conserved in many plant species. Here, we show that in Arabidopsis, DOG1 transcript is subject to alternative polyadenylation. In line with this, mutants in RNA 3' processing complex display weakened seed dormancy in parallel with defects in DOG1 proximal polyadenylation site selection, suggesting that the short DOG1 transcript is functional. This is corroborated by the finding that the proximally polyadenylated short DOG1 mRNA is translated in vivo and complements the dog1 mutant. In summary, our findings indicate that the short DOG1 protein isoform produced from the proximally polyadenylated DOG1 mRNA is a key player in the establishment of seed dormancy in Arabidopsis and characterizes a set of mutants in RNA 3' processing complex required for production of proximally polyadenylated functional DOG1 transcript.

Citing Articles

Revisiting CPSF30-mediated alternative polyadenylation in Arabidopsis thaliana.

Hao G, Zhou L, Liu H, Kachroo P, Hunt A PLoS One. 2025; 20(2):e0319180.

PMID: 39992955 PMC: 11849871. DOI: 10.1371/journal.pone.0319180.

Paving the way to secondary dormancy: mind the DOG's tail.

Cao D Plant Physiol. 2025; 197(2).

PMID: 39774942 PMC: 11809578. DOI: 10.1093/plphys/kiaf008.

The BRAHMA-associated SWI/SNF chromatin remodeling complex controls Arabidopsis seed quality and physiology.

Wrona M, Zinsmeister J, Krzyszton M, Villette C, Zumsteg J, Mercier P Plant Physiol. 2024; 197(1).

PMID: 39661382 PMC: 11668257. DOI: 10.1093/plphys/kiae642.

Dynamics of alternative polyadenylation in single root cells of .

Bi X, Zhu S, Liu F, Wu X Front Plant Sci. 2024; 15:1437118.

PMID: 39372861 PMC: 11449893. DOI: 10.3389/fpls.2024.1437118.

The Arabidopsis U1 snRNP regulates mRNA 3'-end processing.

Mangilet A, Weber J, Schuler S, Adler M, Mjema E, Heilmann P Nat Plants. 2024; 10(10):1514-1531.

PMID: 39313562 PMC: 11489095. DOI: 10.1038/s41477-024-01796-8.

References

Jiang S, Kumar S, Eu Y, Jami S, Stasolla C, Hill R . The Arabidopsis mutant, fy-1, has an ABA-insensitive germination phenotype. J Exp Bot. 2012; 63(7):2693-703. PMC: 3346229. DOI: 10.1093/jxb/err452. View

Zheng J, Chen F, Wang Z, Cao H, Li X, Deng X . A novel role for histone methyltransferase KYP/SUVH4 in the control of Arabidopsis primary seed dormancy. New Phytol. 2011; 193(3):605-616. DOI: 10.1111/j.1469-8137.2011.03969.x. View

Wu X, Zeng Y, Guan J, Ji G, Huang R, Li Q . Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana. BMC Genomics. 2015; 16:511. PMC: 4568572. DOI: 10.1186/s12864-015-1691-1. View

Manzano D, Marquardt S, Jones A, Baurle I, Liu F, Dean C . Altered interactions within FY/AtCPSF complexes required for Arabidopsis FCA-mediated chromatin silencing. Proc Natl Acad Sci U S A. 2009; 106(21):8772-7. PMC: 2689023. DOI: 10.1073/pnas.0903444106. View

Sun Y, Fu Y, Li Y, Xu A . Genome-wide alternative polyadenylation in animals: insights from high-throughput technologies. J Mol Cell Biol. 2012; 4(6):352-61. DOI: 10.1093/jmcb/mjs041. View

Di Giammartino D, Nishida K, Manley J . Mechanisms and consequences of alternative polyadenylation. Mol Cell. 2011; 43(6):853-66. PMC: 3194005. DOI: 10.1016/j.molcel.2011.08.017. View

