A Specialized Histone H1 Variant Is Required for Adaptive Responses to Complex Abiotic Stress and Related DNA Methylation in Arabidopsis.

PubWeight™: 0.85‹?›

🔗 View Article (PMC 4634048)

Published in Plant Physiol on September 08, 2015

Authors

Kinga Rutowicz1, Marcin Puzio1, Joanna Halibart-Puzio1, Maciej Lirski1, Maciej Kotliński1, Magdalena A Kroteń1, Lukasz Knizewski1, Bartosz Lange1, Anna Muszewska1, Katarzyna Śniegowska-Świerk1, Janusz Kościelniak1, Roksana Iwanicka-Nowicka1, Krisztián Buza1, Franciszek Janowiak1, Katarzyna Żmuda1, Indrek Jõesaar1, Katarzyna Laskowska-Kaszub1, Anna Fogtman1, Hannes Kollist1, Piotr Zielenkiewicz1, Jerzy Tiuryn1, Paweł Siedlecki1, Szymon Swiezewski1, Krzysztof Ginalski1, Marta Koblowska1, Rafał Archacki1, Bartek Wilczynski1, Marcin Rapacz1, Andrzej Jerzmanowski2

Author Affiliations

1: Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.).
2: Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.) andyj@ibb.waw.pl.

Articles citing this

Histone H1 Variants in Arabidopsis Are Subject to Numerous Post-Translational Modifications, Both Conserved and Previously Unknown in Histones, Suggesting Complex Functions of H1 in Plants. PLoS One (2016) 0.77

Characterization of DNA methyltransferase and demethylase genes in Fragaria vesca. Mol Genet Genomics (2016) 0.77

BRR2a Affects Flowering Time via FLC Splicing. PLoS Genet (2016) 0.76

The Histone Deacetylase Complex 1 Protein of Arabidopsis Has the Capacity to Interact with Multiple Proteins Including Histone 3-Binding Proteins and Histone 1 Variants. Plant Physiol (2016) 0.75

Crop epigenetics and the molecular hardware of genotype × environment interactions. Front Plant Sci (2015) 0.75

Seed Production Affects Maternal Growth and Senescence in Arabidopsis. Plant Physiol (2016) 0.75

Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression. Nucleic Acids Res (2017) 0.75

Concerted Flexibility of Chromatin Structure, Methylome, and Histone Modifications along with Plant Stress Responses. Biology (Basel) (2017) 0.75

Chromatin and epigenetics in all their states: Meeting report of the first conference on Epigenetic and Chromatin Regulation of Plant Traits - January 14 - 15, 2016 - Strasbourg, France. Epigenetics (2016) 0.75

Plant Stress Responses and Phenotypic Plasticity in the Epigenomics Era: Perspectives on the Grapevine Scenario, a Model for Perennial Crop Plants. Front Plant Sci (2017) 0.75

Phylogeny-Based Systematization of Arabidopsis Proteins with Histone H1 Globular Domain. Plant Physiol (2017) 0.75

Multilevel Regulation of Abiotic Stress Responses in Plants. Front Plant Sci (2017) 0.75

Articles cited by this

(truncated to the top 100)

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J (1998) 97.93

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature (2000) 70.33

Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol (1993) 64.61

WebLogo: a sequence logo generator. Genome Res (2004) 59.58

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol (2010) 53.37

Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng (1997) 38.38

Predicting coiled coils from protein sequences. Science (1991) 38.18

MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol (2013) 34.34

GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol (2004) 19.29

CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res (2010) 19.07

A gene expression map of Arabidopsis thaliana development. Nat Genet (2005) 17.39

SMART 5: domains in the context of genomes and networks. Nucleic Acids Res (2006) 17.13

Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol (2006) 12.96

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res (2011) 10.82

agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res (2010) 10.53

Role of transposable elements in heterochromatin and epigenetic control. Nature (2004) 10.51

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics (2009) 9.81

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics (2011) 9.79

The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J (2007) 8.09

3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics (2003) 7.99

Ancestral polyploidy in seed plants and angiosperms. Nature (2011) 7.00

Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet (2009) 6.50

Histone H1 depletion in mammals alters global chromatin structure but causes specific changes in gene regulation. Cell (2005) 6.17

