Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
PLoS One
2011 Jan 01;67:e22548. doi: 10.1371/journal.pone.0022548.
Show Gene links
Show Anatomy links
Stage-specific histone modification profiles reveal global transitions in the Xenopus embryonic epigenome.
Schneider TD
,
Arteaga-Salas JM
,
Mentele E
,
David R
,
Nicetto D
,
Imhof A
,
Rupp RA
.
???displayArticle.abstract???
Vertebrate embryos are derived from a transitory pool of pluripotent cells. By the process of embryonic induction, these precursor cells are assigned to specific fates and differentiation programs. Histone post-translational modifications are thought to play a key role in the establishment and maintenance of stable gene expression patterns underlying these processes. While on gene level histone modifications are known to change during differentiation, very little is known about the quantitative fluctuations in bulk histone modifications during development. To investigate this issue we analysed histones isolated from four different developmental stages of Xenopus laevis by mass spectrometry. In toto, we quantified 59 modification states on core histones H3 and H4 from blastula to tadpole stages. During this developmental period, we observed in general an increase in the unmodified states, and a shift from histone modifications associated with transcriptional activity to transcriptionally repressive histone marks. We also compared these naturally occurring patterns with the histone modifications of murine ES cells, detecting large differences in the methylation patterns of histone H3 lysines 27 and 36 between pluripotent ES cells and pluripotent cells from Xenopus blastulae. By combining all detected modification transitions we could cluster their patterns according to their embryonic origin, defining specific histone modification profiles (HMPs) for each developmental stage. To our knowledge, this data set represents the first compendium of covalent histone modifications and their quantitative flux during normogenesis in a vertebrate model organism. The HMPs indicate a stepwise maturation of the embryonic epigenome, which may be causal to the progressing restriction of cellular potency during development.
???displayArticle.pubmedLink???
21814581
???displayArticle.pmcLink???PMC3142184 ???displayArticle.link???PLoS One
Figure 1. Histone modification profiling for Xenopus embryogenesis.A) Time line of Xenopus laevis embryonic development – NF stages according to Nieuwkoop and Faber [25] and by hours after fertilization (hpf). The stages selected for mass spec analysis are characterized by the following embryonic and cellular features: Blastula (NF9) naivé/multipotent cells; Gastrula (NF12) germ layers specified; Neurula (NF18) germ layer patterning and differentiation; Tadpole (NF37) embryonic development completed, larvae hatched. B) Flow chart for quantitative mass spectrometric analysis of histone modifications from normal X. leavis embryos. C) Elution profile of differentially acetylated histone H4 4-17 peptides of X. laevis Blastulae from a reversed-phase C18 micro-column of the LC-MS/MS. Shown are the extracted ion chromatograms at corresponding retention times (x-axis), the y-axis represents the intensity of ion currents of the quadrupole Orbi-Trap mass spectrometer. The areas under the peaks are used for quantification of different modification states of a peptide. X-axis: elution time in minutes. Y-axis: intensity of peptides according to ion current of the quadrupole Mass Spectrometer (unmod = unmodified peptide, 1Ac = monoacetylated, 2Ac = diacetylated, 3Ac = triacetylated, 4Ac = quatruple-acetylated peptides, RT = retention time).
Figure 2. Histone modifications of cell proliferation and active transcription in Xenopus embryos.Bar-Charts showing the relative abundance of histone modifications, identified either by Orbi-Trap LC-MS/MS mass spectrometry (A-D; error bars indicate SD of two independent biological replicates) or MALDI-TOF mass spectrometry (E - error bars indicate SD of three independent biological replicates). Abbreviations: unmod = unmodified peptide, Kac = acetylated lysine residue, Kme1 = mono-methylated, Kme2 = di-methylated, Kme3 = tri-methylated lysine residue. Where applicable, p values are given by numbers above brackets to indicate significant differences in the abundance of a histone modification between samples.
Figure 3. Histone Modifications of transcriptionally repressed chromatin and constitutive heterochromatin in Xenopus embryos.Bar-Charts of repressive lysine methylation states on histone H3K9 and H4K20. A) Data from Orbi-Trap mass spectrometry - error bars: SD of two independent biological replicates. B) Data from MALDI-TOF mass spectrometry - error bars: SD of three independent biological replicates. C) Immunoblotting for total Histone H3 and histone H4 trimethylated at lysine 20. Left panel – western blot Odyssey infrared imaging signals; right panel – bar chart showing increase of H4K20me3 levels relative to total histone H3 protein during development. Abbreviations: unmod = unmodified peptide, Kac = acetylated lysine residue, Kme1 = mono-methylated lysine residue, Kme2 = di-methylated lysine residue, Kme3 = tri-methylated lysine residue. Where applicable, p values are given by numbers above brackets to indicate significant differences in the abundance of a histone modification between samples.
