Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem

Hussey, Steven G.; Mizrachi, Eshchar; Groover, Andrew; Berger, Dave K.; Myburg, Alexander A.

doi:10.1186/s12870-015-0499-0

Title: Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem

Journal Article · Sun May 10 00:00:00 EDT 2015 · BMC Plant Biology

DOI:https://doi.org/10.1186/s12870-015-0499-0· OSTI ID:1626838

Hussey, Steven G. ^[1]; Mizrachi, Eshchar ^[1]; Groover, Andrew ^[2]; Berger, Dave K. ^[3]; Myburg, Alexander A. ^[1]

Univ. of Pretoria (South Africa). Genomics Research Inst. (GRI). Dept. of Genetics, Forestry and Agricultural Biotechnology Inst. (FABI)
USDA Forest Service, Davis, CA (United States). Pacific Southwest Research Station; Univ. of California, Davis, CA (United States). Dept. of Plant Biology
Univ. of Pretoria (South Africa). Genomics Research Inst. (GRI). Dept. of Plant Science, Forestry and Agricultural Biotechnology Inst. (FABI)

Background: Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. We investigated the role of the modified histone H3K4me3 (trimethylated lysine 4 of histone H3) in gene expression during the early stages of wood formation using ChIP-seq in Eucalyptus grandis, a woody biomass model. Results: Plant chromatin fixation and isolation protocols were optimized for developing xylem tissue collected from field-grown E. grandis trees. A “nano-ChIP-seq” procedure was employed for ChIP DNA amplification. Over 9 million H3K4me3 ChIP-seq and 18 million control paired-end reads were mapped to the E. grandis reference genome for peak-calling using Model-based Analysis of ChIP-Seq. The 12,177 significant H3K4me3 peaks identified covered ~1.5% of the genome and overlapped some 9,623 protein-coding genes and 38 noncoding RNAs. H3K4me3 library coverage, peaking ~600 - 700 bp downstream of the transcription start site, was highly correlated with gene expression levels measured with RNA-seq. Overall, H3K4me3-enriched genes tended to be less tissue-specific than unenriched genes and were overrepresented for general cellular metabolism and development gene ontology terms. Relative expression of H3K4me3-enriched genes in developing secondary xylem was higher than unenriched genes, however, and highly expressed secondary cell wall-related genes were enriched for H3K4me3 as validated using ChIP-qPCR. Conclusions: In this first genome-wide analysis of a modified histone in a woody tissue, we optimized a ChIP-seq procedure suitable for field-collected samples. In developing E. grandis xylem, H3K4me3 enrichment is an indicator of active transcription, consistent with its known role in sustaining pre-initiation complex formation in yeast. The H3K4me3 ChIP-seq data from this study paves the way to understanding the chromatin landscape and epigenomic architecture of xylogenesis in plants, and complements RNA-seq evidence of gene expression for the future improvement of the E. grandis genome annotation.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1626838

Journal Information:: BMC Plant Biology, Vol. 15, Issue 1; ISSN 1471-2229

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (80)