Wu F, Shen S, Lee L, Lee S, Chan M, Lin C . Tape-Arabidopsis Sandwich - a simpler Arabidopsis protoplast isolation method. Plant Methods. 2009; 5:16. PMC: 2794253. DOI: 10.1186/1746-4811-5-16. View

Graeber K, Linkies A, Steinbrecher T, Mummenhoff K, Tarkowska D, Tureckova V . DELAY OF GERMINATION 1 mediates a conserved coat-dormancy mechanism for the temperature- and gibberellin-dependent control of seed germination. Proc Natl Acad Sci U S A. 2014; 111(34):E3571-80. PMC: 4151772. DOI: 10.1073/pnas.1403851111. View

Castellana N, Payne S, Shen Z, Stanke M, Bafna V, Briggs S . Discovery and revision of Arabidopsis genes by proteogenomics. Proc Natl Acad Sci U S A. 2008; 105(52):21034-8. PMC: 2605632. DOI: 10.1073/pnas.0811066106. View

10.

Shi Y . Alternative polyadenylation: new insights from global analyses. RNA. 2012; 18(12):2105-17. PMC: 3504663. DOI: 10.1261/rna.035899.112. View

11.

Liu F, Marquardt S, Lister C, Swiezewski S, Dean C . Targeted 3' processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing. Science. 2009; 327(5961):94-7. DOI: 10.1126/science.1180278. View

12.

Gruber A, Martin G, Keller W, Zavolan M . Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors. Wiley Interdiscip Rev RNA. 2013; 5(2):183-96. PMC: 4282565. DOI: 10.1002/wrna.1206. View

13.

Grasser M, Kane C, Merkle T, Melzer M, Emmersen J, Grasser K . Transcript elongation factor TFIIS is involved in arabidopsis seed dormancy. J Mol Biol. 2009; 386(3):598-611. DOI: 10.1016/j.jmb.2008.12.066. View

14.

Mandel C, Bai Y, Tong L . Protein factors in pre-mRNA 3'-end processing. Cell Mol Life Sci. 2007; 65(7-8):1099-122. PMC: 2742908. DOI: 10.1007/s00018-007-7474-3. View

15.

Wu X, Liu M, Downie B, Liang C, Ji G, Li Q . Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc Natl Acad Sci U S A. 2011; 108(30):12533-8. PMC: 3145732. DOI: 10.1073/pnas.1019732108. View

16.

Liu Y, Koornneef M, Soppe W . The absence of histone H2B monoubiquitination in the Arabidopsis hub1 (rdo4) mutant reveals a role for chromatin remodeling in seed dormancy. Plant Cell. 2007; 19(2):433-44. PMC: 1867323. DOI: 10.1105/tpc.106.049221. View

17.

Ji G, Li L, Li Q, Wu X, Fu J, Chen G . PASPA: a web server for mRNA poly(A) site predictions in plants and algae. Bioinformatics. 2015; 31(10):1671-3. DOI: 10.1093/bioinformatics/btv004. View

18.

Nakabayashi K, Bartsch M, Xiang Y, Miatton E, Pellengahr S, Yano R . The time required for dormancy release in Arabidopsis is determined by DELAY OF GERMINATION1 protein levels in freshly harvested seeds. Plant Cell. 2012; 24(7):2826-38. PMC: 3426117. DOI: 10.1105/tpc.112.100214. View

19.

Bentsink L, Jowett J, Hanhart C, Koornneef M . Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis. Proc Natl Acad Sci U S A. 2006; 103(45):17042-7. PMC: 1636575. DOI: 10.1073/pnas.0607877103. View

20.

Lin Y, Li Z, Ozsolak F, Kim S, Arango-Argoty G, Liu T . An in-depth map of polyadenylation sites in cancer. Nucleic Acids Res. 2012; 40(17):8460-71. PMC: 3458571. DOI: 10.1093/nar/gks637. View