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Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells

Abstract

Transposable elements comprise roughly 40% of mammalian genomes1. They have an active role in genetic variation, adaptation and evolution through the duplication or deletion of genes or their regulatory elements2,3,4, and transposable elements themselves can act as alternative promoters for nearby genes, resulting in non-canonical regulation of transcription5,6. However, transposable element activity can lead to detrimental genome instability7, and hosts have evolved mechanisms to silence transposable element mobility appropriately8,9. Recent studies have demonstrated that a subset of transposable elements, endogenous retroviral elements (ERVs) containing long terminal repeats (LTRs), are silenced through trimethylation of histone H3 on lysine 9 (H3K9me3) by ESET (also known as SETDB1 or KMT1E)10 and a co-repressor complex containing KRAB-associated protein 1 (KAP1; also known as TRIM28)11 in mouse embryonic stem cells. Here we show that the replacement histone variant H3.3 is enriched at class I and class II ERVs, notably those of the early transposon (ETn)/MusD family and intracisternal A-type particles (IAPs). Deposition at a subset of these elements is dependent upon the H3.3 chaperone complex containing α-thalassaemia/mental retardation syndrome X-linked (ATRX)12 and death-domain-associated protein (DAXX)12,13,14. We demonstrate that recruitment of DAXX, H3.3 and KAP1 to ERVs is co-dependent and occurs upstream of ESET, linking H3.3 to ERV-associated H3K9me3. Importantly, H3K9me3 is reduced at ERVs upon H3.3 deletion, resulting in derepression and dysregulation of adjacent, endogenous genes, along with increased retrotransposition of IAPs. Our study identifies a unique heterochromatin state marked by the presence of both H3.3 and H3K9me3, and establishes an important role for H3.3 in control of ERV retrotransposition in embryonic stem cells.

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Figure 1: H3.3 is co‐enriched with H3K9me3 at class I and II ERV‐associated heterochromatin.
Figure 2: DAXX–ATRX is responsible for H3.3 deposition at a subset of ERVs and co‐localizes with ERV‐specific heterochromatic factors.
Figure 3: H3.3 is required for the maintenance of H3K9me3 at specific class I and II ERVs.
Figure 4: Loss of H3.3 leads to ERV derepression.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

The ChIP-seq and RNA-seq data sets have been deposited in the Gene Expression Omnibus under accession number GSE59189.

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Acknowledgements

This work was supported by the Rockefeller University Fund and the Tri-Institutional Stem Cell Initiative. S.J.E. acknowledges funding from EMBO ALTF 1232-2011 and the Cambridge University Herchel Smith Fund. We thank D. Pickett, D. Trono and D. Shinkai for cell lines. We thank A. Goldberg and C. Li for technical assistance and members of the Allis laboratory for helpful discussions.

Author information

Affiliations

Authors

Contributions

S.J.E. and L.A.B. contributed equally to this project. S.J.E. and L.A.B. conceived, performed and interpreted most experiments with guidance from C.D.A. K.-M.N. and N.D contributed to experiments. S.J.E. and L.A.B. wrote the manuscript with input from all authors.

Corresponding authors

Correspondence to Simon J. Elsässer, C. David Allis or Laura A. Banaszynski.

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Competing interests

The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 H3.3 and H3K9me3 correlate within the mouse repetitive ES cell genome.

Related to Fig. 1. Hierarchically (Spearman rank) clustered heat map showing occupancy of histone H3.3 and known heterochromatic histone modification and factors over a comprehensive set of mouse repetitive sequences (see Methods for details). Published data sets used are listed in the Methods section. Data are represented as log2 fold enrichment over matched inputs for each ChIP data set. Repeats with less then 0.01% abundance are omitted.

Extended Data Figure 2 H3.3 and H3K9me3 co‐occupy class I and II ERVs.

