A Genomic View of Alternative Splicing of Long Non-coding RNAs during Rice Seed Development Reveals Extensive Splicing and lncRNA Gene Families

Frontiers in Plant Science
Edward A KiegleMartin M Kater

Abstract

Alternative splicing (AS) is a key modulator of development in many eukaryotic organisms. In plants, alternative splice forms of non-coding RNAs (ncRNAs) are known to modulate flowering time in Arabidopsis and fertility in rice. Here we demonstrate that alternative splicing of coding and long non-coding RNAs occurs during rice seed development by comparing AS in immature seeds vs. embryo and endosperm of mature seeds. Based on computational predictions of AS events determined from a Bayesian analysis of junction counts of RNA-seq datasets, differential splicing of protein-coding, and non-coding RNAs was determined. In contrast to roots, leaves, flowers, buds, and reproductive meristems, developing seeds had 5.8-57 times more predicted AS. Primers designed to span introns and exons were used to detect AS events predicted by rMATs in cDNA derived from early (milk) seed, embryo, and endosperm. Comparing milk seed vs. mature embryo and endosperm, AS ofMORC7(a gene implicated in epigenetic gene silencing), was markedly different. Long non-coding RNAs (lncRNAs) also underwent AS during the transition from milk seed to mature embryo and endosperm, with a complex gene structure, and were more extensively processed than predicted by cur...Continue Reading

References

May 16, 2000·Plant Molecular Biology·G Lazar, H M Goodman
Aug 31, 2000·Journal of Molecular Biology·C NotredameJ Heringa
Jan 16, 2007·Annual Review of Plant Biology·Anireddy S N Reddy
Aug 9, 2008·Genome Research·Qian-Hao ZhuChris Helliwell
Dec 24, 2008·Nucleic Acids Research·Liang-Jiao XueHong-Wei Xue
Oct 13, 2010·Proceedings of the National Academy of Sciences of the United States of America·Assaf ZemachDaniel Zilberman
Jul 9, 2011·Phytochemical Analysis : PCA·Guifeng WangRentao Song
Feb 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Jihua DingQifa Zhang
May 5, 2012·Science·Guillaume MoissiardSteven E Jacobsen
Apr 25, 2013·Proceedings of the National Academy of Sciences of the United States of America·Jessica A RodriguesDaniel Zilberman
Nov 28, 2013·Nucleic Acids Research·Ana Kozomara, Sam Griffiths-Jones
Dec 21, 2013·Molecular Biology and Evolution·Hypaitia B RauchShailesh K Lal
Mar 19, 2014·The Plant Journal : for Cell and Molecular Biology·Reina KomiyaKen-Ichi Nonomura
Apr 15, 2014·Molecular Cell·Sebastian MarquardtCaroline Dean
Apr 22, 2014·Genomics, Proteomics & Bioinformatics·Collin TokheimYi Xing
May 7, 2014·Proceedings of the National Academy of Sciences of the United States of America·Zhi-Wei WangCaroline Dean
Jul 30, 2014·Developmental Cell·Florian BardouMartin Crespi
Oct 29, 2014·Proceedings of the National Academy of Sciences of the United States of America·Tibor CsorbaCaroline Dean
Dec 7, 2014·Proceedings of the National Academy of Sciences of the United States of America·Shihao ShenYi Xing
Jan 13, 2015·Evolutionary Bioinformatics Online·Feng-Chi ChenHsuan-Yu Lin
Sep 22, 2015·The Plant Journal : for Cell and Molecular Biology·Huan WangNam-Hai Chua
Feb 13, 2016·Methods in Molecular Biology·Craig G SimpsonDorothee Staiger
Mar 5, 2016·The Plant Journal : for Cell and Molecular Biology·Thomas W R HarropMartin M Kater
Sep 25, 2016·The Plant Journal : for Cell and Molecular Biology·Yu LingMagdy M Mahfouz
Dec 14, 2016·Proceedings of the National Academy of Sciences of the United States of America·Kyunghyuk ParkStefan Scholten
May 26, 2017·Frontiers in Plant Science·Wenbin MeiWilliam B Barbazuk
Aug 18, 2017·Advances in Experimental Medicine and Biology·Hsiao-Lin V Wang, Julia A Chekanova

❮ Previous
Next ❯

Citations

Nov 26, 2018·The Plant Journal : for Cell and Molecular Biology·Jun CuiYushi Luan
May 18, 2019·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Dana C PriceDebashish Bhattacharya
May 22, 2019·The Plant Journal : for Cell and Molecular Biology·Barbara Téllez-RobledoJ Carlos Del Pozo
Jan 4, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Yue LuYu Zhao
Sep 16, 2020·Wiley Interdisciplinary Reviews. RNA·Bingbing XuYongfeng Jin
Oct 20, 2020·Frontiers in Plant Science·Zhonghua TuHuogen Li

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE56463
PRJNA306226
GSE50777

Methods Mentioned

BETA
RNA-seq
PCR

Software Mentioned

BLAST
Cufflinks gffread
CuffDiff
PANTHER
DesSeq
rMATS
rFAM
PrimerSeq
DiffSplice
STAR

Related Concepts

Related Feeds

Alternative splicing

Alternative splicing a regulated gene expression process that allows a single genetic sequence to code for multiple proteins. Here is that latest research.