H1 is necessary for stable repression of <i>Oct4</i> pluripotency gene during embryogenesis and ESC differentiation.

<p>(A) Elevated <i>Oct4</i> expression and hypomethylation of CpG sites at <i>Oct4</i> promoters in H1 TKO embryos compared with littermates at E8.5. (i) qRT-PCR analysis of mRNA expression levels of <i>Oct4</i>. Values are means ± SEM, n = 5 for each genotype. Expression levels were normalized over <i>GAPDH</i>. *: P<0.05. (ii) Bisulfite sequencing analysis of DNA methylation status at <i>Oct4</i> promoter regions. Results of two wild-type and two knockout E8.5 embryos are shown. The positions of CpG sites analyzed are depicted schematically as vertical ticks on the line. TSS: transcription start site. (iii) Percentage of methylated CpG sites at <i>Oct4</i> promoter regions in WT and H1 TKO embryos. Statistical analysis was performed using Fisher's exact test. ***: P<0.001; ****: P<0.0001. (B) Analysis of expression and epigenetic marks at <i>Oct4</i> pluripotency gene during EB differentiation in rotary suspension culture. Analyses of expression (i), DNA methylation (ii), % of mCpG (iii); and occupancy of H1 and three histone marks (iv) of <i>Oct4</i> in WT, H1 TKO and RES cells during EB differentiation. Relative expression levels were normalized over <i>GAPDH</i>. Relative fold enrichment is calculated by normalizing the qChIP values (as described in Material and Methods) of ESCs (day 0) or EBs at each time point by that of WT ESCs (WT D0). Values are presented as mean ± S.D. *: P<0.05; **: P<0.01; ***: P<0.001. (C) Model for H1 in repression of <i>Oct4</i> during ESC differentiation. ESCs have low H1 content with an relatively “open” chromatin. During differentiation, total H1 content increases, which facilitates local chromatin compaction at <i>Oct4</i> gene and contributes to establishment and/or maintenance of epigenetic changes necessary for stable silencing of <i>Oct4</i> pluripotency gene.</p

H1c/H1d/H1e triple knockout ESCs are impaired in EB differentiation.

<p>(A) Hematoxylin and eosin (H&E) staining of sections of WT EBs (top panels) and H1 TKO EBs (bottom panels) at 7 days, 10 days and 14 days in rotary suspension culture. High magnification images of H&E staining of sections of WT EB (top right) and H1 TKO EBs (bottom right) show that TKO EBs failed to cavitate. WT EBs showed more differentiated morphologies with cysts forming (black arrows). (B) Quantitative RT-PCR analysis of mRNA expression levels of <i>AFP</i> in ESCs (day 0) and EBs throughout 14 days of rotary suspension culture. Data were normalized over the expression level of <i>GAPDH</i> and are presented as average ± S.D. (C) Hierarchical clustering analysis of qRT-PCR SuperArray gene expression profiling of ESCs (day 0) and EBs (day 10) formed from WT and H1 TKO ESCs. Red, green or black represent higher, lower, or no change in relative expression. (D) Scatter Plot analysis of gene expression comparisons of: (i) WT <i>vs.</i> H1 TKO ESCs (day 0); (ii) WT EBs (day 10) <i>vs.</i> WT ESCs (day 0); (iii) H1 TKO EBs (day 10) <i>vs.</i> H1 TKO ESCs (day 0). X- and y- axes are delta CTs using <i>GAPDH</i> to normalize. Genes with more than 2-fold differences lie outside of the blue lines.</p

Loss of H1c/H1d/H1e inhibits spontaneous ESC differentiation.

<p>(A) Western blot analysis of OCT4 level in WT and H1 TKO ESCs cultured under indicated conditions for 2 days. (B) Phase images of WT and H1 TKO ESCs cultured either on MEF with LIF (left panel), gelatin coated plate with LIF (middle panel), or gelatin coated plate without LIF (right panel) for 2 days. Scale bar: 100 µm. (C) Growth curves of WT and H1 TKO ESCs cultured on gelatin coated plate with or without LIF. Data are presented as average ± S.D.</p

Expression profiles of linker histones in WT and H1 TKO cultures during EB differentiation.

<p>(A) Reverse-phase HPLC and Mass Spectrometry (inset) analysis of histones from WT and H1 TKO ESCs. X axis: elution time; Y axis: absorbency at A₂₁₄. mAU, milli-absorbency units. Inset shows the relative signal intensity of H1d and H1e mass spectral peaks in the H1d/H1e fraction collected from HPLC eluates of WT histones. (B,C) H1/nucleosome ratio of the total H1 (B) and individual H1 subtype (C) during EB formation and differentiation. Day 0, day 7 and day 10 of EB cultures were collected and HPLC analyses as shown in (A) were performed. The ratio of total H1 (or individual H1 subtype) to nucleosome was calculated as described in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002691#s4" target="_blank">Materials and Methods</a>. Values are means ± S.D., n = 4. *: P<0.05; **: P<0.01; ***: P<0.001; ****: P<0.0001.</p

H1 TKO ESCs fail to undergo neural differentiation.

