Genome-wide identification of histone methylation (H3K9me2) and acetylation (H4K12ac) marks in two ecotypes of switchgrass (Panicum virgatum L.)
Abstract
Background: Histone modifications play a significant role in the regulation of transcription and various biological processes, such as development and regeneration. Though a few genomic (including DNA methylation patterns) and transcriptomic studies are currently available in switchgrass, the genome-wide distribution of histone modifications has not yet been studied to help elucidate gene regulation and its application to switchgrass improvement. Results: This study provides a comprehensive epigenomic analyses of two contrasting switchgrass ecotypes, lowland (AP13) and upland (VS16), by employing chromatin immunoprecipitation sequencing (ChIP-Seq) with two histone marks (suppressive- H3K9me2 and active- H4K12ac). In this study, most of the histone binding was in non-genic regions, and the highest enrichment was seen between 0 and 2 kb regions from the transcriptional start site (TSS). Considering the economic importance and potential of switchgrass as a bioenergy crop, we focused on genes, transcription factors (TFs), and pathways that were associated with C4-photosynthesis, biomass, biofuel production, biotic stresses, and abiotic stresses. Using quantitative real-time PCR (qPCR) the relative expression of five genes selected from the phenylpropanoid-monolignol pathway showed preferential binding of acetylation marks in AP13 rather than in VS16. Conclusions: The genome-wide histone modifications reported here can be utilized in understanding the regulation of genesmore »
- Authors:
-
- Delaware State Univ., Dover, DE (United States). College of Agriculture and Related Sciences. Molecular Genetics and Epigenomics Lab.
- Alabama A&M Univ., Normal, AL (United States). Life and Natural Sciences. Molecular Biology and Bioinformatics Lab.
- (. Kal) [Delaware State Univ., Dover, DE (United States). College of Agriculture and Related Sciences. Molecular Genetics and Epigenomics Lab.; Delaware State Univ., Dover, DE (United States). Center for Integrated Biological and Environmental Research
- Noble Research Ins., Ardmore, OK (United States)
- Purdue Univ., West Lafayette, IN (United States). Bioinformatics Core
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1626825
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Genomics
- Additional Journal Information:
- Journal Volume: 20; Journal Issue: 1; Journal ID: ISSN 1471-2164
- Publisher:
- Springer
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Biotechnology & Applied Microbiology; Genetics & Heredity; Switchgrass; Epigenome; ChIP-Seq; Histone modifications; Differential binding; Phenylpropanoid pathway; And monolignols
Citation Formats
Ayyappan, Vasudevan, Sripathi, Venkateswara R., Kalavacharla, Venu, Saha, Malay C., Thimmapuram, Jyothi, Bhide, Ketaki P., and Fiedler, Elizabeth. Genome-wide identification of histone methylation (H3K9me2) and acetylation (H4K12ac) marks in two ecotypes of switchgrass (Panicum virgatum L.). United States: N. p., 2019.
Web. doi:10.1186/s12864-019-6038-x.
Ayyappan, Vasudevan, Sripathi, Venkateswara R., Kalavacharla, Venu, Saha, Malay C., Thimmapuram, Jyothi, Bhide, Ketaki P., & Fiedler, Elizabeth. Genome-wide identification of histone methylation (H3K9me2) and acetylation (H4K12ac) marks in two ecotypes of switchgrass (Panicum virgatum L.). United States. https://doi.org/10.1186/s12864-019-6038-x
Ayyappan, Vasudevan, Sripathi, Venkateswara R., Kalavacharla, Venu, Saha, Malay C., Thimmapuram, Jyothi, Bhide, Ketaki P., and Fiedler, Elizabeth. Thu .
"Genome-wide identification of histone methylation (H3K9me2) and acetylation (H4K12ac) marks in two ecotypes of switchgrass (Panicum virgatum L.)". United States. https://doi.org/10.1186/s12864-019-6038-x. https://www.osti.gov/servlets/purl/1626825.