A Mathematical Theory of Communication Shannon, C. E. Bell System Technical Journal, Vol. 27, Issue 3 https://doi.org/10.1002/j.1538-7305.1948.tb01338.x	journal	July 1948
Two Phases of Chromatin Decondensation during Dedifferentiation of Plant Cells: DISTINCTION BETWEEN COMPETENCE FOR CELL FATE SWITCH AND A COMMITMENT FOR S PHASE Zhao, Jing; Morozova, Nadya; Williams, Leor Journal of Biological Chemistry, Vol. 276, Issue 25 https://doi.org/10.1074/jbc.M101756200	journal	March 2001
Model-based Analysis of ChIP-Seq (MACS) Zhang, Yong; Liu, Tao; Meyer, Clifford A. Genome Biology, Vol. 9, Issue 9 https://doi.org/10.1186/gb-2008-9-9-r137	journal	January 2008
Chromatin Modifications and Their Function Kouzarides, Tony Cell, Vol. 128, Issue 4 https://doi.org/10.1016/j.cell.2007.02.005	journal	February 2007
Systematic analysis of gene expression level with tissue-specificity, function and protein subcellular localization in human transcriptome Li, Qiang; Liu, Xianghua; He, Quanyuan Molecular Biology Reports, Vol. 38, Issue 4 https://doi.org/10.1007/s11033-010-0400-z	journal	November 2010
Coordinated histone modifications are associated with gene expression variation within and between species Ha, M.; Ng, D. W. -K.; Li, W. -H. Genome Research, Vol. 21, Issue 4 https://doi.org/10.1101/gr.116467.110	journal	February 2011
KEGG: Kyoto Encyclopedia of Genes and Genomes Kanehisa, Minoru; Goto, Susumu Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30 https://doi.org/10.1093/nar/28.1.27	journal	January 2000
In plants, expression breadth and expression level distinctly and non-linearly correlate with gene structure Yang, Hangxing Biology Direct, Vol. 4, Issue 1 https://doi.org/10.1186/1745-6150-4-45	journal	January 2009
Design and analysis of ChIP-seq experiments for DNA-binding proteins Kharchenko, Peter V.; Tolstorukov, Michael Y.; Park, Peter J. Nature Biotechnology, Vol. 26, Issue 12 https://doi.org/10.1038/nbt.1508	journal	November 2008
Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast Sun, Zu-Wen; Allis, C. David Nature, Vol. 418, Issue 6893 https://doi.org/10.1038/nature00883	journal	June 2002
Systematic evaluation of factors influencing ChIP-seq fidelity Chen, Yiwen; Negre, Nicolas; Li, Qunhua Nature Methods, Vol. 9, Issue 6 https://doi.org/10.1038/nmeth.1985	journal	April 2012
Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production Luo, Chongyuan; Sidote, David J.; Zhang, Yi The Plant Journal, Vol. 73, Issue 1 https://doi.org/10.1111/tpj.12017	journal	October 2012
Bur1/Bur2 and the Ctk Complex in Yeast: The Split Personality of Mammalian P-TEFb Wood, Adam; Shilatifard, Ali Cell Cycle, Vol. 5, Issue 10 https://doi.org/10.4161/cc.5.10.2769	journal	May 2006
The Plant Vascular System: Evolution, Development and Functions ^F Lucas, William J.; Groover, Andrew; Lichtenberger, Raffael Journal of Integrative Plant Biology, Vol. 55, Issue 4 https://doi.org/10.1111/jipb.12041	journal	April 2013
High-Resolution Profiling of Histone Methylations in the Human Genome Barski, Artem; Cuddapah, Suresh; Cui, Kairong Cell, Vol. 129, Issue 4 https://doi.org/10.1016/j.cell.2007.05.009	journal	May 2007
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Heintzman, Nathaniel D.; Stuart, Rhona K.; Hon, Gary Nature Genetics, Vol. 39, Issue 3 https://doi.org/10.1038/ng1966	journal	February 2007
Wood formation in Angiosperms Déjardin, Annabelle; Laurans, Françoise; Arnaud, Dominique Comptes Rendus Biologies, Vol. 333, Issue 4 https://doi.org/10.1016/j.crvi.2010.01.010	journal	April 2010