Figure 4. Opposing Histone Modifications on the H3 27-40 peptide in Xenopus embryos.A) Amino-acid sequence of the H3 27-40 peptide and its isobaric modification forms, which have identical mass although beeing differently modified at K27 and K36 residues. Panels B+C - Extracted ion chromatograms (XICs) showing separation of isobaric H3 27–40 peptides from the four Xenopus embryonic stages by differential elution from a C18 micro-column on the reversed-phase HPLC of on-line mass spectrometry. X-axis represents retention time, y-axis the intensity of ion currents in the quadrupole Orbi-Trap mass spectrometer. Peak separation was called by the ICIS peak detection algorithm program (Thermo), indicated here by the vertical black lines. B) XICs of isobaric di-methylated peptides, modified at either K27 or K36. C) XICs of isobaric tri-methylated peptides representing K27me3/K36me3, K27me2+K36me1 and K27me1+K36me2. D) Bar-Chart of H3K27 and K36 modification states. Note that isobaric mono- (data not shown) and tri-methylated peptides, which are methylated either at K27 or K36, elute simultanously and cannot be distinguished. E) Bar-Chart of combinatorial K27/K36-methylated peptides. Abbreviations: unmod = unmodified peptide, me1 = single mono-methylated lysine at position 27 or 36, K27me2 = di-methylated lysine 27, K36me2 = di-methylated lysine 36, Kme3 = single tri-methylated lysine at position 27 or 36, K27me1/K36me1 = double mono-methylated, K27me2/K36me2 = double di-methylated, K27me1/K36me2 = combinatorial triple-methylated peptide with dimethlyted K36, K27me2/K36me1 = combinatorial triple-methylated peptide with dimethlyted K27. Error bars represent SD. Where applicable, p values are given by numbers above brackets to indicate significant differences in the abundance of a histone modification between samples.
Figure 5. Comparison of opposing histone modifications on histone H3 from Xenopus blastulae, murine ES cells and MEFs.A) Bar-Charts showing H3K4 methylation states of X.laevis blastulae, GS-1 ES cells and mouse embryo fibroblasts. Data obtained by MALDI-TOF mass spectrometry, error bars indicate SD of three independent biological replicates. B) XIC profiles of K27me2 and K36me2 modification states of the H3 27–40 peptide of X.laevis blastulae, murine ES Cells and MEFs on a C18 micro-column on a reversed-phase HPLC during Orbi-Trap on-line mass spectrometry. C) XIC profiles for K27/K36me3, K27me2+K36me1 and K27me1+K36me2 of the H3 27–40 peptides from the same samples. In B and C, x-axis gives relative elution times of peptides, the y-axis shows their intensity according to the ion current of the quadrupole Mass Spectrometer. In B and C, X-axis represents retention time, y-axis the intensity of ion currents of the quadrupole Orbi-Trap mass spectrometer. Peak separation was called by the ICIS peak detection algorithm program (Thermo), indicated here by vertical black lines. D) Bar-Chart of mutually exclusive H3K27 and K36 methyl states. E) Bar-Chart of peptides with combinatorial H3K27 and K36 methylation. D and E - data from Orbi-Trap Mass Spectrometry, error bars indicate SEM of two independent biological replicates. F) Immunoblotting for total histone H3 and histone H3 trimethylated at lysine 27. Upper panel – western blot Odyssey infrared imaging signals; lower panel – bar chart showing the abundance of H3K27me3 levels relative to total histone H3 protein in Blastulae (NF9), Tadpoles (NF37) and murine GS-1 ES cells. Abbr.: unmod = unmodified peptide, Kme1 = mono-methylated lysine residue, Kme2 = di-methylated lysine residue, Kme3 = tri-methylated lysine residue. Where applicable, p values are given by numbers above brackets to indicate significant differences in histone modifications between samples.