@article{osti_1626825,
title = {Genome-wide identification of histone methylation (H3K9me2) and acetylation (H4K12ac) marks in two ecotypes of switchgrass (Panicum virgatum L.)},
author = {Ayyappan, Vasudevan and Sripathi, Venkateswara R. and Kalavacharla, Venu and Saha, Malay C. and Thimmapuram, Jyothi and Bhide, Ketaki P. and Fiedler, Elizabeth},
abstractNote = {Background: Histone modifications play a significant role in the regulation of transcription and various biological processes, such as development and regeneration. Though a few genomic (including DNA methylation patterns) and transcriptomic studies are currently available in switchgrass, the genome-wide distribution of histone modifications has not yet been studied to help elucidate gene regulation and its application to switchgrass improvement. Results: This study provides a comprehensive epigenomic analyses of two contrasting switchgrass ecotypes, lowland (AP13) and upland (VS16), by employing chromatin immunoprecipitation sequencing (ChIP-Seq) with two histone marks (suppressive- H3K9me2 and active- H4K12ac). In this study, most of the histone binding was in non-genic regions, and the highest enrichment was seen between 0 and 2 kb regions from the transcriptional start site (TSS). Considering the economic importance and potential of switchgrass as a bioenergy crop, we focused on genes, transcription factors (TFs), and pathways that were associated with C4-photosynthesis, biomass, biofuel production, biotic stresses, and abiotic stresses. Using quantitative real-time PCR (qPCR) the relative expression of five genes selected from the phenylpropanoid-monolignol pathway showed preferential binding of acetylation marks in AP13 rather than in VS16. Conclusions: The genome-wide histone modifications reported here can be utilized in understanding the regulation of genes important in the phenylpropanoid–monolignol biosynthesis pathway, which in turn, may help understand the recalcitrance associated with conversion of biomass to biofuel, a major roadblock in utilizing lignocellulosic feedstocks.},
doi = {10.1186/s12864-019-6038-x},
journal = {BMC Genomics},
number = 1,
volume = 20,
place = {United States},
year = {Thu Aug 22 00:00:00 EDT 2019},
month = {Thu Aug 22 00:00:00 EDT 2019}
}
Works referenced in this record:
Transcriptome Analysis of Nodes and Buds from High and Low Tillering Switchgrass Inbred Lines
journal, December 2013
- Wang, Yixing; Zeng, Xin; Peal, Lila
- PLoS ONE, Vol. 8, Issue 12
Epigenetic Control of Cell Cycle-Dependent Histone Gene Expression Is a Principal Component of the Abbreviated Pluripotent Cell Cycle
journal, July 2012
- Medina, R.; Ghule, P. N.; Cruzat, F.
- Molecular and Cellular Biology, Vol. 32, Issue 19
Transcriptome analysis of heat stress response in switchgrass (Panicum virgatum L.)
journal, January 2013
- Li, Yong-Fang; Wang, Yixing; Tang, Yuhong
- BMC Plant Biology, Vol. 13, Issue 1
PAVIS: a tool for Peak Annotation and Visualization
journal, September 2013
- Huang, Weichun; Loganantharaj, Rasiah; Schroeder, Bryce
- Bioinformatics, Vol. 29, Issue 23
siRNAs regulate DNA methylation and interfere with gene and lncRNA expression in the heterozygous polyploid switchgrass
journal, July 2018
- Yan, Haidong; Bombarely, Aureliano; Xu, Bin
- Biotechnology for Biofuels, Vol. 11, Issue 1
Chloroplast DNA and Nuclear DNA Content Variations among Cultivars of Switchgrass, Panicum virgatum L.
journal, January 1996
- Hultquist, Sherry J.; Vogel, K. P.; Lee, D. J.
- Crop Science, Vol. 36, Issue 4
An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum
journal, May 2015
- Veluchamy, Alaguraj; Rastogi, Achal; Lin, Xin
- Genome Biology, Vol. 16, Issue 1
Coordinated histone modifications are associated with gene expression variation within and between species
journal, February 2011
- Ha, M.; Ng, D. W. -K.; Li, W. -H.
