Seasonal plasticity and diel stability of h3k27me3 in natural fluctuating environments

ABSTRACT Diel and seasonal oscillations are two major environmental changes in nature. While organisms cope with the former by the well-characterized mechanism of the circadian clock1,2,

there is limited information on the molecular mechanisms underlying long-term responses to the latter3,4,5. Histone H3 lysine 27 trimethylation (H3K27me3), a repressive histone modification,

imparts stability and plasticity to gene regulation during developmental transitions6,7,8,9. Here we studied the seasonal and diel dynamics of H3K27me3 at the genome-wide level in a natural

population of perennial _Arabidopsis halleri_ and compared these dynamics with those of histone H3 lysine 4 trimethylation (H3K4me3), an active histone modification. Chromatin

immunoprecipitation sequencing revealed that H3K27me3 exhibits seasonal plasticity and diel stability. Furthermore, we found that the seasonal H3K27me3 oscillation is delayed in phase

relative to the H3K4me3 oscillation, particularly for genes associated with environmental memory. Our findings suggest that H3K27me3 monitors past transcriptional activity to create

long-term gene expression trends during organismal responses over weeks in natural fluctuating environments. Access through your institution Buy or subscribe This is a preview of

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ACCESS OPTIONS: * Log in * Learn about institutional subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS THE RATE OF EPIGENETIC DRIFT SCALES WITH

MAXIMUM LIFESPAN ACROSS MAMMALS Article Open access 25 November 2023 RESPONSE STRATEGIES TO ACUTE AND CHRONIC ENVIRONMENTAL STRESS IN THE ARCTIC BREEDING LAPLAND LONGSPUR (_CALCARIUS

LAPPONICUS_) Article Open access 19 December 2024 CIRCADIAN CLOCK MECHANISM DRIVING MAMMALIAN PHOTOPERIODISM Article Open access 27 August 2020 DATA AVAILABILITY The ChIP-seq dataset has

been deposited in the DNA Data Bank of Japan (DDBJ) under accession numbers DRA007511 (diel) and DRA007520 (seasonal). The ChIP-seq graph files are available at

http://sohi.ecology.kyoto-u.ac.jp/AhgRNAseq/AhgChIPseq_bigwig.zip. The genome browser session is available at http://sohi.ecology.kyoto-u.ac.jp/jbrowse-ahg-chip/. All other data in this

study are available at http://sohi.ecology.kyoto-u.ac.jp/AhgRNAseq/Nishio_Nat.Plants_script_data.zip. CODE AVAILABILITY The R code used in this study is available at

https://github.com/hnishio/Nishio_Nat.Plants_script. CHANGE HISTORY * _ 23 NOVEMBER 2020 A Correction to this paper has been published: https://doi.org/10.1038/s41477-020-00757-1. _

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transcript quantification from RNA-seq data with or without a reference genome. _BMC Bioinform._ 12, 323 (2011). CAS  Google Scholar  Download references ACKNOWLEDGEMENTS We thank T. Kawagoe

and J. Sugisaka for support during fieldwork; S. Sugano, M. Tosaka, T. Horiuchi, T. Kikuchi and K. Imamura for support in genome sequencing; and D. M. Buzas, K. Iwayama and A. Dodd for

comments on the manuscript. The computations were performed partially on the NIG supercomputer at the ROIS National Institute of Genetics. This study was supported by JST CREST grant no.

JPMJCR15O1, JSPS Grant-in-Aid for Scientific Research (S) no. 26221106 and (A) no. 19H01001, and MEXT KAKENHI grant no. 221S0002. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Center for

Ecological Research, Kyoto University, Otsu, Japan Haruki Nishio, Atsushi J. Nagano, Tasuku Ito & Hiroshi Kudoh * Faculty of Agriculture, Ryukoku University, Otsu, Japan Atsushi J.

Nagano * Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan Yutaka Suzuki * Department of Computational

Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan Yutaka Suzuki Authors * Haruki Nishio View author publications You can also search for

this author inPubMed Google Scholar * Atsushi J. Nagano View author publications You can also search for this author inPubMed Google Scholar * Tasuku Ito View author publications You can

also search for this author inPubMed Google Scholar * Yutaka Suzuki View author publications You can also search for this author inPubMed Google Scholar * Hiroshi Kudoh View author

publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS H.N., A.J.N. and H.K. designed the study. H.N. and Y.S. performed the ChIP-seq experiments. H.N. and

T.I. analysed the ChIP-seq data. H.N. and H.K. wrote the paper. CORRESPONDING AUTHORS Correspondence to Haruki Nishio or Hiroshi Kudoh. ETHICS DECLARATIONS COMPETING INTERESTS The authors

declare no competing interests. ADDITIONAL INFORMATION PUBLISHER’S NOTE Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