Figure 6. Stage-specific histone modification profiles.The heatmap visualizes clusters of histone modifications according to their relative abundance at the four developmental stages, which we have investigated. The hierarchical clustering analysis produces a dendrogram, shown on the left side, with four major branches that correspond to specific developmental stages. Modifications associated with transcriptional activity are highlighted in green, while modifications associated with repressed/silent states are shown in magenta. The four clusters define histone modifications profiles (HMPs), which reflect the gradual transition from uncomitted to determined cell fates.
Akkers,
A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos.
2009, Pubmed,
Xenbase
Akkers,
A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos.
2009,
Pubmed
,
Xenbase
Aldiri,
Characterization of the expression pattern of the PRC2 core subunit Suz12 during embryonic development of Xenopus laevis.
2009,
Pubmed
,
Xenbase
Azuara,
Chromatin signatures of pluripotent cell lines.
2006,
Pubmed
Barski,
High-resolution profiling of histone methylations in the human genome.
2007,
Pubmed
Bell,
Transcription-coupled methylation of histone H3 at lysine 36 regulates dosage compensation by enhancing recruitment of the MSL complex in Drosophila melanogaster.
2008,
Pubmed
Bernstein,
A bivalent chromatin structure marks key developmental genes in embryonic stem cells.
2006,
Pubmed
Bernstein,
The mammalian epigenome.
2007,
Pubmed
Bhaumik,
Covalent modifications of histones during development and disease pathogenesis.
2007,
Pubmed
Buszczak,
Drosophila stem cells share a common requirement for the histone H2B ubiquitin protease scrawny.
2009,
Pubmed
Chambeyron,
Nuclear re-organisation of the Hoxb complex during mouse embryonic development.
2005,
Pubmed
Clayton,
Enhanced histone acetylation and transcription: a dynamic perspective.
2006,
Pubmed
Creyghton,
Histone H3K27ac separates active from poised enhancers and predicts developmental state.
2010,
Pubmed
Cui,
Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation.
2009,
Pubmed
Dahl,
Histone H3 lysine 27 methylation asymmetry on developmentally-regulated promoters distinguish the first two lineages in mouse preimplantation embryos.
2010,
Pubmed
Dai,
Global epiproteomic signatures distinguish embryonic stem cells from differentiated cells.
2007,
Pubmed
Das,
CBP/p300-mediated acetylation of histone H3 on lysine 56.
2009,
Pubmed
David,
MesP1 drives vertebrate cardiovascular differentiation through Dkk-1-mediated blockade of Wnt-signalling.
2008,
Pubmed
,
Xenbase
De Robertis,
Spemann's organizer and the self-regulation of embryonic fields.
2009,
Pubmed
,
Xenbase
Garcia,
Organismal differences in post-translational modifications in histones H3 and H4.
2007,
Pubmed
Guenther,
A chromatin landmark and transcription initiation at most promoters in human cells.
2007,
Pubmed
Hajkova,
Chromatin dynamics during epigenetic reprogramming in the mouse germ line.
2008,
Pubmed
Hake,
Histone H3 variants and their potential role in indexing mammalian genomes: the "H3 barcode hypothesis".
2006,
Pubmed
Hammoud,
Distinctive chromatin in human sperm packages genes for embryo development.
2009,
Pubmed
Han,
Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication.
2007,
Pubmed
Heasman,
Patterning the early Xenopus embryo.
2006,
Pubmed
,
Xenbase
Hemberger,
Epigenetic dynamics of stem cells and cell lineage commitment: digging Waddington's canal.
2009,
Pubmed
Jasencakova,
Replication stress interferes with histone recycling and predeposition marking of new histones.
2010,
Pubmed
Jung,
Quantitative mass spectrometry of histones H3.2 and H3.3 in Suz12-deficient mouse embryonic stem cells reveals distinct, dynamic post-translational modifications at Lys-27 and Lys-36.
2010,
Pubmed
Kouzarides,
Chromatin modifications and their function.
2007,
Pubmed
Kurth,
Establishment of mesodermal gene expression patterns in early Xenopus embryos: the role of repression.
2005,
Pubmed
,
Xenbase
Lee,
Stability of histone modifications across mammalian genomes: implications for 'epigenetic' marking.
2009,
Pubmed
Li,
Acetylation of histone H3 lysine 56 regulates replication-coupled nucleosome assembly.
2008,
Pubmed
Loyola,
PTMs on H3 variants before chromatin assembly potentiate their final epigenetic state.