- Genome Research, Vol. 21, Issue 4
Changes in Histone Methylation and Acetylation during Microspore Reprogramming to Embryogenesis Occur Concomitantly with BnHKMT and BnHAT Expression and Are Associated with Cell Totipotency, Proliferation, and Differentiation in Brassica napus
journal, January 2014
- Rodríguez-Sanz, Héctor; Moreno-Romero, Jordi; Solís, María-Teresa
- Cytogenetic and Genome Research, Vol. 143, Issue 1-3
Switchgrass (Panicum virgatum L) flag leaf transcriptomes reveal molecular signatures of leaf development, senescence, and mineral dynamics
journal, August 2014
- Palmer, Nathan A.; Donze-Reiner, Teresa; Horvath, David
- Functional & Integrative Genomics, Vol. 15, Issue 1
Identification and validation of promoters and cis-acting regulatory elements
journal, March 2014
- Hernandez-Garcia, Carlos M.; Finer, John J.
- Plant Science, Vol. 217-218
A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus
journal, May 2015
- Liu, Lijun; Ramsay, Trevor; Zinkgraf, Matthew
- The Plant Journal, Vol. 82, Issue 5
The basic helix loop helix domain of maize R links transcriptional regulation and histone modifications by recruitment of an EMSY-related factor
journal, October 2007
- Hernandez, J. M.; Feller, A.; Morohashi, K.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 43
Epigenetics in cancer
journal, September 2009
- Sharma, S.; Kelly, T. K.; Jones, P. A.
- Carcinogenesis, Vol. 31, Issue 1
Analyses of methylomes of upland and lowland switchgrass (Panicum virgatum) ecotypes using MeDIP-seq and BS-seq
journal, November 2017
- Dworkin, Mollee; Xie, Shaojun; Saha, Malay
- BMC Genomics, Vol. 18, Issue 1
High-resolution mapping of open chromatin in the rice genome
journal, November 2011
- Zhang, W.; Wu, Y.; Schnable, J. C.
- Genome Research, Vol. 22, Issue 1
DNA Methylation and Histone Modifications Regulate De Novo Shoot Regeneration in Arabidopsis by Modulating WUSCHEL Expression and Auxin Signaling
journal, August 2011
- Li, Wei; Liu, Hui; Cheng, Zhi Juan
- PLoS Genetics, Vol. 7, Issue 8
H3K36ac Is an Evolutionary Conserved Plant Histone Modification That Marks Active Genes
journal, January 2016
- Mahrez, Walid; Arellano, Minerva Susana Trejo; Moreno-Romero, Jordi
- Plant Physiology, Vol. 170, Issue 3
Complete Switchgrass Genetic Maps Reveal Subgenome Collinearity, Preferential Pairing and Multilocus Interactions
journal, April 2010
- Okada, Miki; Lanzatella, Christina; Saha, Malay C.
- Genetics, Vol. 185, Issue 3
Advances in modifying lignin for enhanced biofuel production
journal, June 2010
- Simmons, Blake A.; Loqué, Dominique; Ralph, John
- Current Opinion in Plant Biology, Vol. 13, Issue 3, p. 312-319
Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription
journal, April 2015
- Bornelöv, Susanne; Komorowski, Jan; Wadelius, Claes
- BMC Genomics, Vol. 16, Issue 1
Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency
journal, December 2016
- Serba, Desalegn D.; Uppalapati, Srinivasa Rao; Krom, Nick
- BMC Genomics, Vol. 17, Issue 1
Histone modifications facilitate the coexpression of bidirectional promoters in rice
journal, September 2016
- Fang, Yuan; Wang, Lei; Wang, Ximeng
- BMC Genomics, Vol. 17, Issue 1
Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem
journal, May 2015
- Hussey, Steven G.; Mizrachi, Eshchar; Groover, Andrew
- BMC Plant Biology, Vol. 15, Issue 1
Downregulation of Cinnamyl Alcohol Dehydrogenase (CAD) Leads to Improved Saccharification Efficiency in Switchgrass
journal, January 2011
- Fu, Chunxiang; Xiao, Xirong; Xi, Yajun
- BioEnergy Research, Vol. 4, Issue 3, p. 153-164
The potential of C4 grasses for cellulosic biofuel production
journal, January 2013
- van der Weijde, Tim; Alvim Kamei, Claire L.; Torres, Andres F.
