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Defining chromatin state transitions predicts a network that modulates cell wall remodeling in phosphate-starved rice shoots

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/bies.201600095openalex-snapshot

Is H3K4me3 instructive for transcription activation?

inferredcites →https://doi.org/10.1007/s00425-007-0612-1openalex-snapshot

Up-regulation of stress-inducible genes in tobacco and Arabidopsis cells in response to abiotic stresses and ABA treatment correlates with dynamic changes in histone H3 and H4 modifications

inferredcites →https://doi.org/10.1007/s11103-012-9990-2openalex-snapshot

Genome-wide profiling of histone H3K4-tri-methylation and gene expression in rice under drought stress

inferredcites →https://doi.org/10.1007/s11105-012-0485-8openalex-snapshot

Comparative Analysis of Differentially Expressed Genes in Rice Under Nitrogen and Phosphorus Starvation Stress Conditions

inferredcites →https://doi.org/10.1016/j.cell.2006.02.041openalex-snapshot

A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells

inferredcites →https://doi.org/10.1016/j.cell.2007.05.009openalex-snapshot

High-Resolution Profiling of Histone Methylations in the Human Genome

inferredcites →https://doi.org/10.1016/j.cell.2009.02.006openalex-snapshot

Evolution and Functions of Long Noncoding RNAs

inferredcites →https://doi.org/10.1016/j.cell.2009.11.006openalex-snapshot

H2A.Z-Containing Nucleosomes Mediate the Thermosensory Response in Arabidopsis

inferredcites →https://doi.org/10.1016/j.cell.2014.06.006openalex-snapshot

The Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis

inferredcites →https://doi.org/10.1016/j.celrep.2017.03.078openalex-snapshot

Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression

inferredcites →https://doi.org/10.1016/j.cub.2018.01.023openalex-snapshot

The FERONIA Receptor Kinase Maintains Cell-Wall Integrity during Salt Stress through Ca2+ Signaling

inferredcites →https://doi.org/10.1016/j.gpb.2012.05.001openalex-snapshot

The Association Between H3K4me3 and Antisense Transcription

inferredcites →https://doi.org/10.1016/j.molcel.2005.05.009openalex-snapshot

Dynamic Lysine Methylation on Histone H3 Defines the Regulatory Phase of Gene Transcription

inferredcites →https://doi.org/10.1016/j.molcel.2014.07.004openalex-snapshot

Lysine Acetylation Controls Local Protein Conformation by Influencing Proline Isomerization

inferredcites →https://doi.org/10.1016/j.molcel.2015.02.002openalex-snapshot

High-Resolution Chromatin Dynamics during a Yeast Stress Response

inferredcites →https://doi.org/10.1016/j.molp.2016.04.003openalex-snapshot

SWR1 Chromatin-Remodeling Complex Subunits and H2A.Z Have Non-overlapping Functions in Immunity and Gene Regulation in Arabidopsis

inferredcites →https://doi.org/10.1016/j.molp.2017.09.007openalex-snapshot

H2A.Z Represses Gene Expression by Modulating Promoter Nucleosome Structure and Enhancer Histone Modifications in Arabidopsis

inferredcites →https://doi.org/10.1038/38444openalex-snapshot

Crystal structure of the nucleosome core particle at 2.8 Å resolution

inferredcites →https://doi.org/10.1038/embor.2010.186openalex-snapshot

Chromatin modification acts as a memory for systemic acquired resistance in the plant stress response

inferredcites →https://doi.org/10.1038/nature01080openalex-snapshot

Active genes are tri-methylated at K4 of histone H3

inferredcites →https://doi.org/10.1038/nature07324openalex-snapshot

Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks

inferredcites →https://doi.org/10.1038/ncomms12284openalex-snapshot

Writing of H3K4Me3 overcomes epigenetic silencing in a sustained but context-dependent manner

inferredcites →https://doi.org/10.1038/ncomms1732openalex-snapshot

Multiple exposures to drought 'train' transcriptional responses in Arabidopsis

inferredcites →https://doi.org/10.1038/nmeth.1906openalex-snapshot

ChromHMM: automating chromatin-state discovery and characterization

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nprot.2012.016openalex-snapshot