<p>(A) Neural differentiation scheme for ESCs. (B) Characterization of WT and H1 TKO cultures on day 6+7 under neural differentiation protocol. i). Phase contrast images shows that H1 TKO mutants were unable to adequately form neurites and neural networks. Right panels: zoom-in images of the areas encircled with black rectangles. Scale bar: 100 µm (left panels) and 50 µm (right panels). ii). Left panel: Percentage of neurite-forming EBs. Numbers were averaged from 6 experiments. 80 EBs were counted per experiment. Right panel: Numbers of neurites per neurite-forming EB. Number of neurites was counted from EBs that produced neurites. 58 and 28 neurite-forming EBs from respective WT and TKO were selected and counted for neurite numbers. **: P<0.01; ****: P<0.0001. iii). Immunostaining for expression of TUBB3 and GFAP. Nuclei were stained with Hoechst 33342. Scale bars: 50 µm (left panels) and 20 µm (right panels). Results are representative of three independent experiments. (C) H1 TKO ESCs were unable to adequately repress the pluripotency genes and to efficiently induce the expression of neural genes. Expression levels of pluripotency genes (<i>Oct4</i> and <i>Nanog</i>), neural marker (<i>Nestin</i>), neuronal marker (<i>Tyrosine hydroxylase (TH)</i>), astrocyte marker (<i>GFAP</i>) from WT and H1 TKO cultures at indicated days in differentiation cultures were determined by qRT-PCR. Data were normalized over the expression level of <i>GAPDH</i> and are presented as average ± S.D.</p

High-Resolution Mapping of H1 Linker Histone Variants in Embryonic Stem Cells

<div><p>H1 linker histones facilitate higher-order chromatin folding and are essential for mammalian development. To achieve high-resolution mapping of H1 variants H1d and H1c in embryonic stem cells (ESCs), we have established a knock-in system and shown that the N-terminally tagged H1 proteins are functionally interchangeable to their endogenous counterparts <i>in vivo</i>. H1d and H1c are depleted from GC- and gene-rich regions and active promoters, inversely correlated with H3K4me3, but positively correlated with H3K9me3 and associated with characteristic sequence features. Surprisingly, both H1d and H1c are significantly enriched at major satellites, which display increased nucleosome spacing compared with bulk chromatin. While also depleted at active promoters and enriched at major satellites, overexpressed H1⁰ displays differential binding patterns in specific repetitive sequences compared with H1d and H1c. Depletion of H1c, H1d, and H1e causes pericentric chromocenter clustering and de-repression of major satellites. These results integrate the localization of an understudied type of chromatin proteins, namely the H1 variants, into the epigenome map of mouse ESCs, and we identify significant changes at pericentric heterochromatin upon depletion of this epigenetic mark.</p> </div

H1 depletion leads to chromocenter clustering.

<p>(A) Typical images of WT (top), H1 TKO (middle), and RES ESCs (bottom) of FISH with a major satellite probe (left), DNA stain DAPI (middle), and merged images (right). Scale bar: 10 µm. (B) Box plots of chromocenter numbers in the nuclei of WT, H1 TKO, and RES ESCs. The line in the box indicates the median, while the bottom and top of the boxes are the 25^th and 75^th percentiles, respectively. ****: P<0.000001.</p

Generation of H1d^FLAG knock-in ESCs.

<p>(A) Schematic representation of the H1d^FLAG targeting construct and the knock-in strategy for insertion of the FLAG tag at N-terminus of the endogenous H1d gene. (B) Identification of ESC clones containing the modified FLAG-H1d allele. DNA isolated from Blasticidin resistant ESC clones were analyzed by Southern blotting. <i>Cis vs. trans</i> configurations of the homologous recombination events are schematically illustrated in the diagram above the Southern blotting image. (C) Reverse phase HPLC profiles of histone extracts from ce^het (left panel) and <i>cis</i>-targeted H1d^FLAG ESCs (right panel). mU, milliunits of absorbency at 214 nm. (D) Coomassie staining and Western blotting analysis of individual H1 fractions eluted from HPLC of histone extracts of ce^het (1) and H1d^FLAG (2) ESCs. (E) Calculated ratio of each H1 variant (and total H1) to nucleosome of ce^het and H1d^FLAG ESCs.</p

Increased nucleosome repeat length at major satellite repeats in ESCs.

<p>(A) Nucleosome repeat length analyses of bulk chromatin (left), major satellite sequences (middle) and minor satellite sequences (right) in WT ESCs. DNA isolated from ESC nuclei digested with MNase at different time points were analyzed by ethidium bromide (EB) –stained gel (left), transferred to membrane which was sequentially probed with major satellites (middle) and minor satellites (right) using Southern blotting. The positions of di-nucleosomes with 10-minute MNase digestion are marked by *. The dashed line indicates di-nucleosome position of major satellites, which is higher than that of bulk chromatin and minor satellites. (B) The NRLs were calculated from the images presented in (A) by extrapolating the corresponding curves to time “0” as described <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003417#pgen.1003417-Gilbert2" target="_blank">[72]</a>.</p

H1 depletion leads to increased expression of major satellite repeats independent of multiple epigenetic marks.

<p>(A) Analyses of expression of selected repeats in WT, H1 TKO, and RES ESCs by qRT-PCR. Data are represented as mean +/− S. D.. *: P<0.05; **: P<0.01. (B) qChIP analysis of three repressive histone marks and one active histone mark at selected repetitive sequences in WT and H1 TKO ESCs. Dashed lines indicate the highest level of signals detected by qChIP with IgG antibody. (C) Bisulfite sequencing analysis (i) and percent of methylated CpG (ii) of major, minor satellite sequences. The positions of CpG sites analyzed are marked as vertical ticks on the line.</p