Charting histone modifications and the functional organization of mammalian genomes Zhou, Vicky W.; Goren, Alon; Bernstein, Bradley E. Nature Reviews Genetics, Vol. 12, Issue 1 https://doi.org/10.1038/nrg2905	journal	November 2010
The accessible chromatin landscape of the human genome Thurman, Robert E.; Rynes, Eric; Humbert, Richard Nature, Vol. 489, Issue 7414 https://doi.org/10.1038/nature11232	journal	September 2012
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository Edgar, R. Nucleic Acids Research, Vol. 30, Issue 1 https://doi.org/10.1093/nar/30.1.207	journal	January 2002
Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors Adli, Mazhar; Zhu, Jiang; Bernstein, Bradley E. Nature Methods, Vol. 7, Issue 8 https://doi.org/10.1038/nmeth.1478	journal	July 2010
High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression Li, Xueyong; Wang, Xiangfeng; He, Kun The Plant Cell, Vol. 20, Issue 2 https://doi.org/10.1105/tpc.107.056879	journal	February 2008
De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq Mizrachi, Eshchar; Hefer, Charles A.; Ranik, Martin BMC Genomics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2164-11-681	journal	January 2010
The Populus ARBORKNOX1 homeodomain transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function Liu, Lijun; Zinkgraf, Matthew; Petzold, H. Earl New Phytologist, Vol. 205, Issue 2 https://doi.org/10.1111/nph.13151	journal	November 2014
H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation Lauberth, Shannon M.; Nakayama, Takahiro; Wu, Xiaolin Cell, Vol. 152, Issue 5 https://doi.org/10.1016/j.cell.2013.01.052	journal	February 2013
Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana Zhang, Xiaoyu; Bernatavichute, Yana V.; Cokus, Shawn Genome Biology, Vol. 10, Issue 6 https://doi.org/10.1186/gb-2009-10-6-r62	journal	January 2009
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Goecks, Jeremy; Nekrutenko, Anton; Taylor, James Genome Biology, Vol. 11, Issue 8 https://doi.org/10.1186/gb-2010-11-8-r86	journal	January 2010
Genome-wide profiling of histone H3K4-tri-methylation and gene expression in rice under drought stress Zong, Wei; Zhong, Xiaochao; You, Jun Plant Molecular Biology, Vol. 81, Issue 1-2 https://doi.org/10.1007/s11103-012-9990-2	journal	November 2012
Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP) Kaufmann, Kerstin; Muiño, Jose M.; Østerås, Magne Nature Protocols, Vol. 5, Issue 3 https://doi.org/10.1038/nprot.2009.244	journal	February 2010
The genome of Eucalyptus grandis Myburg, Alexander A.; Grattapaglia, Dario; Tuskan, Gerald A. Nature, Vol. 510, Issue 7505 https://doi.org/10.1038/nature13308	journal	June 2014
An integrated encyclopedia of DNA elements in the human genome Nature, Vol. 489, Issue 7414, p. 57-74 https://doi.org/10.1038/nature11247	journal	September 2012
psRNATarget: a plant small RNA target analysis server Dai, Xinbin; Zhao, Patrick Xuechun Nucleic Acids Research, Vol. 39, Issue suppl_2 https://doi.org/10.1093/nar/gkr319	journal	May 2011
Dynamic Changes in Genome-Wide Histone H3 Lysine 4 Methylation Patterns in Response to Dehydration Stress in Arabidopsis thaliana van Dijk, Karin; Ding, Yong; Malkaram, Sridhar BMC Plant Biology, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2229-10-238	journal	January 2010
Selective Anchoring of TFIID to Nucleosomes by Trimethylation of Histone H3 Lysine 4 Vermeulen, Michiel; Mulder, Klaas W.; Denissov, Sergei Cell, Vol. 131, Issue 1 https://doi.org/10.1016/j.cell.2007.08.016	journal	October 2007