Improved prediction of protein side-chain conformations with SCWRL4. Proteins (2009) 5.67

Crystal structure of globular domain of histone H5 and its implications for nucleosome binding. Nature (1993) 4.81

Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins. Mol Cell Biol (2004) 4.41

Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem (1994) 4.36

Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell. Ann Bot (2008) 4.15

KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics (2006) 4.15

CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics (2004) 4.14

Microarray expression analyses of Arabidopsis guard cells and isolation of a recessive abscisic acid hypersensitive protein phosphatase 2C mutant. Plant Cell (2004) 3.85

Accurate formula for P-values of gapped local sequence and profile alignments. J Mol Biol (2000) 3.51

The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell (2013) 3.27

PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics (2003) 3.23

ABA-mediated transcriptional regulation in response to osmotic stress in plants. J Plant Res (2011) 2.98

Transcription factor control of asymmetric cell divisions that establish the stomatal lineage. Nature (2006) 2.91

The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis. Genes Dev (1998) 2.41

Fast chromatin immunoprecipitation assay. Nucleic Acids Res (2006) 2.39

Network of dynamic interactions between histone H1 and high-mobility-group proteins in chromatin. Mol Cell Biol (2004) 2.33

Differential expression of two P5CS genes controlling proline accumulation during salt-stress requires ABA and is regulated by ABA1, ABI1 and AXR2 in Arabidopsis. Plant J (1997) 2.13

Plant development. Signals from mature to new leaves. Nature (2001) 2.04

Characterization of somatic cell nuclear reprogramming by oocytes in which a linker histone is required for pluripotency gene reactivation. Proc Natl Acad Sci U S A (2010) 2.01

MORC family ATPases required for heterochromatin condensation and gene silencing. Science (2012) 1.97

Mapping the interaction surface of linker histone H1(0) with the nucleosome of native chromatin in vivo. Nat Struct Mol Biol (2006) 1.94

Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment. Proteins (2003) 1.87

Detecting distant homology with Meta-BASIC. Nucleic Acids Res (2004) 1.86

A unified phylogeny-based nomenclature for histone variants. Epigenetics Chromatin (2012) 1.82

Citrullination regulates pluripotency and histone H1 binding to chromatin. Nature (2014) 1.81

Determinants of histone H1 mobility and chromatin binding in living cells. Nat Struct Mol Biol (2006) 1.64

Nucleotide sequence and spatial expression pattern of a drought- and abscisic Acid-induced gene of tomato. Plant Physiol (1991) 1.62

The embryonic linker histone H1 variant of Drosophila, dBigH1, regulates zygotic genome activation. Dev Cell (2013) 1.60

Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin-remodeling factors. J Biol Chem (2002) 1.51

The stomatal response to reduced relative humidity requires guard cell-autonomous ABA synthesis. Curr Biol (2012) 1.48

Histone H1 binding is inhibited by histone variant H3.3. EMBO J (2009) 1.47

H1 histones: current perspectives and challenges. Nucleic Acids Res (2013) 1.35

AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol (2009) 1.33

Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression. Plant Mol Biol (2010) 1.33

Histone h1 depletion impairs embryonic stem cell differentiation. PLoS Genet (2012) 1.32

Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC Genomics (2007) 1.29

Dissecting the binding mechanism of the linker histone in live cells: an integrated FRAP analysis. EMBO J (2010) 1.29

Dynamic changes in genome-wide histone H3 lysine 4 methylation patterns in response to dehydration stress in Arabidopsis thaliana. BMC Plant Biol (2010) 1.28

Photosynthetic redox control of nuclear gene expression. J Exp Bot (2005) 1.26

Stomatal development: a plant's perspective on cell polarity, cell fate transitions and intercellular communication. Development (2012) 1.25

Genetic manipulation of stomatal density influences stomatal size, plant growth and tolerance to restricted water supply across a growth carbon dioxide gradient. Philos Trans R Soc Lond B Biol Sci (2012) 1.25

Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production. Plant J (2012) 1.24

Arabidopsis transcriptome reveals control circuits regulating redox homeostasis and the role of an AP2 transcription factor. Plant Physiol (2008) 1.21

