Struhl, K. Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 98, 1–4 (1999).
Kornberg, R. D. & Lorch, Y. Primary role of the nucleosome. Mol. Cell 79, 371–375 (2020).
Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43–49 (2011).
Ho, J. W. K. et al. Comparative analysis of metazoan chromatin organization. Nature 512, 449–452 (2014).
Montgomery, S. A. et al. Chromatin organization in early land plants reveals an ancestral association between H3K27me3, transposons, and constitutive heterochromatin. Curr. Biol. 30, 573–588 (2020).
Wang, Z. et al. AraENCODE: a comprehensive epigenomic database of Arabidopsis thaliana. Mol. Plant 16, 1113–1116 (2023).
Kharchenko, P. V. et al. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471, 480–485 (2011).
Jamge, B. et al. Histone variants shape chromatin states in Arabidopsis. Elife 12, RP87714 (2023).
Lara-Astiaso, D. et al. In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis. Nat. Genet. 55, 1542–1554 (2023).
Spracklin, G. et al. Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers. Nat. Struct. Mol. Biol. 30, 38–51 (2023).
Lara-Astiaso, D. et al. Immunogenetics. Chromatin state dynamics during blood formation. Science 345, 943–949 (2014).
Sebé-Pedrós, A. et al. The dynamic regulatory genome of Capsaspora and the origin of animal multicellularity. Cell 165, 1224–1237 (2016).
Wenger, A. et al. Symmetric inheritance of parental histones governs epigenome maintenance and embryonic stem cell identity. Nat. Genet. 55, 1567–1578 (2023).
Sultana, T. et al. The landscape of L1 retrotransposons in the human genome is shaped by pre-insertion sequence biases and post-insertion selection. Mol. Cell 74, 555–570 (2019).
Gangadharan, S., Mularoni, L., Fain-Thornton, J., Wheelan, S. J. & Craig, N. L. DNA transposon Hermes inserts into DNA in nucleosome-free regions in vivo. Proc. Natl Acad. Sci. USA 107, 21966–21972 (2010).
Shinn, P. et al. HIV-1 integration in the human genome favors active genes and local hotspots. Cell 110, 521–529 (2002).
Goodier, J. L. Restricting retrotransposons: a review. Mob. DNA 7, 16 (2016).
Molaro, A. & Malik, H. S. Hide and seek: how chromatin-based pathways silence retroelements in the mammalian germline. Curr. Opin. Genet. Dev. 37, 51–58 (2016).
Zentner, G. E. & Henikoff, S. Regulation of nucleosome dynamics by histone modifications. Nat. Struct. Mol. Biol. 20, 259–266 (2013).
Huang, H., Sabari, B. R., Garcia, B. A., Allis, C. D. & Zhao, Y. SnapShot: histone modifications. Cell 159, 458–458 (2014).
Strahl, B. D. & Allis, C. D. The language of covalent histone modifications. Nature 403, 41–45 (2000).
Zhou, V. W., Goren, A. & Bernstein, B. E. Charting histone modifications and the functional organization of mammalian genomes. Nat. Rev. Genet. 12, 7–18 (2011).
Millán-Zambrano, G., Burton, A., Bannister, A. J. & Schneider, R. Histone post-translational modifications—cause and consequence of genome function. Nat. Rev. Genet. 23, 563–580 (2022).
Nardelli, S. C. et al. The histone code of Toxoplasma gondii comprises conserved and unique posttranslational modifications. mBio 4, e00922-13 (2013).
Wang, S. Y. et al. Role of epigenetics in unicellular to multicellular transition in Dictyostelium. Genome Biol. 22, 134 (2021).
Garcia, B. et al. Organismal differences in post-translational modifications in histones H3 and H4. J. Biol. Chem. 282, 7641–7655 (2007).
Bourdareau, S. et al. Histone modifications during the life cycle of the brown alga Ectocarpus. Genome Biol. 22, 12 (2021).
Schwaiger, M. et al. Evolutionary conservation of the eumetazoan gene regulatory landscape. Genome Res. 24, 639–650 (2014).
Grau-Bové, X. et al. A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution. Nat. Ecol. Evol. 6, 1007–1023 (2022).
Ernst, J. & Kellis, M. ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods 9, 215–216 (2012).
Roudier, F. et al. Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J. 30, 1928–1938 (2011).
Kanno, T. et al. BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones. Nat. Struct. Mol. Biol. 21, 1047–1057 (2014).
Nguyen, A. T. & Zhang, Y. The diverse functions of Dot1 and H3K79 methylation. Genes Dev. 25, 1345–1358 (2011).
Vigneau, J. et al. Interactions between U and V sex chromosomes during the life cycle of Ectocarpus. Development 151, dev202677 (2024).
Gueno, J. et al. Chromatin landscape associated with sexual differentiation in a UV sex determination system. Nucleic Acids Res. 50, 3307–3322 (2022).
Vigneau, J. et al. Evolution of a distinct chromatin regulatory landscape in brown algae. Nat. Ecol. Evol. 10, 779–793 (2026).
Dindar, G., Anger, A. M., Mehlhorn, C., Hake, S. B. & Janzen, C. J. Structure-guided mutational analysis reveals the functional requirements for product specificity of DOT1 enzymes. Nat. Commun. 5, 5313 (2014).
Ou, S. et al. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol. 20, 275 (2019).
Carlier, F. et al. Loss of EZH2-like or SU(VAR)3–9-like proteins causes simultaneous perturbations in H3K27 and H3K9 tri-methylation and associated developmental defects in the fungus Podospora anserina. Epigenetics Chromatin 14, 22 (2021).
Kramer, H. M., Seidl, M. F., Thomma, B. P. H. J. & Cook, D. E. Local rather than global H3K27me3 dynamics are associated with differential gene expression in Verticillium dahliae. mBio 13, e0356621 (2021).