Architecture of the human regulatory network derived from ENCODE data Gerstein, Mark B.; Kundaje, Anshul; Hariharan, Manoj Nature, Vol. 489, Issue 7414 https://doi.org/10.1038/nature11245	journal	September 2012
Modeling gene expression using chromatin features in various cellular contexts Dong, Xianjun; Greven, Melissa C.; Kundaje, Anshul Genome Biology, Vol. 13, Issue 9 https://doi.org/10.1186/gb-2012-13-9-r53	journal	January 2012
Dynamic and stable histone H3 methylation patterns at the Arabidopsis FLC and AP1 loci Saleh, Abdelaty; Alvarez-Venegas, Raul; Avramova, Zoya Gene, Vol. 423, Issue 1 https://doi.org/10.1016/j.gene.2008.06.022	journal	October 2008
Dissection of the Transcriptional Program Regulating Secondary Wall Biosynthesis during Wood Formation in Poplar Zhong, Ruiqin; McCarthy, Ryan L.; Lee, Chanhui Plant Physiology, Vol. 157, Issue 3 https://doi.org/10.1104/pp.111.181354	journal	September 2011
microRNA biogenesis and function in plants Chen, Xuemei FEBS Letters, Vol. 579, Issue 26 https://doi.org/10.1016/j.febslet.2005.07.071	journal	August 2005
Comprehensive Genome-Wide Survey, Genomic Constitution and Expression Profiling of the NAC Transcription Factor Family in Foxtail Millet (Setaria italica L.) Puranik, Swati; Sahu, Pranav Pankaj; Mandal, Sambhu Nath PLoS ONE, Vol. 8, Issue 5 https://doi.org/10.1371/journal.pone.0064594	journal	May 2013
Fast gapped-read alignment with Bowtie 2 Langmead, Ben; Salzberg, Steven L. Nature Methods, Vol. 9, Issue 4 https://doi.org/10.1038/nmeth.1923	journal	March 2012
BEDTools: a flexible suite of utilities for comparing genomic features Quinlan, Aaron R.; Hall, Ira M. Bioinformatics, Vol. 26, Issue 6 https://doi.org/10.1093/bioinformatics/btq033	journal	January 2010
Measuring reproducibility of high-throughput experiments Li, Qunhua; Brown, James B.; Huang, Haiyan The Annals of Applied Statistics, Vol. 5, Issue 3 https://doi.org/10.1214/11-AOAS466	journal	September 2011
A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells Guenther, Matthew G.; Levine, Stuart S.; Boyer, Laurie A. Cell, Vol. 130, Issue 1 https://doi.org/10.1016/j.cell.2007.05.042	journal	July 2007
Galaxy: A platform for interactive large-scale genome analysis Giardine, B. Genome Research, Vol. 15, Issue 10 https://doi.org/10.1101/gr.4086505	journal	September 2005
Histone modifications and dynamic regulation of genome accessibility in plants Pfluger, Jennifer; Wagner, Doris Current Opinion in Plant Biology, Vol. 10, Issue 6 https://doi.org/10.1016/j.pbi.2007.07.013	journal	December 2007
Methylation patterns of histone H3 Lys 4, Lys 9 and Lys 27 in transcriptionally active and inactive Arabidopsis genes and in atx1 mutants Alvarez-Venegas, R. Nucleic Acids Research, Vol. 33, Issue 16 https://doi.org/10.1093/nar/gki830	journal	September 2005
Structural Insight into the Recognition of the H3K4me3 Mark by the TFIID Subunit TAF3 van Ingen, Hugo; van Schaik, Frederik M. A.; Wienk, Hans Structure, Vol. 16, Issue 8 https://doi.org/10.1016/j.str.2008.04.015	journal	August 2008
ARABIDOPSIS TRITHORAX1 Dynamically Regulates FLOWERING LOCUS C Activation via Histone 3 Lysine 4 Trimethylation Pien, Stéphane; Fleury, Delphine; Mylne, Joshua S. The Plant Cell, Vol. 20, Issue 3 https://doi.org/10.1105/tpc.108.058172	journal	March 2008
A robust chromatin immunoprecipitation protocol for studying transcription factor–DNA interactions and histone modifications in wood-forming tissue Li, Wei; Lin, Ying-Chung; Li, Quanzi Nature Protocols, Vol. 9, Issue 9 https://doi.org/10.1038/nprot.2014.146	journal	August 2014