- Frontiers in Plant Science, Vol. 4
Phytozome: a comparative platform for green plant genomics
journal, November 2011
- Goodstein, David M.; Shu, Shengqiang; Howson, Russell
- Nucleic Acids Research, Vol. 40, Issue D1
Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA-Seq Analysis
journal, January 2015
- Serba, Desalegn D.; Uppalapati, Srinivasa Rao; Mukherjee, Shreyartha
- The Plant Genome, Vol. 8, Issue 2
Integrative genomics viewer
journal, January 2011
- Robinson, James T.; Thorvaldsdóttir, Helga; Winckler, Wendy
- Nature Biotechnology, Vol. 29, Issue 1
Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass ( Panicum virgatum L.)
journal, February 2013
- Zhang, Ji-Yi; Lee, Yi-Ching; Torres-Jerez, Ivone
- The Plant Journal, Vol. 74, Issue 1
Histone H3 Lysine 4 Methylation Marks Postreplicative Human Cytomegalovirus Chromatin
journal, July 2012
- Nitzsche, Alexandra; Steinhäußer, Charlotte; Mücke, Katrin
- Journal of Virology, Vol. 86, Issue 18
Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method
journal, December 2001
- Livak, Kenneth J.; Schmittgen, Thomas D.
- Methods, Vol. 25, Issue 4
High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression
journal, February 2008
- Li, Xueyong; Wang, Xiangfeng; He, Kun
- The Plant Cell, Vol. 20, Issue 2
Contrasting Metabolism in Perenniating Structures of Upland and Lowland Switchgrass Plants Late in the Growing Season
journal, August 2014
- Palmer, Nathan A.; Saathoff, Aaron J.; Tobias, Christian M.
- PLoS ONE, Vol. 9, Issue 8
Linkage Maps of Lowland and Upland Tetraploid Switchgrass Ecotypes
journal, March 2013
- Serba, Desalegn; Wu, Limin; Daverdin, Guillaume
- BioEnergy Research, Vol. 6, Issue 3
Genome-Wide Profiling of Histone Modifications (H3K9me2 and H4K12ac) and Gene Expression in Rust (Uromyces appendiculatus) Inoculated Common Bean (Phaseolus vulgaris L.)
journal, July 2015
- Ayyappan, Vasudevan; Kalavacharla, Venu; Thimmapuram, Jyothi
- PLOS ONE, Vol. 10, Issue 7
Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana
journal, January 2009
- Zhang, Xiaoyu; Bernatavichute, Yana V.; Cokus, Shawn
- Genome Biology, Vol. 10, Issue 6
DNA methylation pathways and their crosstalk with histone methylation
journal, August 2015
- Du, Jiamu; Johnson, Lianna M.; Jacobsen, Steven E.
- Nature Reviews Molecular Cell Biology, Vol. 16, Issue 9
DNA Methylation: Superior or Subordinate in the Epigenetic Hierarchy?
journal, January 2011
- Jin, B.; Li, Y.; Robertson, K. D.
- Genes & Cancer, Vol. 2, Issue 6
The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote
journal, June 2004
- Schubeler, D.
- Genes & Development, Vol. 18, Issue 11
Dynamic Landscapes of Four Histone Modifications during Deetiolation in Arabidopsis
journal, December 2009
- Charron, Jean-Benoit F.; He, Hang; Elling, Axel A.
