Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops

Franke, Karl R.; Schmidt, Skye A.; Park, Sunhee; Jeong, Dong-Hoon; Accerbi, Monica; Green, Pamela J.

doi:10.1186/s12864-018-4911-7

Title: Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops

Abstract

Since the proposal of Brachypodium distachyon as a model for the grasses, over 500 Bdi-miRNAs have been annotated in miRBase making Brachypodium second in number only to rice. Other monocots, such as switchgrass, are completely absent from the miRBase database. While a significant number of miRNAs have been identified which are highly conserved across plants, little research has been done with respect to the conservation of miRNA targets. Plant responses to abiotic stresses are regulated by diverse pathways many of which involve miRNAs; however, it can be difficult to identify miRNA guided gene regulation when the miRNA is not the primary regulator of the target mRNA.

Authors:

Franke, Karl R.; Schmidt, Skye A.; Park, Sunhee; Jeong, Dong-Hoon; Accerbi, Monica;

Publication Date:: Fri Jul 20 00:00:00 EDT 2018

Research Org.:: Univ. of Delaware, Newark, DE (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:: 1618562

Alternate Identifier(s):: OSTI ID: 1504900

Grant/Contract Number:: FG02-07ER64450

Resource Type:: Published Article

Journal Name:: BMC Genomics

Additional Journal Information:: Journal Name: BMC Genomics Journal Volume: 19 Journal Issue: 1; Journal ID: ISSN 1471-2164

Publisher:: Springer Science + Business Media

Country of Publication:: United Kingdom

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; 09 BIOMASS FUELS; PARE; Degradome; SmRNA; miRNA; Abiotic stress; Brachypodium; Sorghum; Switchgrass; Bioenergy

Citation Formats


                    Franke, Karl R., Schmidt, Skye A., Park, Sunhee, Jeong, Dong-Hoon, Accerbi, Monica, and Green, Pamela J. Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops.  United Kingdom: N. p., 2018. 
Web.  doi:10.1186/s12864-018-4911-7.

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                    Franke, Karl R., Schmidt, Skye A., Park, Sunhee, Jeong, Dong-Hoon, Accerbi, Monica, & Green, Pamela J. Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops.  United Kingdom.  https://doi.org/10.1186/s12864-018-4911-7

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                    Franke, Karl R., Schmidt, Skye A., Park, Sunhee, Jeong, Dong-Hoon, Accerbi, Monica, and Green, Pamela J. Fri .  
"Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops".  United Kingdom.  https://doi.org/10.1186/s12864-018-4911-7.

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@article{osti_1618562,

  title        = {Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops},

  author       = {Franke, Karl R. and Schmidt, Skye A. and Park, Sunhee and Jeong, Dong-Hoon and Accerbi, Monica and Green, Pamela J.},

  abstractNote = {Since the proposal of Brachypodium distachyon as a model for the grasses, over 500 Bdi-miRNAs have been annotated in miRBase making Brachypodium second in number only to rice. Other monocots, such as switchgrass, are completely absent from the miRBase database. While a significant number of miRNAs have been identified which are highly conserved across plants, little research has been done with respect to the conservation of miRNA targets. Plant responses to abiotic stresses are regulated by diverse pathways many of which involve miRNAs; however, it can be difficult to identify miRNA guided gene regulation when the miRNA is not the primary regulator of the target mRNA.},

  doi          = {10.1186/s12864-018-4911-7},

  journal      = {BMC Genomics},

  number       = 1,

  volume       = 19,

  place        = {United Kingdom},

  year         = {Fri Jul 20 00:00:00 EDT 2018},

  month        = {Fri Jul 20 00:00:00 EDT 2018}

}

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Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects
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Title: Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops

Abstract

Citation Formats

MicroRNAs: Target Recognition and Regulatory Functions journal, January 2009

Origin, Biogenesis, and Activity of Plant MicroRNAs journal, February 2009

Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response journal, January 2009