2006,
Pubmed
Maisonneuve,
Bicaudal C, a novel regulator of Dvl signaling abutting RNA-processing bodies, controls cilia orientation and leftward flow.
2009,
Pubmed
,
Xenbase
Meissner,
Epigenetic modifications in pluripotent and differentiated cells.
2010,
Pubmed
Meshorer,
Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells.
2006,
Pubmed
Mikkelsen,
Dissecting direct reprogramming through integrative genomic analysis.
2008,
Pubmed
Mikkelsen,
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.
2007,
Pubmed
Neilson,
Less label, more free: approaches in label-free quantitative mass spectrometry.
2011,
Pubmed
Nicklay,
Analysis of histones in Xenopus laevis. II. mass spectrometry reveals an index of cell type-specific modifications on H3 and H4.
2009,
Pubmed
,
Xenbase
Pasini,
Characterization of an antagonistic switch between histone H3 lysine 27 methylation and acetylation in the transcriptional regulation of Polycomb group target genes.
2010,
Pubmed
Pauler,
H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome.
2009,
Pubmed
Phanstiel,
Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells.
2008,
Pubmed
Pudney,
Establishment of a cell line (XTC-2) from the South African clawed toad, Xenopus laevis.
1973,
Pubmed
,
Xenbase
Rando,
Genome-wide views of chromatin structure.
2009,
Pubmed
Rugg-Gunn,
Distinct histone modifications in stem cell lines and tissue lineages from the early mouse embryo.
2010,
Pubmed
Rupp,
Ubiquitous MyoD transcription at the midblastula transition precedes induction-dependent MyoD expression in presumptive mesoderm of X. laevis.
1991,
Pubmed
,
Xenbase
Scharf,
Every methyl counts--epigenetic calculus.
2011,
Pubmed
Schotta,
A chromatin-wide transition to H4K20 monomethylation impairs genome integrity and programmed DNA rearrangements in the mouse.
2008,
Pubmed
Sharov,
Human ES cell profiling broadens the reach of bivalent domains.
2007,
Pubmed
Shechter,
Analysis of histones in Xenopus laevis. I. A distinct index of enriched variants and modifications exists in each cell type and is remodeled during developmental transitions.
2009,
Pubmed
,
Xenbase
Shimamura,
The assembly of regularly spaced nucleosomes in the Xenopus oocyte S-150 extract is accompanied by deacetylation of histone H4.
1989,
Pubmed
,
Xenbase
Silva,
Capturing pluripotency.
2008,
Pubmed
Snape,
Changes in states of commitment of single animal pole blastomeres of Xenopus laevis.
1987,
Pubmed
,
Xenbase
Sobel,
Conservation of deposition-related acetylation sites in newly synthesized histones H3 and H4.
1995,
Pubmed
Surani,
Genetic and epigenetic regulators of pluripotency.
2007,
Pubmed
Swigut,
H3K27 demethylases, at long last.
2007,
Pubmed
Szutorisz,
Formation of an active tissue-specific chromatin domain initiated by epigenetic marking at the embryonic stem cell stage.
2005,
Pubmed
Taipale,
hMOF histone acetyltransferase is required for histone H4 lysine 16 acetylation in mammalian cells.
2005,
Pubmed
Thomas,
Mass spectrometric characterization of human histone H3: a bird's eye view.
2006,
Pubmed
Tie,
CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing.
2009,
Pubmed
Vastenhouw,
Chromatin signature of embryonic pluripotency is established during genome activation.
2010,
Pubmed
Villar-Garea,
Analysis of histone modifications by mass spectrometry.
2008,
Pubmed
Wardle,
Refinement of gene expression patterns in the early Xenopus embryo.
2004,
Pubmed
,
Xenbase
Waterborg,
Dynamic methylation of alfalfa histone H3.
1993,
Pubmed
Wu,
Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm.
2011,
Pubmed
Wylie,
Vegetal pole cells and commitment to form endoderm in Xenopus laevis.
1987,
Pubmed
,
Xenbase
Xie,
Histone h3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells.
2009,
Pubmed
Young,
Control of the embryonic stem cell state.
2011,
Pubmed
Zhang,
Histone acetylation and deacetylation: identification of acetylation and methylation sites of HeLa histone H4 by mass spectrometry.
2002,
Pubmed