- The Plant Cell, Vol. 21, Issue 12
Dynamic Changes in Genome-Wide Histone H3 Lysine 4 Methylation Patterns in Response to Dehydration Stress in Arabidopsis thaliana
journal, January 2010
- van Dijk, Karin; Ding, Yong; Malkaram, Sridhar
- BMC Plant Biology, Vol. 10, Issue 1
Sequencing quality assessment tools to enable data-driven informatics for high throughput genomics
journal, January 2013
- Leggett, Richard M.; Ramirez-Gonzalez, Ricardo H.; Clavijo, Bernardo J.
- Frontiers in Genetics, Vol. 4
Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome
journal, August 2014
- West, Patrick T.; Li, Qing; Ji, Lexiang
- PLoS ONE, Vol. 9, Issue 8
Molecular breeding of switchgrass for use as a biofuel crop
journal, December 2007
- Bouton, Joseph H.
- Current Opinion in Genetics & Development, Vol. 17, Issue 6
Fast gapped-read alignment with Bowtie 2
journal, March 2012
- Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 9, Issue 4
BEDTools: a flexible suite of utilities for comparing genomic features
journal, January 2010
- Quinlan, Aaron R.; Hall, Ira M.
- Bioinformatics, Vol. 26, Issue 6
Genome-wide analysis of local chromatin packing in Arabidopsis thaliana
journal, November 2014
- Wang, Congmao; Liu, Chang; Roqueiro, Damian
- Genome Research, Vol. 25, Issue 2
Histone Modifications Define Expression Bias of Homoeologous Genomes in Allotetraploid Cotton
journal, September 2016
- Zheng, Dewei; Ye, Wenxue; Song, Qingxin
- Plant Physiology, Vol. 172, Issue 3
Histone modifications and dynamic regulation of genome accessibility in plants
journal, December 2007
- Pfluger, Jennifer; Wagner, Doris
- Current Opinion in Plant Biology, Vol. 10, Issue 6
Transcriptional networks for lignin biosynthesis: more complex than we thought?
journal, April 2011
- Zhao, Qiao; Dixon, Richard A.
- Trends in Plant Science, Vol. 16, Issue 4, p. 227-233
Genome-Wide Analysis of Histone Modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica
journal, September 2013
- Du, Zhou; Li, Hui; Wei, Qiang
- Molecular Plant, Vol. 6, Issue 5
A Common Histone Modification Code on C4 Genes in Maize and Its Conservation in Sorghum and Setaria italica
journal, April 2013
- Heimann, Louisa; Horst, Ina; Perduns, Renke
- Plant Physiology, Vol. 162, Issue 1
Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression
journal, January 2010
- Zhou, Junli; Wang, Xiangfeng; He, Kun
- Plant Molecular Biology, Vol. 72, Issue 6
Comparative transcriptome profiling of upland (VS16) and lowland (AP13) ecotypes of switchgrass
journal, November 2016
- Ayyappan, Vasudevan; Saha, Malay C.; Thimmapuram, Jyothi
- Plant Cell Reports, Vol. 36, Issue 1
Chromatin state analysis of the barley epigenome reveals a higher‐order structure defined by H3K27me1 and H3K27me3 abundance
journal, September 2015
- Baker, Katie; Dhillon, Taniya; Colas, Isabelle
- The Plant Journal, Vol. 84, Issue 1
Correction: Temporal Expression of Pelp1 during Proliferation and Osteogenic Differentiation of Rat Bone Marrow Mesenchymal Stem Cells
journal, December 2013
- Wang, Jing; Song, Shujun; Shi, Liang
- PLoS ONE, Vol. 8, Issue 12
Correction: A High Throughput In Vivo Assay for Taste Quality and Palatability
journal, January 2014
- Palmer, R. Kyle; Long, Daniel; Brennan, Francis
- PLoS ONE, Vol. 9, Issue 1
H3K36ac is an evolutionary conserved plant histone modification that marks active genes
text, January 2016
- Mahrez, Walid; Arellano, Minerva Susana Trejo; Moreno-Romero, Jordi
- American Society of Plant Biologists
Genome-wide analysis of local chromatin packing in Arabidopsis thaliana
dataset, January 2019
- Liu, Chang
- figshare