EXTENDED DATA EXTENDED DATA FIG. 1 GENOME-WIDE ENRICHMENT PATTERNS OF H3K27ME3 AND H3K4ME3 IN SEASONAL AND DIEL CHIP-SEQ. A, Genome browser view of the H3K27me3 and H3K4me3 density at

_AhgCCA1_ (left) and _AhgTOC1_ (right) from diel ChIP-seq, shown in rpkm on the y axis. Black arrows indicate gene orientation and represent 1 kbp. B, C, Metagene plots of the H3K27me3 and

H3K4me3 accumulation in the genes (B) and at the TSS (C) and their ±2-kbp flanking regions. Rpm was calculated for 50 bp sliding windows along each region. Annual means of rpm in the

seasonal ChIP-seq are shown. The grey shading in B indicates standardised gene lengths. D–F, Seasonal and diel changes in H3K27me3 and H3K4me3 at genes with seasonal oscillations of both

modifications (D), at genes with seasonal oscillations of either H3K27me3 or H3K4me3 (E), and at genes with diel oscillations of H3K4me3 (F). The values represent log2 rpkm at gene regions

(H3K27me3) and 1 kbp-downstream regions from TSS (H3K4me3). Circles represent observations of seasonal and diel changes, and solid lines represent spline curves. The spline curves are shown

irrespective of presence/absence of oscillations. The grey shading indicates time between sunset and sunrise. G, The seasonal and diel amplitudes were compared for H3K27me3- and

H3K4me3-enriched genes. The boxes span from the first to the third quartiles, the lines inside the boxes represent the medians, and the whiskers above and below the boxes represent 1.5 × the

interquartile range from the quartiles; Brunner-Munzel tests (two-sided). EXTENDED DATA FIG. 2 COMPARISON BETWEEN SEASONAL AND DIEL OSCILLATION AMPLITUDES. A, Scatter plots comparing

seasonal and diel amplitudes of H3K27me3 (left) and H3K4me3 (right) for H3K27me3- and H3K4me3-enriched genes, respectively. B, The ratio of seasonal amplitude to diel amplitude for H3K27me3

and H3K4me3. C–H, Four out of 12 time points [three months intervals starting from Nov. (C, D), Dec. (E, F), and Jan. (G, H)] were used to calculate seasonal amplitudes of H3K27me3 and

H3K4me3 for all genes, otherwise the same as A and B. We compared seasonal and diel data with the same number of time points per cycle by reducing data points of seasonal data. In B, D, F,

H, The boxes span from the first to the third quartiles, the bands inside the boxes represent the medians, and the whiskers above and below the boxes represent 1.5 × the interquartile range

from the quartiles; Brunner-Munzel tests (two-sided). EXTENDED DATA FIG. 3 DEFINITION OF THE GENES WITH H3K27ME3 AND H3K4ME3 SEASONAL OSCILLATIONS. A, B, The distribution of H3K27me3 and

H3K4me3 enrichment for all genes in seasonal (A) and diel (B) ChIP-seq. Enriched genes were defined by the threshold of log2 (maximum rpkm) > 2 (red lines). C, D, The distribution of

seasonal (C) and diel (D) amplitudes of H3K27me3 and H3K4me3 for the enriched genes. As one of the criteria of the genes with the seasonal and diel oscillations of H3K27me3 or H3K4me3, the

threshold of log2 (amplitude) > 1 (red lines) was set. E, Seasonal and diel changes in H3K27me3 and H3K4me3 at _AhgFLC_, _AhgLTI30_, _AhgCCA1_, and _AhgTOC1_. The values represent the

standardised levels at gene regions (H3K27me3) and 1 kbp-downstream regions from the TSS (H3K4me3). Circles represent observations of seasonal and diel changes, and solid lines represent

significant seasonal patterns estimated by cosinor models (_P_ < 0.05 for the coefficients of sine and cosine terms; n.s., not significant). The grey shading indicates time between sunset

and sunrise. F, G, The genes with seasonal oscillations of H3K27me3 and H3K4me3 were defined as the overlap of the three categories: maximum/minimum rpkm > 2, FDR < 0.05 in the

generalised linear model likelihood ratio test using edgeR, and _P_ < 0.05 for the coefficients of sine and cosine terms using cosinor models. The statistical tests were two sided. H, I,

The genes with diel oscillations of H3K27me3 and H3K4me3 were defined in the same way as F and G. EXTENDED DATA FIG. 4 H3K27ME3 AND H3K4ME3 ACCUMULATION PATTERNS REVEALED BY THE SEASONAL