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

inferredcites →https://doi.org/10.1038/nrm3941openalex-snapshot

Histone exchange, chromatin structure and the regulation of transcription

inferredcites →https://doi.org/10.1038/s41598-017-09680-6openalex-snapshot

Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation

inferredcites →https://doi.org/10.1038/srep15708openalex-snapshot

The histone deacetylase HDA19 controls root cell elongation and modulates a subset of phosphate starvation responses in Arabidopsis

inferredcites →https://doi.org/10.1046/j.1469-8137.2003.00695.xopenalex-snapshot

Phosphorus acquisition and use: critical adaptations by plants for securing a nonrenewable resource

inferredcites →https://doi.org/10.1071/s96047openalex-snapshot

Soil phosphorus: its measurement, and its uptake by plants

inferredcites →https://doi.org/10.1073/pnas.082249499openalex-snapshot

Methylation of histone H3 Lys 4 in coding regions of active genes

inferredcites →https://doi.org/10.1073/pnas.1010478107openalex-snapshot

SET DOMAIN GROUP2 is the major histone H3 lysine 4 trimethyltransferase in Arabidopsis

inferredcites →https://doi.org/10.1073/pnas.1816991115openalex-snapshot

Leucine-rich repeat extensin proteins regulate plant salt tolerance in Arabidopsis

inferredcites →https://doi.org/10.1093/bioinformatics/bti551openalex-snapshot

BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks

inferredcites →https://doi.org/10.1093/bioinformatics/btp340openalex-snapshot

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

inferredcites →https://doi.org/10.1093/bioinformatics/btp479openalex-snapshot

CEAS: cis-regulatory element annotation system

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/glycob/cww029openalex-snapshot

Cell wall integrity signaling in plants: “To grow or not to grow that's the question”

inferredcites →https://doi.org/10.1093/jxb/ery244openalex-snapshot

Rice H2A.Z negatively regulates genes responsive to nutrient starvation but promotes expression of key housekeeping genes

inferredcites →https://doi.org/10.1093/mp/ssp019openalex-snapshot

The Beauty of Being a Variant: H2A.Z and the SWR1 Complex in Plants

inferredcites →https://doi.org/10.1093/mp/sst018openalex-snapshot

Genome-Wide Analysis of Histone Modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica

inferredcites →https://doi.org/10.1093/nar/gkw257openalex-snapshot

deepTools2: a next generation web server for deep-sequencing data analysis

inferredcites →https://doi.org/10.1093/pcp/pcj072openalex-snapshot

Dynamic and Reversible Changes in Histone H3-Lys4 Methylation and H3 Acetylation Occurring at Submergence-inducible Genes in Rice

inferredcites →https://doi.org/10.1093/pcp/pcn133openalex-snapshot

Alterations of Lysine Modifications on the Histone H3 N-Tail under Drought Stress Conditions in Arabidopsis thaliana

inferredcites →https://doi.org/10.1093/pcp/pcx048openalex-snapshot

FERONIA Receptor Kinase at the Crossroads of Hormone Signaling and Stress Responses

inferredcites →https://doi.org/10.1093/pcp/pcz095openalex-snapshot

Salt-Responsive Genes are Differentially Regulated at the Chromatin Levels Between Seedlings and Roots in Rice

inferredcites →https://doi.org/10.1101/gad.194209.112openalex-snapshot

Cfp1 integrates both CpG content and gene activity for accurate H3K4me3 deposition in embryonic stem cells

inferredcites →https://doi.org/10.1104/pp.109.145532openalex-snapshot

Histone H2A.Z Regulates the Expression of Several Classes of Phosphate Starvation Response Genes But Not as a Transcriptional Activator

inferredcites →https://doi.org/10.1104/pp.110.166520openalex-snapshot

Coexpression-Based Clustering of Arabidopsis Root Genes Predicts Functional Modules in Early Phosphate Deficiency Signaling

inferredcites →https://doi.org/10.1104/pp.15.01336openalex-snapshot

Arabidopsis PHL2 and PHR1 Act Redundantly as the Key Components of the Central Regulatory System Controlling Transcriptional Responses to Phosphate Starvation

inferredcites →https://doi.org/10.1104/pp.16.01944openalex-snapshot

ATX3, ATX4, and ATX5 Encode Putative H3K4 Methyltransferases and Are Critical for Plant Development

inferredcites →https://doi.org/10.1104/pp.17.00413openalex-snapshot

Dynamic Cytology and Transcriptional Regulation of Rice Lamina Joint Development

inferredcites →https://doi.org/10.1105/tpc.106.048447openalex-snapshot

Repression of Flowering in Arabidopsis Requires Activation of FLOWERING LOCUS C Expression by the Histone Variant H2A.Z

inferredcites →https://doi.org/10.1105/tpc.113.117325openalex-snapshot

Spatio-Temporal Transcript Profiling of Rice Roots and Shoots in Response to Phosphate Starvation and Recovery