Jamieson, K., Rountree, M. R., Lewis, Z. A., Stajich, J. E. & Selker, E. U. Regional control of histone H3 lysine 27 methylation in Neurospora. Proc. Natl Acad. Sci. USA 110, 6027–6032 (2013).
Turck, F. et al. Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet. 3, e86 (2007).
Jackson, J. P. et al. Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma 112, 308–315 (2004).
Widiez, T. et al. The chromatin landscape of the moss Physcomitrella patens and its dynamics during development and drought stress. Plant J. 79, 67–81 (2014).
Petroll, R. et al. The expansion and diversification of epigenetic regulatory networks underpins major transitions in the evolution of land plants. Mol. Biol. Evol. 42, msaf064 (2025).
Hisanaga, T. et al. The Polycomb repressive complex 2 deposits H3K27me3 and represses transposable elements in a broad range of eukaryotes. Curr. Biol. 33, 4367–4380 (2023).
Gahan, J. M. et al. Chromatin profiling identifies putative dual roles for H3K27me3 in regulating cell type-specific genes and transposable elements in choanoflagellates. Nat. Commun. 16, 9549 (2025).
De Mendoza, A., Lister, R. & Bogdanovic, O. Evolution of DNA methylome diversity in eukaryotes. J. Mol. Biol. 432, 1687–1705 (2020).
Huff, J. T. & Zilberman, D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell 156, 1286–1297 (2014).
Gao, X., Hou, Y., Ebina, H., Levin, H. L. & Voytas, D. F. Chromodomains direct integration of retrotransposons to heterochromatin. Genome Res. 18, 359–369 (2008).
Sarre, L. A. et al. DNA methylation enables recurrent endogenization of giant viruses in an animal relative. Sci. Adv. 10, eado6406 (2024).
Lewin, H. A. et al. Earth BioGenome Project: sequencing life for the future of life. Proc. Natl Acad. Sci. USA 115, 4325–4333 (2018).
Maile, T. M. et al. Mass spectrometric quantification of histone post-translational modifications by a hybrid chemical labeling method. Mol. Cell. Proteomics 14, 1148–1158 (2015).
Perkins, D. N., Pappin, D. J. C., Creasy, D. M. & Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551–3567 (1999).
MacLean, B. et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26, 966–968 (2010).
Payá-Milans, M. et al. Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa, Gigascience https://doi.org/10.1093/gigascience/giz147 (2019).
Keren-Shaul, H. et al. MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing. Nat. Protoc. 14, 1841–1862 (2019).
Matthey-Doret, C. et al. Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection-related chromatin reorganization. Genome Res. 32, 1698–1710 (2022).
Naish, M. et al. The genetic and epigenetic landscape of the Arabidopsis centromeres. Science 374, eabi7489 (2025).
Curtis, B. A. et al. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature 492, 59–65 (2012).
De Mendoza, A., Suga, H., Permanyer, J., Irimia, M. & Ruiz-Trillo, I. Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals. Elife 4, e08904 (2015).
Eichinger, L. et al. The genome of the social amoeba Dictyostelium discoideum. Nature 435, 43–57 (2005).
Fritz-Laylin, L. K. et al. The genome of Naegleria gruberi illuminates early eukaryotic versatility. Cell 140, 631–642 (2010).
Fletcher, C. & Pereira da Conceicoa, L. The genome sequence of the starlet sea anemone, Nematostella vectensis (Stephenson, 1935). Wellcome Open Res. 8, 79 (2023).
Bi, G. et al. Near telomere-to-telomere genome of the model plant Physcomitrium patens. Nat. Plants 10, 327–343 (2024).
Russ, C. et al. Genome sequence of Spizellomyces punctatus. Genome Announc. 4, e00849-16 (2016).
Ye, F. et al. Comprehensive genome annotation of the model ciliate Tetrahymena thermophila by in-depth epigenetic and transcriptomic profiling. Nucleic Acids Res. 53, gkae1177 (2025).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Tarasov, A., Vilella, A. J., Cuppen, E., Nijman, I. J. & Prins, P. Sambamba: fast processing of NGS alignment formats. Bioinformatics 31, 2032–2034 (2015).
Ramírez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160–W165 (2016).
Zhang, Y. et al. Model-based analysis of ChIP-seq (MACS). Genome Biol. 9, R137 (2008).
Landt, S. G. et al. ChIP–seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22, 1813–1831 (2012).
Kharchenko, P. V., Tolstorukov, M. Y. & Park, P. J. Design and analysis of ChIP–seq experiments for DNA-binding proteins. Nat. Biotechnol. 26, 1351–1359 (2008).
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Wickham, H. et al. Welcome to the tidyverse. J. Open Source Softw. 4, 1686 (2019).
Wickham, H. Reshaping data with the reshape package. J. Stat. Softw. 21, 1–20 (2007).
Riemondy, K. A. et al. valr: reproducible genome interval analysis in R. F1000Res. 6, 1025 (2017).
Lawrence, M. et al. Software for computing and annotating genomic ranges. PLoS Comput. Biol. 9, e1003118 (2013).
Zolotarov, G., Grau-Bové, X. & Sebé-Pedrós, A. GeneExt: a gene model extension tool for enhanced single-cell RNA-seq analysis. Bioinformatics 42, btag094 (2026).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Hahne, F. & Ivanek, R. Visualizing genomic data using Gviz and Bioconductor. Methods Mol. Biol. 1418, 335–351 (2016).
Montgomery, S., Mendieta, J. & Sebé-Pedrós, A. sebepedroslab/iChIPv2: iChIPv2 pipeline. Zenodo https://doi.org/10.5281/zenodo.20049133 (2026).