CHIP-SEQ. A, The enriched gene ontology terms of the genes that exhibited winter accumulation of H3K27me3. B, The enriched gene ontology terms of the genes that exhibited winter (upper) and

summer (lower) accumulation of H3K4me3. C, Monthly patterns of histone modification levels for the genes with dual seasonal oscillations. The genes were aligned according to the H3K27me3

peak date. D, The genes were aligned according to the H3K4me3 peak date, otherwise the same as B. EXTENDED DATA FIG. 5 CORRELATION BETWEEN SEASONAL PATTERNS OF HISTONE MODIFICATIONS AND

ENVIRONMENTAL FACTORS. A, Simple moving averages (SMAs) of environmental factors (temperature, precipitation, day length, and sunlight hours) for past 1 week (black) and 1 month (red). B,

The number of genes which showed the highest correlation between histone modifications (left, H3K27me3; right, H3K4me3) and SMAs of one of the environmental factors for past 1 month. Genes

are shown that have significant correlations with one of the environmental factors (_P_ < 0.001; Spearman’s rank correlation, two-sided; corrected by the Benjamini-Hochberg method): 89%

and 83% of the genes with seasonal oscillations of H3K27me3 and H3K4me3, respectively. EXTENDED DATA FIG. 6 THE EFFECTS OF H3K27ME3 AND H3K4ME3 SEASONAL OSCILLATIONS ON GENE EXPRESSION. A,

Venn diagram displaying all categories in which genes are classified by enrichment and seasonality of histone modifications. B, C, The mean of mRNA accumulation for the gene categories with

different combinations of enrichment and seasonality of histone modifications. The presence and absence of H3K27me3 (B) and H3K4me3 (C) seasonality was compared. Brunner-Munzel tests

(one-sided; corrected by the Benjamini-Hochberg method). D, E, The seasonal amplitude (D) and mean (E) of transcript accumulation for all gene categories with different combinations of

enrichment and seasonality of histone modifications. Steel-Dwass tests (two-sided), _P_ < 0.05. In B–E, the boxes span from the first to the third quartiles, the bands inside the boxes

represent the medians, and the whiskers above and below the boxes represent 1.5 × the interquartile range from the quartiles. EXTENDED DATA FIG. 7 PHASE DIFFERENCE BETWEEN THE H3K27ME3 AND

H3K4ME3 DYNAMICS. A, Frequency distribution of the temporal differences between the trough of H3K27me3 and the peak of H3K4me3 estimated using cosinor models, illustrating genes with

advanced (left) and delayed (right) H3K27me3 relative to no difference (vertical line). Because the trough appears six months later after the peak in the cosinor model, the temporal

differences between the peak of H3K27me3 and the trough of H3K4me3 shows the identical distribution. B, Conceptual diagrams illustrating the relationship between the degree of phase

difference and Lissajous curves. C–E, The Lissajous curve (red line) drawn as a spline of observed values (black dots) of H3K27me3 against H3K4me3 for _AhgVIN3_ (C), _AhgMAF1_ (D), and

_AhgRAB18_ (E). The area inside the curve represents the degree of phase difference. Grey dots: all values for the genes with dual seasonal oscillations. EXTENDED DATA FIG. 8 DIRECTION OF

PHASE DIFFERENCE BETWEEN THE H3K27ME3 AND H3K4ME3 DYNAMICS FOR THE TOP 20 GENES WITH THE LARGEST AREAS OF THE LISSAJOUS CURVES. The values at the 12 sampling time points were estimated using

smoothing splines and were connected by lines. The numbers next to the data points are chronological ordinals (1: November 6, 2012, 12: September 24, 2013). Open circles, filled circles,

open squares, and filled squares represent the data points in autumn, winter, spring, and summer, respectively. EXTENDED DATA FIG. 9 REPRODUCIBILITY OF THE CHIP-SEQ EXPERIMENTS. A, B,

Correlation of log2 rpkm between replicates 1 and 2 in the seasonal ChIP-seq for H3K27me3 (A) and H3K4me3 (B). C, D, Correlation of log2 rpkm between replicates 1 and 2, 1 and 3, and 1 and 4

in the diel ChIP-seq for H3K27me3 (C) and H3K4me3 (D). In A–D, log2 rpkm was calculated from the number of reads overlapping the transcribed region (H3K27me3) and the region from TSS to

1,000 bp downstream (H3K4me3) for each gene. SUPPLEMENTARY INFORMATION REPORTING SUMMARY SUPPLEMENTARY DATA 1 The list of the genes with the seasonal oscillations of H3K27me3. SUPPLEMENTARY

DATA 2 The list of the genes with the seasonal oscillations of H3K4me3. SUPPLEMENTARY DATA 3 The list of the genes with the dual seasonal oscillations. RIGHTS AND PERMISSIONS Reprints and

permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Nishio, H., Nagano, A.J., Ito, T. _et al._ Seasonal plasticity and diel stability of H3K27me3 in natural fluctuating environments. _Nat.

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