inferredcites →https://doi.org/10.1105/tpc.16.00573openalex-snapshot

Dual Role of the Histone Variant H2A.Z in Transcriptional Regulation of Stress-Response Genes

inferredcites →https://doi.org/10.1105/tpc.17.00867openalex-snapshot

The Chromatin Remodelers PKL and PIE1 Act in an Epigenetic Pathway That Determines H3K27me3 Homeostasis in Arabidopsis

inferredcites →https://doi.org/10.1111/j.1365-313x.2010.04375.xopenalex-snapshot

Dissection of local and systemic transcriptional responses to phosphate starvation in Arabidopsis

inferredcites →https://doi.org/10.1111/j.1365-313x.2011.04534.xopenalex-snapshot

The Arabidopsis trithorax‐like factor ATX1 functions in dehydration stress responses via ABA‐dependent and ABA‐independent pathways

inferredcites →https://doi.org/10.1111/nph.12194openalex-snapshot

ALFIN ‐ LIKE 6 is involved in root hair elongation during phosphate deficiency in Arabidopsis

inferredcites →https://doi.org/10.1111/nph.15306openalex-snapshot

Epigenetic regulation of anthocyanin biosynthesis by an antagonistic interaction between H2A.Z and H3K4me3

inferredcites →https://doi.org/10.1111/tpj.13381openalex-snapshot

Differential deposition of H2A.Z in combination with histone modifications within related genes in Oryza sativa callus and seedling

inferredcites →https://doi.org/10.1126/science.aal2541openalex-snapshot

The receptor kinase FER is a RALF-regulated scaffold controlling plant immune signaling

inferredcites →https://doi.org/10.1155/2008/420747openalex-snapshot

Genevestigator V3: A Reference Expression Database for the Meta‐Analysis of Transcriptomes

inferredcites →https://doi.org/10.1186/1471-2105-14-91openalex-snapshot

A comparison of methods for differential expression analysis of RNA-seq data

inferredcites →https://doi.org/10.1186/1471-2164-15-284openalex-snapshot

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

inferredcites →https://doi.org/10.1186/1471-2229-10-238openalex-snapshot

Dynamic changes in genome-wide histone H3 lysine 4 methylation patterns in response to dehydration stress in Arabidopsis thaliana

inferredcites →https://doi.org/10.1186/1939-8433-6-4openalex-snapshot

Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data

inferredcites →https://doi.org/10.1186/gb-2009-10-6-r62openalex-snapshot

Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana

inferredcites →https://doi.org/10.1186/s12864-017-4172-xopenalex-snapshot

Chromatin states responsible for the regulation of differentially expressed genes under 60Co~γ ray radiation in rice

inferredcites →https://doi.org/10.1186/s12864-017-4397-8openalex-snapshot

Rice nucleosome patterns undergo remodeling coincident with stress-induced gene expression

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1186/s13059-019-1731-2openalex-snapshot

Cold stress induces enhanced chromatin accessibility and bivalent histone modifications H3K4me3 and H3K27me3 of active genes in potato

inferredcites →https://doi.org/10.1242/dev.152868openalex-snapshot

H2A.Z promotes the transcription of MIR156A and MIR156C in Arabidopsis by facilitating the deposition of H3K4me3

inferredcites →https://doi.org/10.1371/journal.pbio.0030328openalex-snapshot

Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae

inferredcites →https://doi.org/10.1371/journal.pgen.1002952openalex-snapshot

Two Distinct Repressive Mechanisms for Histone 3 Lysine 4 Methylation through Promoting 3′-End Antisense Transcription

inferredcites →https://doi.org/10.1371/journal.pgen.1002988openalex-snapshot

Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes

inferredcites →https://doi.org/10.1586/14789450.2.5.719openalex-snapshot

Histone structure and nucleosome stability

inferredcites →https://doi.org/10.3389/fgene.2019.00306openalex-snapshot

Chromatin State-Based Analysis of Epigenetic H3K4me3 Marks of Arabidopsis in Response to Dark Stress

inferredcites →https://doi.org/10.3389/fpls.2017.00037openalex-snapshot

A Comprehensive Analysis of RALF Proteins in Green Plants Suggests There Are Two Distinct Functional Groups

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s00425-020-03520-0openalex-snapshot

H3K4 trimethylation dynamics impact diverse developmental and environmental responses in plants

inferred← citeshttps://doi.org/10.1016/j.gene.2021.145742openalex-snapshot

Expression of potential reference genes in response to macronutrient stress in rice and soybean

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