Uniform, optimal signal processing of mapped deep-sequencing data Kumar, Vibhor; Muratani, Masafumi; Rayan, Nirmala Arul Nature Biotechnology, Vol. 31, Issue 7 https://doi.org/10.1038/nbt.2596	journal	June 2013
The Highly Similar Arabidopsis Homologs of Trithorax ATX1 and ATX2 Encode Proteins with Divergent Biochemical Functions Saleh, Abdelaty; Alvarez-Venegas, Raul; Yilmaz, Mehtap The Plant Cell, Vol. 20, Issue 3 https://doi.org/10.1105/tpc.107.056614	journal	March 2008
Targeted Recruitment of Set1 Histone Methylase by Elongating Pol II Provides a Localized Mark and Memory of Recent Transcriptional Activity Ng, Huck Hui; Robert, François; Young, Richard A. Molecular Cell, Vol. 11, Issue 3 https://doi.org/10.1016/S1097-2765(03)00092-3	journal	March 2003
A High-Resolution Transcript Profile across the Wood-Forming Meristem of Poplar Identifies Potential Regulators of Cambial Stem Cell Identity Schrader, Jarmo; Nilsson, Jeanette; Mellerowicz, Ewa The Plant Cell, Vol. 16, Issue 9 https://doi.org/10.1105/tpc.104.024190	journal	August 2004
Methylation of Lysine 4 on Histone H3: Intricacy of Writing and Reading a Single Epigenetic Mark Ruthenburg, Alexander J.; Allis, C. David; Wysocka, Joanna Molecular Cell, Vol. 25, Issue 1 https://doi.org/10.1016/j.molcel.2006.12.014	journal	January 2007
Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression Zhou, Junli; Wang, Xiangfeng; He, Kun Plant Molecular Biology, Vol. 72, Issue 6 https://doi.org/10.1007/s11103-009-9594-7	journal	January 2010
The transcriptional regulatory code of eukaryotic cells – insights from genome-wide analysis of chromatin organization and transcription factor binding Barrera, Leah O.; Ren, Bing Current Opinion in Cell Biology, Vol. 18, Issue 3 https://doi.org/10.1016/j.ceb.2006.04.002	journal	June 2006
Dynamic Regulation of Histone Lysine Methylation by Demethylases Shi, Yang; Whetstine, Johnathan R. Molecular Cell, Vol. 25, Issue 1 https://doi.org/10.1016/j.molcel.2006.12.010	journal	January 2007
Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq Adli, Mazhar; Bernstein, Bradley E. Nature Protocols, Vol. 6, Issue 10 https://doi.org/10.1038/nprot.2011.402	journal	September 2011
Tails of Intrigue Hampsey, Michael; Reinberg, Danny Cell, Vol. 113, Issue 4 https://doi.org/10.1016/S0092-8674(03)00360-X	journal	May 2003
Histone Methylation in Higher Plants Liu, Chunyan; Lu, Falong; Cui, Xia Annual Review of Plant Biology, Vol. 61, Issue 1 https://doi.org/10.1146/annurev.arplant.043008.091939	journal	June 2010
ATX-1, an Arabidopsis Homolog of Trithorax, Activates Flower Homeotic Genes Alvarez-Venegas, Raul; Pien, Stephane; Sadder, Monther Current Biology, Vol. 13, Issue 8 https://doi.org/10.1016/S0960-9822(03)00243-4	journal	April 2003
Predictive chromatin signatures in the mammalian genome Hon, G. C.; Hawkins, R. D.; Ren, B. Human Molecular Genetics, Vol. 18, Issue R2 https://doi.org/10.1093/hmg/ddp409	journal	October 2009
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia Landt, S. G.; Marinov, G. K.; Kundaje, A. Genome Research, Vol. 22, Issue 9 https://doi.org/10.1101/gr.136184.111	journal	September 2012
Promoter features related to tissue specificity as measured by Shannon entropy Schug, Jonathan; Schuller, Winfried-Paul; Kappen, Claudia Genome Biology, Vol. 6, Issue 4 https://doi.org/10.1186/gb-2005-6-4-r33	journal	March 2005
