Cloning and Expression Pattern Analysis of Rice <i>OsJMJ718</i> Alternative Polyadenylation Sequences During Reproductive Developmental Stage

Lu Dan, Wang Li, Song Fan, Tao Juhong, Zhang Dabing, Yuan Zheng

doi:10.11983/CBB17114

2018 , Vol. 53 >Issue 5: 594 - 602

DOI: https://doi.org/10.11983/CBB17114

EXPERIMENTAL COMMUNICATIONS

Cloning and Expression Pattern Analysis of Rice OsJMJ718 Alternative Polyadenylation Sequences During Reproductive Developmental Stage

Expand

School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China

† These authors contributed equally to this paper

Received date: 2017-06-07

Accepted date: 2017-10-07

Online published: 2018-11-29

Fold

Abstract

Alternative polyadenylation (APA) is one of the important regulatory pathways of eukaryotic gene expression. By forming different lengths of 3' untranslated regions, APA affects the stability, localization and translation efficiency of mRNA and increases the complexity of transcripts. The expression of the Arabidopsis gene increased polyadenylation of BONSAI methylation 1 (IBM1) is regulated by chromatin regulatory factor enhanced downy mildew 2 (EDM2), which can further affect the CHG methylation level of the Arabidopsis thaliana genome. However, whether such regulatory mechanisms exist in other species is unknown. To answer this question, we selected OsJMJ718, an IBM1 homologous gene of rice, for research. By using bioinformatics analysis and 3'RACE experiments, we found that homologous genes of IBM1 also had APA modification. Among them, the OsJMJ718 gene may have 9 alternative polyadenylation sequences. Further sequence alignment analysis revealed that the 3' terminal sequence of OsJMJ718 in the existing Japonica genome in the NCBI database may be different from that of the other ecotype genome sequences, such as 9522 and Minghui 63. Quantitative real-time PCR showed that the 9 transcripts of OsJMJ718 present diverse dynamic expression patterns in different stages of rice reproductive development. The expression of OsJMJ718-TVX5 was higher than that of other transcripts. In summary, this work provides information for APA sequences of OsJMJ718, and the expression pattern analysis of these transcripts would also help further study of the mechanism of APA and biological function of OsJMJ718.

Key words： rice; OsJMJ718; alternative polyadenylation; 3'RACE; expression pattern

Cite this article

Lu Dan, Wang Li, Song Fan, Tao Juhong, Zhang Dabing, Yuan Zheng . Cloning and Expression Pattern Analysis of Rice OsJMJ718 Alternative Polyadenylation Sequences During Reproductive Developmental Stage[J]. Chinese Bulletin of Botany, 2018 , 53(5) : 594 -602 . DOI: 10.11983/CBB17114

[an error occurred while processing this directive]

References

1	Elkon R, Ugalde AP, Agami R (2013). Alternative cleavage and polyadenylation: extent, regulation and function.Nat Rev Genet 14, 496-506.
2	Inagaki S, Miura-Kamio A, Nakamura Y, Lu FL, Cui X, Cao XF, Kimura H, Saze H, Kakutani T (2010). Autocatalytic differentiation of epigenetic modifications within the Ara- bidopsis genome.EMBO J 29, 3496-3506.
3	Itoh JI, Nonomura KI, Ikeda K, Yamaki S, Inukai Y, Yamagishi H, Kitano H, Nagato Y (2005). Rice plant development: from zygote to spikelet.Plant Cell Physiol 46, 23-47.
4	Lei MG, La HG, Lu K, Wang PC, Miki D, Ren ZZ, Duan CG, Wang XG, Tang K, Zeng L, Yang L, Zhang H, Nie WF, Liu P, Zhou JP, Liu RY, Zhong YL, Liu D, Zhu JK (2014). Arabidopsis EDM2 promotes IBM1 distal poly- adenylation and regulates genome DNA methylation pat- terns. Proc Natl Acad Sci USA 111, 527-532.
5	Licatalosi DD, Darnell RB (2010). RNA processing and its regulation: global insights into biological networks.Nat Rev Genet 11, 75-87.
6	Liu Y, Cui SJ, Wu F, Yan S, Lin XL, Du XQ, Chong K, Schilling S, Theissen G, Meng Z (2013). Functional conservation of MIKC*-type MADS box genes in Ara- bidopsis and rice pollen maturation.Plant Cell 25, 1288-1303.
7	Ma LY, Guo C, Li QQ (2014). Role of alternative poly- adenylation in epigenetic silencing and antisilencing.Proc Natl Acad Sci USA 111, 9-10.
8	Mayr C, Bartel DP (2009). Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates onco- genes in cancer cells.Cell 138, 673-684.
9	Rigal M, Kevei Z, Pélissier T, Mathieu O (2012). DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns.EMBO J 31, 2981-2993.
10	Rosonina E, Manley JL (2010). Alternative polyadenylation blooms.Dev Cell 18, 172-174.
11	Saze H, Shiraishi A, Miura A, Kakutani T (2008). Control of genic DNA methylation by a jmjC domain-containing pro- tein in Arabidopsis thaliana. Science 319, 462-465.
12	Shen YJ, Venu RC, Nobuta K, Wu XH, Notibala V, Demirci C, Meyers BC, Wang GL, Ji GL, Li QQ (2011). Transcrip- tome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing.Genome Res 21, 1478-1486.
13	Shi YS (2012). Alternative polyadenylation: new insights from global analyses.RNA 18, 2105-2117.
14	Simpson GG, Dijkwel PP, Quesada V, Henderson I, Dean C (2003). FY is an RNA 3′ end-processing factor that inter- acts with FCA to control the Arabidopsis floral transition.Cell 113, 777-787.
15	Sun Q, Zhou DX (2008). Rice jmjC domain-containing gene JMJ706 encodes H3K9 demethylase required for floral organ development. Proc Natl Acad Sci USA 105, 13679-13684.
16	Wu XH, Liu M, Downie B, Liang C, Ji GL, Li QQ, Hunt AG (2011). Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation.Proc Natl Acad Sci USA 108, 12533-12538.
17	Xing DH, Li QQ (2011). Alternative polyadenylation and gene expression regulation in plants.Wiley Interdiscip Rev RNA 2, 445-458.
18	Yao P, Potdar AA, Arif A, Ray PS, Mukhopadhyay R, Willard B, Xu YC, Yan J, Saidel GM, Fox PL (2012). Coding region polyadenylation generates a truncated tRNA synthetase that counters translation repression.Cell 149, 88-100.
19	Zhang JX, Addepalli B, Yun KY, Hunt AG, Xu RQ, Rao S, Li QQ, Falcone DL (2008). A polyadenylation factor subunit implicated in regulating oxidative signaling in Ara- bidopsis thaliana. PLoS One 3, e2410.
20	Zhang JW, Chen LL, Xing F, Kudrna DA, Yao W, Copetti D, Mu T, Li WM, Song JM, Xie WB, Lee S, Talag J, Shao L, An Y, Zhang CL, Ouyang YD, Sun S, Jiao WB, Lv F, Du BG, Luo MZ, Maldonado CE, Goicoechea JL, Xiong LZ, Wu CY, Xing YZ, Zhou DX, Yu SB, Zhao Y, Wang GW, Yu Y, Luo YJ, Zhou ZW, Hurtado BEP, Danowitz A, Wing RA, Zhang QF (2016). Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proc Natl Acad Sci USA 113, E5163-E5171.

Options

Outlines