Genome organization and characteristics of soybean microRNAs.

BMC Genomics
Marie TurnerSenthil Subramanian

Abstract

microRNAs (miRNAs) are key regulators of gene expression and play important roles in many aspects of plant biology. The role(s) of miRNAs in nitrogen-fixing root nodules of leguminous plants such as soybean is not well understood. We examined a library of small RNAs from Bradyrhizobium japonicum-inoculated soybean roots and identified novel miRNAs. In order to enhance our understanding of miRNA evolution, diversification and function, we classified all known soybean miRNAs based on their phylogenetic conservation (conserved, legume- and soybean-specific miRNAs) and examined their genome organization, family characteristics and target diversity. We predicted targets of these miRNAs and experimentally validated several of them. We also examined organ-specific expression of selected miRNAs and their targets. We identified 120 previously unknown miRNA genes from soybean including 5 novel miRNA families. In the soybean genome, genes encoding miRNAs are primarily intergenic and a small percentage were intragenic or less than 1000 bp from a protein-coding gene, suggesting potential co-regulation between the miRNA and its parent gene. Difference in number and orientation of tandemly duplicated miRNA genes between orthologous genomic lo...Continue Reading

References

Apr 12, 2000·Proceedings of the National Academy of Sciences of the United States of America·D GrantR C Shoemaker
Jul 9, 2002·Genes & Development·Brenda J ReinhartDavid P Bartel
Aug 31, 2002·Cell·Matthew W RhoadesDavid P Bartel
Jun 18, 2004·Molecular Cell·Matthew W Jones-Rhoades, David P Bartel
Jul 20, 2004·The Plant Cell·Ramanjulu Sunkar, Jian-Kang Zhu
Jul 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Koichiro TamuraSudhir Kumar
Feb 12, 2005·Science·Bin YuXuemei Chen
Apr 6, 2005·Developmental Cell·Rebecca SchwabDetlef Weigel
Apr 27, 2005·Cell·Edwards AllenJames C Carrington
Aug 25, 2005·Cell Research·Sreelatha GuddetiLong Mao
Sep 8, 2005·FEBS Letters·Xuemei Chen
Apr 21, 2006·The Plant Journal : for Cell and Molecular Biology·Baohong ZhangTodd A Anderson
May 4, 2006·Annual Review of Plant Biology·Matthew W Jones-RhoadesBonnie Bartel
Oct 5, 2006·The Plant Journal : for Cell and Molecular Biology·Senthil SubramanianOliver Yu
Nov 4, 2006·Cell·Michael J AxtellDavid P Bartel
Dec 22, 2006·Genes & Development·Ramya RajagopalanDavid P Bartel
May 10, 2007·Molecular Biology and Evolution·Koichiro TamuraSudhir Kumar
Oct 6, 2007·Proceedings of the National Academy of Sciences of the United States of America·Robert S AllenAnthony A Millar
Oct 13, 2007·Plant Methods·Erika Varkonyi-GasicRoger P Hellens
Feb 27, 2008·The Plant Journal : for Cell and Molecular Biology·Adnane BoualemFlorian Frugier
Apr 12, 2008·BMC Genomics·Senthil SubramanianOliver Yu
Jun 17, 2008·Trends in Plant Science·John W S BrownManuel Echeverria
Jul 18, 2008·Proceedings of the National Academy of Sciences of the United States of America·Jian-Kang Zhu
Sep 26, 2008·Planta·Baohong ZhangEdmund J Stellwag
Dec 17, 2008·The Plant Cell·Blake C MeyersJian-Kang Zhu
Dec 17, 2008·Biochemical and Biophysical Research Communications·Yanwei WangXia Li
Apr 9, 2009·Plant Molecular Biology·Catalina Arenas-HuerteroJosé Luis Reyes
Jun 23, 2009·Genome Research·Martin KrzywinskiMarco A Marra
Jul 7, 2009·Annual Review of Cell and Developmental Biology·Xuemei Chen
Jul 17, 2009·Plant Physiology·Navdeep GillScott A Jackson
Oct 1, 2009·Plant Physiology·Stacey A SimonD Janine Sherrier
Oct 8, 2009·Nucleic Acids Research·Zhenhai ZhangZhen Su
Nov 12, 2009·The Plant Cell·Liang WuYijun Qi
Nov 26, 2009·PLoS Genetics·Lifang ZhangDoreen Ware
Jan 16, 2010·RNA·Alex Mas MonteysBeverly L Davidson

❮ Previous
Next ❯

Citations

Apr 29, 2014·Annals of Botany·Jamie A O'RourkeCarroll P Vance
Sep 26, 2014·BMC Evolutionary Biology·Pedro Gabriel NachtigallDanillo Pinhal
Aug 20, 2015·The Plant Journal : for Cell and Molecular Biology·Narasimha Rao NizampatnamSenthil Subramanian
Jun 20, 2014·The Plant Journal : for Cell and Molecular Biology·James WongWenbo Ma
Sep 6, 2015·Gene·F R KulcheskiR Margis
Apr 23, 2015·Plant Science : an International Journal of Experimental Plant Biology·Sangeeta SrivastavaRamanjulu Sunkar
Jan 8, 2015·Frontiers in Plant Science·Chu-Yu YeLongjiang Fan
Jun 9, 2016·International Journal of Molecular Sciences·Damien FormeyGeorgina Hernández
Sep 24, 2016·Journal of Experimental Botany·Man-Wah LiHon-Ming Lam
Aug 25, 2017·Genome Biology·Chenjiang YouXuemei Chen
Mar 13, 2020·Journal of Experimental Botany·Nhung T HoangGary Stacey
Aug 28, 2018·Frontiers in Plant Science·José Á Martín-RodríguezGeorgina Hernández
Dec 9, 2016·Journal of Experimental Botany·Jeremy D MurrayAnthony J Miller
Dec 22, 2020·Plant, Cell & Environment·Manish TiwariSabhyata Bhatia
May 1, 2021·Frontiers in Molecular Biosciences·Sarbottam PiyaTarek Hewezi

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR

Software Mentioned

perlscript
circos
miRbase
CLUSTALW
MEGA4
BLAST

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.