Related to Fig. 1. a, Direct comparison of H3.3 enrichment at genic and repetitive sites. Box plot (top) showing enrichment of H3.3 over sets of intervals either representing genic or repetitive elements5 annotated in the reference genome, using inclusive read mapping. H3.3 ChIP was performed using an H3.3 antibody and formaldehyde (FA) crosslinking in H3.3 wild‐type (WT) cell line. H3.3 enrichment is shown as standardized ChIP‐seq read density divided by the standardized input read density on a per‐interval basis. The width of the box is proportional to the number of intervals in each group. TSS, transcription start sites of highly active genes; K27pro, bivalent promoters16. Box plot (bottom) shows the input read density (standardized by scaling to a genome‐wide mean of 1), confirming the even representation of unique and repetitive sequences resulting from the inclusive mapping procedure (see Methods for details). Result of one‐sided Wilcoxon rank sum test against a set of randomly selected genomic intervals (shuffled) is indicated (****P < 0.0001). b, H3K9me3 enrichment at genic and repetitive sites. H3K9me3 ChIP was performed using MNase digestion under native conditions. Box plot (top) showing enrichment of H3K9me3 over sets of intervals either representing genic or repetitive elements analogous to a. Box plot (bottom) shows the input read density analogous to a. Result of one‐sided Wilcoxon rank sum test against a set of randomly selected genomic intervals (shuffled) is indicated (****P < 0.0001). c, Sequential H3.3 and H3K9me3 (re)‐ChIP at genic and repetitive sites. Boxplots showing enrichment of Re‐ChIP inclusive read mapping relative to an input control. Result of one‐sided Wilcoxon rank sum test against a set of randomly selected genomic intervals (shuffled) is indicated (****P < 0.0001). d, Co‐occupancy of H3.3 and H3K9me3 at specific classes of ERVs. H3.3 and H3K9me3 peak intervals were independently intersected with annotated ERVs5 and their co‐occurrences within the same ERV were evaluated. L1Md_F (full) is a subset of L1Md_F, comprising only full length repeats (>5 kb). All pie charts include total number of intervals for each family that had none, (at least) one H3.3 peak (H3.3 only), or H3K9me3 peak(s) (H3K9me3 only), or at least one of each (H3.3+H3K9me3).

Extended Data Figure 3 Generation of H3.3‐isoform‐specific antibodies.

Related to Fig. 1. a, Schematic of amino acid sequence differences for the canonical histones H3.1 and H3.2 versus the histone variant H3.3. H3.3 differs from H3.2 or H3.1 at only 4 or 5 amino acids, positions 31, 87, 89, 90 and 96, as indicated. b, Immunoblot against recombinant histones using the final purified antibody (Millipore 09‐838), confirming specificity of the H3.3‐isoform‐specific antibody. c, ChIP‐qPCR analysis of H3.3 enrichment at various repeat regions in control and H3.3‐knockout ES cells. Error bars represent s.d. from one experiment (n = 3). d, ChIP‐seq enrichment of H3.3 at repetitive regions of the mouse genome in control and H3.3‐knockout ES cells. Data are represented in a heat map of log2 fold enrichment (red) or depletion (blue) over a matched input.

Extended Data Figure 4 H3.3 is enriched in regions flanking ERVs and orphan LTRs.

Related to Fig. 1. a, ChIP‐seq density heat maps for unique sites flanking full‐length IAP ERVs (n = 800) rank ordered by H3K9me3 enrichment. Colour intensity represents normalized and globally scaled tag counts. b, H3.3 (top) and H3K9me3 (bottom) enrichment over regions flanking IAP, ERVK10C, ETn ERVs and L1 elements. H3.3 ChIP‐seq was performed with FA crosslinking, H3K9me3 ChIP‐seq under native conditions. Average profiles were aligned and aggregated at the 5′ and 3′ boundaries of hundreds of annotated elements from standardized unique read count coverage tracks. The profiles are directional with the 5′ ends on the left and 3′ end on the right. c, H3.3 (top) and H3K9me3 (bottom) enrichment over regions flanking single (so‐called orphan) IAP LTRs, ˜500 bp. Orphan LTRs are the result of a recombination event between two LTRs—usually the 3′ and 5′ LTRs of the same ERV—effectively deleting the internal coding sequence. Approximately 600 full‐length LTRs (˜500 bp) enriched in H3.3 and H3K9me3 were identified in the mouse genome and aggregated for the profiles.

