Characterization of unique small RNA populations from rice grain.

PloS One
Sara E HeiselJames K Roberts

Abstract

Small RNAs (approximately 20 to 24 nucleotides) function as naturally occurring molecules critical in developmental pathways in plants and animals. Here we analyze small RNA populations from mature rice grain and seedlings by pyrosequencing. Using a clustering algorithm to locate regions producing small RNAs, we classified hotspots of small RNA generation within the genome. Hotspots here are defined as 1 kb regions within which small RNAs are significantly overproduced relative to the rest of the genome. Hotspots were identified to facilitate characterization of different categories of small RNA regulatory elements. Included in the hotspots, we found known members of 23 miRNA families representing 92 genes, one trans acting siRNA (ta-siRNA) gene, novel siRNA-generating coding genes and phased siRNA generating genes. Interestingly, over 20% of the small RNA population in grain came from a single foldback structure, which generated eight phased 21-nt siRNAs. This is reminiscent of a newly arising miRNA derived from duplication of progenitor genes. Our results provide data identifying distinct populations of small RNAs, including phased small RNAs, in mature grain to facilitate characterization of small regulatory RNA expression i...Continue Reading

References

Oct 23, 1998·Science·M D Gale, K M Devos
Feb 9, 2000·Trends in Biochemical Sciences·I D Small, N Peeters
Jul 18, 2002·The Plant Cell·Cesar LlaveJames C Carrington
Aug 31, 2002·Cell·Matthew W RhoadesDavid P Bartel
Feb 20, 2003·RNA·Victor AmbrosThomas Tuschl
Jan 23, 2004·Proceedings of the National Academy of Sciences of the United States of America·Jerzy JurkaMichael V Jurka
Feb 28, 2004·Science·Simon W-L ChanSteven E Jacobsen
Mar 17, 2004·PLoS Biology·Zhixin XieJames C Carrington
Jun 3, 2004·Plant Physiology·Blake C MeyersLarry D Tindell
Jul 20, 2004·The Plant Cell·Ramanjulu Sunkar, Jian-Kang Zhu
Aug 18, 2004·Proceedings of the National Academy of Sciences of the United States of America·Yukio Kurihara, Yuichiro Watanabe
Apr 1, 2005·Nucleic Acids Research·Shibin QiuTerran Lane
Apr 26, 2005·The Plant Cell·Michael J Axtell, David P Bartel
Apr 27, 2005·Cell·Edwards AllenJames C Carrington
Jul 26, 2005·Plant Physiology·Zhixin XieJames C Carrington
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Aug 4, 2005·Nucleic Acids Research·Ramanjulu SunkarJian-Kang Zhu
Sep 1, 2005·Genes & Development·Manabu YoshikawaR Scott Poethig
Sep 6, 2005·Science·Cheng LuPamela J Green
Dec 31, 2005·Nucleic Acids Research·Sam Griffiths-JonesAnton J Enright
Mar 29, 2006·Trends in Genetics : TIG·Peter Brodersen, Olivier Voinnet
May 4, 2006·Annual Review of Plant Biology·Matthew W Jones-RhoadesBonnie Bartel
Jun 1, 2006·Nature Genetics·Allison C Mallory, Hervé Vaucheret
Jun 27, 2006·Computational Biology and Chemistry·J GorodkinM Fredholm
Sep 8, 2006·Methods in Molecular Biology·Sam Griffiths-Jones
Dec 16, 2006·Nucleic Acids Research·Cameron JohnsonVenkatesan Sundaresan
Dec 22, 2006·Genes & Development·Ramya RajagopalanDavid P Bartel
Feb 15, 2007·PLoS Biology·Kristin D KasschauJames C Carrington
Mar 14, 2007·Nature Biotechnology·Kan NobutaBlake C Meyers
Nov 16, 2007·Genes & Development·Surekha Katiyar-AgarwalHailing Jin

❮ Previous
Next ❯

Citations

Jun 3, 2014·BMC Plant Biology·Fenglong SunYingyin Yao
Nov 8, 2014·Journal of Experimental Botany·Zhiqiang XianZhengguo Li
Jul 9, 2009·Genome Research·Cameron JohnsonLewis H Bowman
Aug 4, 2009·PLoS Computational Biology·Xingyi GuoDeyou Zheng
Nov 12, 2009·The Plant Cell·Liang WuYijun Qi
Apr 22, 2010·The Plant Cell·Noah FahlgrenJames C Carrington
May 1, 2010·BMC Evolutionary Biology·Yu WangLongjiang Fan
Nov 12, 2013·Nature Biotechnology·Brent DickinsonWilliam S Marshall
Dec 14, 2011·Plant Molecular Biology·Ying-Hsuan SunRonald R Sederoff
Feb 6, 2015·International Journal of Molecular Sciences·Xiaoshuang LiuJin Wang
Jun 10, 2014·Journal of Cellular Physiology·Baohong Zhang, Qinglian Wang
Apr 20, 2010·Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association·Wayne ParrottMarci Levine
Apr 3, 2010·Seminars in Cell & Developmental Biology·Edwards Allen, Miya D Howell
Dec 11, 2008·Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association·Sergey I IvashutaJames K Roberts
Mar 6, 2010·The Plant Journal : for Cell and Molecular Biology·Yong-Fang LiRamanjulu Sunkar
Mar 27, 2015·The Plant Journal : for Cell and Molecular Biology·Alberto CarbonellJames C Carrington
Jun 5, 2013·Plant Signaling & Behavior·Yang LiuLongjiang Fan
Jul 11, 2019·Plant & Cell Physiology·Luis Cervera-SecoGustavo Gomez
Jul 16, 2019·Critical Reviews in Biotechnology·P AziziM N Yusuf
Jul 28, 2017·The Plant Journal : for Cell and Molecular Biology·Yuanlong LiuQiang Xu
Mar 8, 2016·Journal of Biosciences·Archana SinghSunil Kumar Mukherjee

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR

Software Mentioned

Tandem Repeats Finder
Foldback
BLAST
RepeatMasker
Perl
scripts

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.