Overexpression of a miR393-Resistant Form of Transport Inhibitor Response Protein 1 (mTIR1) Enhances Salt Tolerance by Increased Osmoregulation and Na+ Exclusion in Arabidopsis thaliana journal, October 2014

MicroRNAs AND THEIR REGULATORY ROLES IN PLANTS journal, June 2006

Modulation of floral development by a gibberellin-regulatedmicroRNA journal, June 2004

MicroRNA-mediated signaling involved in plant root development journal, March 2010

STAR: ultrafast universal RNA-seq aligner journal, October 2012

Brachypodium as a Model for the Grasses: Today and the Future journal, July 2011

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome journal, January 2009

Brachypodium distachyon . A New Model System for Functional Genomics in Grasses journal, December 2001

Characterization of drought- and heat-responsive microRNAs in switchgrass journal, January 2016

A plant microRNA regulates the adaptation of roots to drought stress journal, May 2012

Identification of microRNAs and their targets in switchgrass, a model biofuel plant species journal, July 2010

Massive Analysis of Rice Small RNAs: Mechanistic Implications of Regulated MicroRNAs and Variants for Differential Target RNA Cleavage journal, December 2011

miRNA Target Prediction in Plants book, January 2009

Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing journal, July 2011

Identification of drought-induced microRNAs in rice journal, March 2007

GmNFYA3, a target gene of miR169, is a positive regulator of plant tolerance to drought stress journal, March 2013

Novel and Stress-Regulated MicroRNAs and Other Small RNAs from Arabidopsis journal, July 2004

Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon journal, January 2013

Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum) journal, May 2010

The Arabidopsis NFYA5 Transcription Factor Is Regulated Transcriptionally and Posttranscriptionally to Promote Drought Resistance journal, August 2008

Family-Wide Survey of miR169s and NF-YAs and Their Expression Profiles Response to Abiotic Stress in Maize Roots journal, March 2014

Dehydration Stress-Responsive miRNA in Brachypodium distachyon : Evident by Genome-Wide Screening of microRNAs Expression journal, November 2011

Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor journal, January 2009

miR394 and its target gene LCR are involved in cold stress response in Arabidopsis journal, March 2016

Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends journal, June 2008

Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data journal, January 2018

Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana journal, February 2010

The developmental role of microRNA in plants journal, February 2005

Functional and Transcriptome Analysis Reveals an Acclimatization Strategy for Abiotic Stress Tolerance Mediated by Arabidopsis NF-YA Family Members journal, October 2012

psRNATarget: a plant small RNA target analysis server journal, May 2011

The role of rice microRNAs in abiotic stress responses journal, August 2013

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data journal, November 2009

MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5′ region journal, July 2004

Climate Trends and Global Crop Production Since 1980 journal, May 2011

Methods for validation of miRNA sequence variants and the cleavage of their targets journal, October 2012

Basic local alignment search tool journal, October 1990

Plant nuclear factor Y (NF-Y) B subunits confer drought tolerance and lead to improved corn yields on water-limited acres journal, October 2007

High-throughput deep sequencing shows that microRNAs play important roles in switchgrass responses to drought and salinity stress journal, November 2013

Addressing the Role of microRNAs in Reprogramming Leaf Growth during Drought Stress in Brachypodium distachyon journal, March 2013

High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes journal, February 2007

Conserved and novel miRNAs in the legume Phaseolus vulgaris in response to stress journal, April 2009

Role of MicroRNAs in Plant and Animal Development journal, July 2003

A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon journal, January 2013

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome journal, August 2011

The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development journal, May 2004

Stress-induced early flowering is mediated by miR169 in Arabidopsis thaliana journal, December 2013

miRBase: annotating high confidence microRNAs using deep sequencing data journal, November 2013

Identification of SMG6 cleavage sites and a preferred RNA cleavage motif by global analysis of endogenous NMD targets in human cells journal, November 2014

Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects journal, March 2019

MicroRNAs: Target Recognition and Regulatory Functions
journal, January 2009

Origin, Biogenesis, and Activity of Plant MicroRNAs
journal, February 2009

Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response
journal, January 2009