Extended Data Figure 5 H3.3 at IAPs is not associated with transcription, DNase I or MNase sensitivity.

Related to Fig. 1. a, Direct comparison of chromatin properties at TSSs of highly expressed genes and IAP ERVs. Box plots showing (from left to right) comparable enrichment of H3.3; DNase I sensitivity; MNase sensitivity; elongating RNAP2 occupancy. MNase data sets are from a recent study, showing H3.3 localizing to MNase hypersentitive regions such as active promoters25. In this study, MNase sensitivity was assessed by sequencing nucleosomes released under mild (‘short’) or extensive (‘long’) MNase digestion conditions; MNase hypersensitive sites were shown to be specifically enriched by mild MNase digestion, whereas long digestion released chromatin more evenly25. b, Comparison of kinetics of H3.3 incorporation26 at the TSS of highly expressed genes and IAP ERVs; as control, a randomized set of intervals is shown.

Extended Data Figure 6 H3.3 and ESET‐dependent H3K9me3 enrichment at IAPs is lost upon differentiation.

Related to Fig. 1. a, b, Comparison of H3.3 (a) and H3K9me3 (b) enrichment at the TSS of highly expressed genes and various repeat classes in ES cells and NPCs using inclusive read mapping. H3.3 ChIP was performed using a genomic knock‐in tagged H3.3B–HA and FA crosslinking12. H3K9me3 ChIP was performed using FA crosslinking17. Enrichment is shown as standardized ChIP‐seq read density divided by the standardized input read density on a per interval basis. Result of one‐sided Wilcoxon signed rank test (NPCs versus ES cells) are shown (**** P < 0.0001; ***P < 0.0005; **P < 0.005; *P < 0.05; no annotation = not significant). c, Levels of H3K9me3 enrichment in control and ESET‐knockout ES cells (top) or control and SUV39h1/2‐knockout ES cells27 (bottom) at various repeat classes. DKO, double knockout. Data are represented as in a and b.

Extended Data Figure 7 Contribution of DAXX, ATRX, KAP1 and ESET to H3.3 enrichment at ERVs.

Related to Fig. 2. ad, ChIP‐qPCR analysis of H3.3 enrichment at various repeat regions in control and ATRX‐knockout (a), DAXX‐knockout (b), KAP1‐knockout (c) and ESET‐knockout (d) ES cells. Error bars represent s.d. from one experiment (n = 3). Data are representative of two independent ChIP experiments. e, ChIP‐seq enrichment of KAP1 and H3.3 in control and KAP1‐knockout ES cells at repetitive regions of the mouse genome. Data are represented in a heat map of log2 fold enrichment (red) or depletion (blue) over a matched input. f, Loss of H3.3 reduces nuclear DAXX levels. Immunoblot from whole‐cell extracts (WCE) or nuclear extracts (NE) in the presence and absence of H3.3. Asterisk denotes cross‐reacting band. g, ChIP‐seq enrichment of KAP1 and DAXX in control and H3.3‐knockout ES cells. Data are represented as in e. Note the different colour scale used for KAP1 and DAXX.

Extended Data Figure 8 Effects of H3.3 and corepressor complex depletion on H3K9me3 heterochromatin.

Related to Fig. 3. a, Positive correlation of H3.3 and H3K9me3 at IAP ERVs. H3.3 ChIP‐seq enrichment at 800 unique IAP flanking regions (see Fig. 1e) was binned into three groups by their H3K9me3 ChIP‐seq enrichment (low, medium and high). Wilcoxon rank sum test (****P < 0.0001). b, Immunoblot from ES cell whole‐cell lysates in the presence and absence of H3.3. c, H3.3, H3K9me3 and KAP1 ChIP‐seq density heat maps for peaks classified as H3.3 only (n = 60,925), both H3.3 and H3K9me3 (n = 18,605), or H3K9me3 only (n = 54,204) in control and H3.3‐knockout ES cell. Five‐kilobase intervals around peak centres are shown. Colour intensity represents normalized and globally scaled tag counts. d, Levels of H3K9me3 at IAP, ETn, MusD ERVs and LINE elements in control and KAP1‐knockout ES cells (top) and control and H3.3‐knockout ES cells (bottom). Box plots show enrichment over matched input. eh, ChIP‐qPCR analysis of H3K9me3 at various repeat regions in control and KAP1‐knockout (e), ESET‐knockout (f), ATRX‐knockout (g) and DAXX‐knockout (h) ES cells. Error bars represent s.d. from one experiment (n = 3). Data are representative of two independent ChIP experiments.