GOToolBox: functional analysis of gene datasets based on Gene Ontology Martin, David; Brun, Christine; Remy, Elisabeth Genome Biology, Vol. 5, Issue 12, p. R101 https://doi.org/10.1186/gb-2004-5-12-r101	journal	January 2004
Histone variants and modifications in plant gene regulation Deal, Roger B.; Henikoff, Steven Current Opinion in Plant Biology, Vol. 14, Issue 2 https://doi.org/10.1016/j.pbi.2010.11.005	journal	April 2011
A trithorax-group complex purified from Saccharomyces cerevisiae is required for methylation of histone H3 Nagy, P. L.; Griesenbeck, J.; Kornberg, R. D. Proceedings of the National Academy of Sciences, Vol. 99, Issue 1 https://doi.org/10.1073/pnas.221596698	journal	December 2001
scVAEBGM: Clustering Analysis of Single-Cell ATAC-seq Data Using a Deep Generative Model Duan, Hongyu; Li, Feng; Shang, Junliang Interdisciplinary Sciences: Computational Life Sciences, Vol. 14, Issue 4 https://doi.org/10.1007/s12539-022-00536-w	journal	August 2022
Synergism between IL7R and CXCR4 drives BCR-ABL induced transformation in Philadelphia chromosome-positive acute lymphoblastic leukemia Abdelrasoul, Hend; Vadakumchery, Anila; Werner, Markus Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-16927-w	journal	June 2020
Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens Papalexi, Efthymia; Mimitou, Eleni P.; Butler, Andrew W. Nature Genetics, Vol. 53, Issue 3 https://doi.org/10.1038/s41588-021-00778-2	journal	March 2021
Red versus green leaves: transcriptomic comparison of foliar senescence between two Prunus cerasifera genotypes Vangelisti, Alberto; Guidi, Lucia; Cavallini, Andrea Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-58878-8	journal	February 2020
Advances in biocultural geography of olive tree (Olea europaea L.) landscapes by merging biological and historical assays Russo, Giuseppe; Beritognolo, Isacco; Bufacchi, Marina Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-64063-8	journal	May 2020
Nucleolar RNPs: from genes to functional snoRNAs in plants Rodor, Julie; Letelier, Ingrid; Holuigue, Loreto Biochemical Society Transactions, Vol. 38, Issue 2 https://doi.org/10.1042/bst0380672	journal	March 2010
Methylation of Histone H3 by COMPASS Requires Ubiquitination of Histone H2B by Rad6 Dover, Jim; Schneider, Jessica; Tawiah-Boateng, Mary Anne Journal of Biological Chemistry, Vol. 277, Issue 32 https://doi.org/10.1074/jbc.c200348200	journal	June 2002
A unique program for cell death in xylem fibers of Populus stem Courtois-Moreau, Charleen L.; Pesquet, Edouard; Sjödin, Andreas The Plant Journal, Vol. 58, Issue 2 https://doi.org/10.1111/j.1365-313x.2008.03777.x	journal	April 2009
The floral transcriptome of Eucalyptus grandis Vining, Kelly J.; Romanel, Elisson; Jones, Rebecca C. New Phytologist, Vol. 206, Issue 4 https://doi.org/10.1111/nph.13077	journal	October 2014
The Eucalyptus genome integrative explorer (EucGenIE): a resource for Eucalyptusgenomics and transcriptomics Hefer, Charles; Mizrachi, Eshchar; Joubert, Fourie BMC Proceedings, Vol. 5, Issue S7 https://doi.org/10.1186/1753-6561-5-s7-o49	journal	September 2011
An Improved Filtering Algorithm for Big Read Datasets Wedemeyer, Axel; Kliemann, Lasse; Srivastav, Anand arXiv https://doi.org/10.48550/arxiv.1610.03443	preprint	January 2016
ARABIDOPSIS TRITHORAX1 dynamically regulates FLOWERING LOCUS C activation via histone 3 lysine 4 trimethylation S., Pien,; D., Fleury,; S., Mylne, J. American Society of Plant Biologists https://doi.org/10.5167/uzh-11010	text	January 2008