Overexpression of a miR393-Resistant Form of Transport Inhibitor Response Protein 1 (mTIR1) Enhances Salt Tolerance by Increased Osmoregulation and Na+ Exclusion in Arabidopsis thaliana
journal, October 2014

MicroRNAs AND THEIR REGULATORY ROLES IN PLANTS
journal, June 2006

Modulation of floral development by a gibberellin-regulatedmicroRNA
journal, June 2004

MicroRNA-mediated signaling involved in plant root development
journal, March 2010

STAR: ultrafast universal RNA-seq aligner
journal, October 2012

Brachypodium as a Model for the Grasses: Today and the Future
journal, July 2011

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
journal, January 2009

Brachypodium distachyon . A New Model System for Functional Genomics in Grasses
journal, December 2001

Characterization of drought- and heat-responsive microRNAs in switchgrass
journal, January 2016

A plant microRNA regulates the adaptation of roots to drought stress
journal, May 2012

Identification of microRNAs and their targets in switchgrass, a model biofuel plant species
journal, July 2010

Massive Analysis of Rice Small RNAs: Mechanistic Implications of Regulated MicroRNAs and Variants for Differential Target RNA Cleavage
journal, December 2011

miRNA Target Prediction in Plants
book, January 2009

Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing
journal, July 2011

Identification of drought-induced microRNAs in rice
journal, March 2007

GmNFYA3, a target gene of miR169, is a positive regulator of plant tolerance to drought stress
journal, March 2013

Novel and Stress-Regulated MicroRNAs and Other Small RNAs from Arabidopsis
journal, July 2004

Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon
journal, January 2013

Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum)
journal, May 2010

The Arabidopsis NFYA5 Transcription Factor Is Regulated Transcriptionally and Posttranscriptionally to Promote Drought Resistance
journal, August 2008

Family-Wide Survey of miR169s and NF-YAs and Their Expression Profiles Response to Abiotic Stress in Maize Roots
journal, March 2014

Dehydration Stress-Responsive miRNA in Brachypodium distachyon : Evident by Genome-Wide Screening of microRNAs Expression
journal, November 2011

Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor
journal, January 2009

miR394 and its target gene LCR are involved in cold stress response in Arabidopsis
journal, March 2016

Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends
journal, June 2008

Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data
journal, January 2018

Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana
journal, February 2010

The developmental role of microRNA in plants
journal, February 2005

Functional and Transcriptome Analysis Reveals an Acclimatization Strategy for Abiotic Stress Tolerance Mediated by Arabidopsis NF-YA Family Members
journal, October 2012

psRNATarget: a plant small RNA target analysis server
journal, May 2011

The role of rice microRNAs in abiotic stress responses
journal, August 2013

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
journal, November 2009

MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5′ region
journal, July 2004

Climate Trends and Global Crop Production Since 1980
journal, May 2011

Methods for validation of miRNA sequence variants and the cleavage of their targets
journal, October 2012

Basic local alignment search tool
journal, October 1990

Plant nuclear factor Y (NF-Y) B subunits confer drought tolerance and lead to improved corn yields on water-limited acres
journal, October 2007

High-throughput deep sequencing shows that microRNAs play important roles in switchgrass responses to drought and salinity stress
journal, November 2013

Addressing the Role of microRNAs in Reprogramming Leaf Growth during Drought Stress in Brachypodium distachyon
journal, March 2013

High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes
journal, February 2007

Conserved and novel miRNAs in the legume Phaseolus vulgaris in response to stress
journal, April 2009

Role of MicroRNAs in Plant and Animal Development
journal, July 2003

A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon
journal, January 2013

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
journal, August 2011

The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development
journal, May 2004

Stress-induced early flowering is mediated by miR169 in Arabidopsis thaliana
journal, December 2013

miRBase: annotating high confidence microRNAs using deep sequencing data
journal, November 2013

Identification of SMG6 cleavage sites and a preferred RNA cleavage motif by global analysis of endogenous NMD targets in human cells
journal, November 2014

Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects
journal, March 2019