Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis

BMC Molecular Biology
Hailing JinJian-Kang Zhu

Abstract

In spite of large intergenic spaces in plant and animal genomes, 7% to 30% of genes in the genomes encode overlapping cis-natural antisense transcripts (cis-NATs). The widespread occurrence of cis-NATs suggests an evolutionary advantage for this type of genomic arrangement. Experimental evidence for the regulation of two cis-NAT gene pairs by natural antisense transcripts-generated small interfering RNAs (nat-siRNAs) via the RNA interference (RNAi) pathway has been reported in Arabidopsis. However, the extent of siRNA-mediated regulation of cis-NAT genes is still unclear in any genome. The hallmarks of RNAi regulation of NATs are 1) inverse regulation of two genes in a cis-NAT pair by environmental and developmental cues and 2) generation of siRNAs by cis-NAT genes. We examined Arabidopsis transcript profiling data from public microarray databases to identify cis-NAT pairs whose sense and antisense transcripts show opposite expression changes. A subset of the cis-NAT genes displayed negatively correlated expression profiles as well as inverse differential expression changes under at least one of the examined developmental stages or treatment conditions. By searching the Arabidopsis Small RNA Project (ASRP) and Massively Paralle...Continue Reading

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Apr 7, 1999·Nature Genetics·J T LeeD Warshawsky
Jul 13, 2000·Journal of Molecular Biology·O EmanuelssonG von Heijne
Nov 20, 2001·Molecular and Cellular Biology·S LuikenhuisR Jaenisch
Feb 15, 2002·Nature·Frank SleutelsDenise P Barlow
Jun 22, 2002·Proceedings of the National Academy of Sciences of the United States of America·Elizabeth M Prescott, Nick J Proudfoot
Jul 18, 2002·The Plant Cell·Cesar LlaveJames C Carrington
Dec 6, 2002·Nature·Y OkazakiUNKNOWN RIKEN Genome Exploration Research Group Phase I & II Team
Dec 25, 2002·Human Molecular Genetics·Shinwa Shibata, Jeannie T Lee
Jan 23, 2003·Genome Biology·Sima MisraSuzanna E Lewis
Mar 18, 2003·Nature Biotechnology·Rodrigo YelinGalit Rotman
Jun 24, 2003·Genome Research·Hidenori KiyosawaUNKNOWN GSL Members
Nov 1, 2003·Science·Kayoko YamadaJoseph R Ecker
Jan 8, 2004·Genome Biology·Naoki OsatoYoshihide Hayashizaki
Apr 23, 2004·Trends in Biochemical Sciences·Giovanni LavorgnaGiorgio Casari
Jun 3, 2004·Plant Physiology·Tanya Z BerardiniSeung Y Rhee
Sep 2, 2004·Molecular and Cellular Biology·Noopur ThakurChandrasekhar Kanduri
Sep 3, 2004·Genome Research·Dennis D Y KimAbram Gabriel
Sep 10, 2004·Nucleic Acids Research·Jianjun ChenJanet D Rowley
Oct 2, 2004·Current Biology : CB·Shinwa Shibata, Jeannie T Lee
Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang
Dec 21, 2004·Nucleic Acids Research·Adam M GustafsonKristin D Kasschau
Feb 1, 2005·Computational Biology and Chemistry·Izabela MakalowskaWojciech Makalowski
Feb 11, 2005·Nature Reviews. Genetics·Olivier Voinnet
Jun 14, 2005·Trends in Biochemical Sciences·David Baulcombe
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Sep 6, 2005·Science·S KatayamaUNKNOWN FANTOM Consortium
Sep 6, 2005·Science·Cheng LuPamela J Green
Oct 19, 2005·Physiological Genomics·Andreas Werner, Ariane Berdal
Aug 9, 2006·Trends in Plant Science·Franck Vazquez
Oct 17, 2006·Genome Biology·Huan WangXiu-Jie Wang
Oct 31, 2006·Proceedings of the National Academy of Sciences of the United States of America·Surekha Katiyar-AgarwalHailing Jin
Dec 22, 2006·Genes & Development·Ramya RajagopalanDavid P Bartel
Feb 15, 2007·PLoS Biology·Kristin D KasschauJames C Carrington

❮ Previous
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Citations

Oct 8, 2008·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Paulo P Amaral, John S Mattick
Oct 6, 2009·Functional & Integrative Genomics·Sadegh Azimzadeh Jamalkandi, Ali Masoudi-Nejad
Apr 22, 2009·Science in China. Series C, Life Sciences·Viswanathan Chinnusamy, Jian-Kang Zhu
Jul 30, 2009·Nature Reviews. Molecular Cell Biology·Mohammad Ali Faghihi, Claes Wahlestedt
May 27, 2008·Nature Structural & Molecular Biology·Katsutomo OkamuraEric C Lai
Dec 17, 2008·Proceedings of the National Academy of Sciences of the United States of America·Michael A HeldNicholas C Carpita
Jul 31, 2009·Briefings in Functional Genomics & Proteomics·Frank SchwachTamas Dalmay
Dec 21, 2011·Briefings in Functional Genomics·David J Studholme
Dec 22, 2010·Journal of Experimental Botany·G Le TrionnaireD Twell
Nov 8, 2011·Nucleic Acids Research·Dijun ChenMing Chen
Jun 3, 2010·Genes & Development·Gaël Le Trionnaire, David Twell
Sep 18, 2008·BMC Molecular Biology·Dejun LiLihuang Zhu
Oct 4, 2011·Plant Methods·Nanette CoetzerDave K Berger
Aug 11, 2010·Genome Biology·Weixiong ZhangHailing Jin
Aug 2, 2008·Genes & Genetic Systems·Tomoaki FujiokaMasao Watanabe
Feb 24, 2010·Yi chuan = Hereditas·Zhao-Hui Xie
Nov 5, 2013·Biochimica Et Biophysica Acta·Angel Emilio Martínez de AlbaHervé Vaucheret
Feb 28, 2015·Genetika·R O Cherezov, O B Simonova
Jan 22, 2013·Annual Review of Plant Biology·Michael J Axtell
Oct 27, 2015·International Journal of Molecular Sciences·Yee-Shan KuHon-Ming Lam
Jan 31, 2015·Science China. Life Sciences·Hui HeBingLian Zheng
Jun 1, 2012·Journal of Plant Physiology·Katarzyna KruszkaFranck Vazquez
Nov 23, 2011·Trends in Plant Science·Eun-Deok Kim, Sibum Sung
Jul 12, 2011·Trends in Genetics : TIG·Alex C Tuck, David Tollervey
Mar 30, 2011·Current Opinion in Plant Biology·Damon Lisch, Jeffrey L Bennetzen
Oct 30, 2010·Computational Biology and Chemistry·Ming ChenDijun Chen
May 5, 2010·Biochemical and Biophysical Research Communications·Wen-Yu SuJing-Yuan Fang
Aug 15, 2009·Biochemical and Biophysical Research Communications·Supratim Choudhuri
Jun 3, 2008·Trends in Plant Science·Craig S PikaardAndrzej T Wierzbicki
Jun 20, 2008·Trends in Plant Science·Jay B Hollick
Mar 24, 2009·Birth Defects Research. Part C, Embryo Today : Reviews·Tin-Lap LeeWai-Yee Chan

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Datasets Mentioned

BETA
GSM118374
GSM118375
GSE5228

Methods Mentioned

BETA
chip

Software Mentioned

BLASTCUST
Linear Models for Microarray Data ( Limma )
R scripts
Affymetrix
MPSS
R environment
GOstats
R
BioConductor R scripts
affy package

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