Cited By (8)

ChIP-seq and RNA-seq for complex and low-abundance tree buds reveal chromatin and expression co-dynamics during sweet cherry bud dormancy Vimont, Noémie; Quah, Fu Xiang; Schöepfer, David Guillaume Tree Genetics & Genomes, Vol. 16, Issue 1 https://doi.org/10.1007/s11295-019-1395-9	journal	December 2019
Identification and functional evaluation of accessible chromatin associated with wood formation in Eucalyptus grandis Brown, Katrien; Takawira, Lazarus T.; O'Neill, Marja M. New Phytologist, Vol. 223, Issue 4 https://doi.org/10.1111/nph.15897	journal	April 2019
Genome-wide identification of histone methylation (H3K9me2) and acetylation (H4K12ac) marks in two ecotypes of switchgrass (Panicum virgatum L.) Ayyappan, Vasudevan; Sripathi, Venkateswara R.; Kalavacharla, Venu BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-6038-x	journal	August 2019
Application of Genomic Technologies to the Breeding of Trees Badenes, Maria L.; Fernández i. Martí, Angel; Ríos, Gabino Frontiers in Genetics, Vol. 7 https://doi.org/10.3389/fgene.2016.00198	journal	November 2016
RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism Muhammad, Isiaka Ibrahim; Kong, Sze Ling; Akmar Abdullah, Siti Nor International Journal of Molecular Sciences, Vol. 21, Issue 1 https://doi.org/10.3390/ijms21010167	journal	December 2019
ChIP-seq and RNA-seq for complex and low-abundance tree buds reveal chromatin and expression co-dynamics during sweet cherry bud dormancy Vimont, Noémie; Quah, Fu Xiang; Schöepfer, David Guillaume Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.53464	text	January 2019
ChIP-seq and RNA-seq for complex and low-abundance tree buds reveal chromatin and expression co-dynamics during sweet cherry bud dormancy Vimont, Noémie; Quah, Fu Xiang; Schöepfer, David Guillaume Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.60258	text	January 2019
ChIP-seq and RNA-seq for complex and low-abundance tree buds reveal chromatin and expression co-dynamics during sweet cherry bud dormancy Vimont, Noémie; Quah, Fu Xiang; Schöepfer, David Guillaume Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.62490	text	January 2019

Similar Records

The landscape of Chlamydomonas histone H3 lysine 4 methylation reveals both constant features and dynamic changes during the diurnal cycle

Journal Article · Fri Aug 19 00:00:00 EDT 2022 · The Plant Journal · OSTI ID:1626838

Strenkert, Daniela; Yildirim, Asli; Yan, Juying; +5 more

An optimized ChIP-Seq framework for profiling histone modifications in Chromochloris zofingiensis

Journal Article · Mon Mar 28 00:00:00 EDT 2022 · Plant Direct · OSTI ID:1626838

Strenkert, Daniela; Mingay, Matthew; Schmollinger, Stefan; +3 more

Global epigenomic analysis indicates protocadherin-7 activates osteoclastogenesis by promoting cell–cell fusion

Journal Article · Fri Dec 12 00:00:00 EST 2014 · Biochemical and Biophysical Research Communications · OSTI ID:1626838

Nakamura, Haruhiko; Nakashima, Tomoki; Hayashi, Mikihito; +5 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Plant Sciences
ChIP-seq
H3K4me3
Histone
Secondary cell wall
Xylogenesis
Eucalyptus

Title: Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem

Citation Formats

References (80)

Cited By (8)

Similar Records

Related Subjects