Extended Data Figure 9 Global effects of H3.3 depletion.

Related to Fig. 3. a, H3.3 transcript levels in control, H3.3‐knockdown and H3.3‐knockout ES cells. Data are represented as mean expression relative to Gapdh ± s.d. (n = 3). b, Relative gain/loss upon H3.3 knockdown of H3K9me3, H3.3 and total H3 are shown over a section of chromosome 10 containing the highly transcribed Rps12 gene and several ERVs. Gain/loss tracks are calculated by subtracting the respective control from H3.3 KD1 tracks, both standardized to a global mean of 1. Note that H3.3 ChIP‐seq data in KD1 cells represents the remaining 10% H3.3. The global loss of H3.3 is not directly apparent from the track due to the necessary normalization of the data. The H3.3 difference track thus does not indicate the global loss of H3.3 but merely represent the relative redistribution of the remaining H3.3 from active genes (Rps12) towards repetitive sequences. c, Levels of H3.3 and H3 and IAP, ETn, MusD, and the TSS of highly expressed genes in control, H3.3‐knockdown and H3.3‐knockout ES cells. Box plots show enrichment over matched input. d, Incorporation of exogenous, constitutively expressed, H3.3 and H3.2 added back into H3.3‐knockdown or H3.3‐knockout ES cells. H3.2 cannot substitute for H3.3 at repetitive ERVs but is efficiently incorporated at sites of active transcription. ChIP‐seq was performed on lentivirally integrated H3.3–haemagglutinin (HA) and H3.2–HA in H3.3 KD1 and H3.3 KO1. e, ChIP‐seq density heat maps for peaks classified as enriched with both H3.3 and H3K9me3 (n = 18,605) or H3.3 only (n = 60,925). Colour intensity represents tag counts scaled and normalized globally. Five-kilobase intervals around peak centres are shown. f, Quantification of H3.3–HA and H3.2–HA add‐back in H3.3‐knockout enrichment at low and highly expressed genes, as well as the TSS (±1 kb) of the latter, IAP, ETn and MusD ERVs, and full‐length LINE elements and their 5′ promoter regions. Data are represented as enrichment over input.

Extended Data Figure 10 ERV reactivation upregulates adjacent genes and may be linked to unbalanced chromosomal translocations.

Related to Fig. 4. a, Repetitive elements associated with genes in Fig. 4b. Elements that were found either within or nearby the transcription unit are listed and the closest distance of an ERV to an exon is given (accounting for the possibility that ERVs could initiate a partial transcript from an alternative start site). b, Newly annotated sites of IAP integration in wild‐type and H3.3 KO1 are indicated on karyogram. c, Karyotype analysis of wild‐type and H3.3‐knockout ES cells. Abnormal karyotype is indicated by arrows. All analysed cells in H3.3 KO1 had a small reciprocal translocation between chromosomes 2q and 6q and an unbalanced translocation between chromosomes 6 and 17 resulting in partial gain of chromosomal segment 6qD to 6qG and partial loss of chromosomal segment 17qE2 to 17qE5. Approximately 45% of the cells had chromosomal breaks or gaps (1–2 per cell). Approximately 45% of the H3.3 KO2 ES cells had a duplication of the segment 8qC to 8qD resulting in partial gain of this segment.

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This file contains ChIP-seq Datasets associated with this paper. (PDF 98 kb)

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Elsässer, S., Noh, KM., Diaz, N. et al. Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells. Nature 522, 240–244 (2015). https://doi.org/10.1038/nature14345

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