Organ-Specific and Environmentally Regulated Expression of Two Abscisic Acid-Induced Genes of Tomato : Nucleotide Sequence and Analysis of the Corresponding cDNAs. Plant Physiol (1991) 1.19

Multifunctionality of the linker histones: an emerging role for protein-protein interactions. Cell Res (2010) 1.15

High-resolution mapping of h1 linker histone variants in embryonic stem cells. PLoS Genet (2013) 1.11

Suppression of histone H1 genes in Arabidopsis results in heritable developmental defects and stochastic changes in DNA methylation. Genetics (2004) 1.09

Histone modifications and expression of light-regulated genes in Arabidopsis are cooperatively influenced by changing light conditions. Plant Physiol (2008) 1.08

H1 linker histone promotes epigenetic silencing by regulating both DNA methylation and histone H3 methylation. Proc Natl Acad Sci U S A (2013) 1.08

Arabidopsis chromatin-associated HMGA and HMGB use different nuclear targeting signals and display highly dynamic localization within the nucleus. Plant Cell (2006) 1.05

The genomic landscape of the somatic linker histone subtypes H1.1 to H1.5 in human cells. Cell Rep (2013) 1.04

Molecular dynamics of histone H1. Biochem Cell Biol (2009) 1.03

A drought-stress-inducible histone gene in Arabidopsis thaliana is a member of a distinct class of plant linker histone variants. Plant Mol Biol (1997) 1.03

Chromatin reprogramming during the somatic-to-reproductive cell fate transition in plants. Development (2013) 1.01

Molecular genetic analysis of the drought-inducible linker histone variant in Arabidopsis thaliana. Plant Mol Biol (1999) 0.98

Photoreceptors CRYTOCHROME2 and phytochrome B control chromatin compaction in Arabidopsis. Plant Physiol (2010) 0.97

The histone-like protein H1-S and the response of tomato leaves to water deficit. J Exp Bot (2003) 0.97

ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments. Biochem Biophys Res Commun (2012) 0.96

Genome-wide profiling of histone H3K4-tri-methylation and gene expression in rice under drought stress. Plant Mol Biol (2012) 0.95

Environmental control of plant nuclear gene expression by chloroplast redox signals. Front Plant Sci (2012) 0.93

Effects of salt secretion on psychrometric determinations of water potential of cotton leaves. Plant Physiol (1968) 0.93

The H1 histone variant of tomato, H1-S, is targeted to the nucleus and accumulates in chromatin in response to water-deficit stress. Planta (2000) 0.92

Genome-wide quantitative identification of DNA differentially methylated sites in Arabidopsis seedlings growing at different water potential. PLoS One (2013) 0.91

Temperature dependence of violaxanthin de-epoxidation and non-photochemical fluorescence quenching in intact leaves of Gossypium hirsutum L. and Malva parviflora L. Planta (1991) 0.91

Epigenetic memory for stress response and adaptation in plants. Plant Cell Physiol (2014) 0.91

Histone H1 affects gene imprinting and DNA methylation in Arabidopsis. Plant J (2012) 0.89

Structure and characterization of a putative drought-inducible H1 histone gene. Plant Mol Biol (1996) 0.88

Evidence for a dynamic role of the linker histone variant H1x during retinoic acid-induced differentiation of NT2 cells. FEBS Lett (2010) 0.86

Subnuclear distribution of the entire complement of linker histone variants in Arabidopsis thaliana. Chromosoma (1999) 0.85

Chromatin proteins: key responders to stress. PLoS Biol (2012) 0.85

Characterization of three mRNAs that accumulate in wilted tomato leaves in response to elevated levels of endogenous abscisic acid. Planta (1990) 0.84

Cell differentiation and development in Arabidopsis are associated with changes in histone dynamics at the single-cell level. Plant Cell (2014) 0.84

Retrograde signaling from functionally heterogeneous plastids. Front Plant Sci (2012) 0.81

Meta-analysis of retrograde signaling in Arabidopsis thaliana reveals a core module of genes embedded in complex cellular signaling networks. Mol Plant (2014) 0.81

The "drought-inducible" histone H1s of tobacco play no role in male sterility linked to alterations in H1 variants. Planta (2002) 0.81

Expression of enzymes involved in chlorophyll catabolism in Arabidopsis is light controlled. Plant Physiol (2011) 0.81