Roy, S. W. & Gilbert, W. The evolution of spliceosomal introns: patterns, puzzles and progress. Nat. Rev. Genet. 7, 211–221 (2006).Article PubMed Google Scholar Le Hir, H., Nott, A. & Moore, M. J. How introns influence and enhance eukaryotic gene expression. Trends Biochem. Sci. 28, 215–220 (2003).Article PubMed Google Scholar Kumari, A., Sedehizadeh, S., Brook, J. D., Kozlowski, P. & Wojciechowska, M. Differential fates of introns in gene expression due to global alternative splicing. Hum. Genet. 141, 31–47 (2022).Article CAS PubMed Google Scholar Kaul, S. et al. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815 (2000).Article CAS Google Scholar Wu, J. et al. Systematic analysis of intron size and abundance parameters in diverse lineages. Sci. China Life Sci. 56, 968–974 (2013).Article CAS PubMed Google Scholar Castillo-Davis, C. I., Mekhedov, S. L., Hartl, D. L., Koonin, E. V. & Kondrashov, F. A. Selection for short introns in highly expressed genes. Nat. Genet. 31, 415–418 (2002).Article CAS PubMed Google Scholar Liu, H. et al. The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution. Nat. Plants 7, 748–756 (2021).Article CAS PubMed Google Scholar Nystedt, B. et al. The Norway spruce genome sequence and conifer genome evolution. Nature 497, 579–584 (2013).Article CAS PubMed Google Scholar Niu, S. et al. The Chinese pine genome and methylome unveil key features of conifer evolution. Cell 185, 204–217.e14 (2022).Article CAS PubMed Google Scholar Liu, Y. et al. The Cycas genome and the early evolution of seed plants. Nat. Plants 8, 389–401 (2022).Article CAS PubMed PubMed Central Google Scholar Moabbi, A. M., Agarwal, N., El Kaderi, B. & Ansari, A. Role for gene looping in intron-mediated enhancement of transcription. Proc. Natl. Acad. Sci. USA 109, 8505–8510 (2012).Article CAS PubMed PubMed Central Google Scholar Voelker, R. B. & Berglund, J. A. A comprehensive computational characterization of conserved mammalian intronic sequences reveals conserved motifs associated with constitutive and alternative splicing. Genome Res. 17, 1023–1033 (2007).Article CAS PubMed PubMed Central Google Scholar Yeo, G. W., Van Nostrand, E. L. & Liang, T. Y. Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements. PLoS Genet. 3, 814–829 (2007).CAS Google Scholar Mirny, L. A. & Solovei, I. Keeping chromatin in the loop(s). Nat. Rev. Mol. Cell Biol. 22, 439–440 (2021).Article CAS PubMed Google Scholar Long, Y., Wendel, J. F., Zhang, X. & Wang, M. Evolutionary insights into the organization of chromatin structure and landscape of transcriptional regulation in plants. Trends Plant Sci. 29, 638–649 (2024).Article CAS PubMed Google Scholar Tang, Z. et al. CTCF-mediated human 3D genome architecture reveals chromatin topology for transcription. Cell 163, 1611–1627 (2015).Article CAS PubMed PubMed Central Google Scholar Ong, C. T. & Corces, V. G. CTCF: an architectural protein bridging genome topology and function. Nat. Rev. Genet. 15, 234–246 (2014).Article CAS PubMed PubMed Central Google Scholar Gabriele, M. et al. Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging. Science 376, 496–501 (2022).Article CAS PubMed PubMed Central Google Scholar Yin, M. et al. Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites. Cell Res. 27, 1365–1377 (2017).Article CAS PubMed PubMed Central Google Scholar Beernink, B. M., Vogel, J. P. & Lei, L. Enhancers in plant development, adaptation and evolution. Plant Cell Physiol. 66, 461–476 (2025).Article CAS PubMed PubMed Central Google Scholar Zhu, B., Zhang, W., Zhang, T., Liu, B. & Jiang, J. Genome-wide prediction and validation of intergenic enhancers in Arabidopsis using open chromatin signatures. Plant Cell 27, 2415–2426 (2015).Article CAS PubMed PubMed Central Google Scholar Zhao, H. et al. Identification and functional validation of super-enhancers in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 119, e2215328119 (2022).Article CAS PubMed PubMed Central Google Scholar Nabeel-Shah, S. et al. C2H2-zinc-finger transcription factors bind RNA and function in diverse post-transcriptional regulatory processes. Mol. Cell 84, 3810–3825.e10 (2024).Article CAS PubMed Google Scholar Nishiyama, T. et al. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell 174, 448–464.e24 (2018).Article CAS PubMed Google Scholar Marchant, D. B. et al. Dynamic genome evolution in a model fern. Nat. Plants 8, 1038–1051 (2021).Article Google Scholar Weintraub, A. S. et al. YY1 is a structural regulator of enhancer-promoter loops. Cell 171, 1573–1588.e28 (2017).Article CAS PubMed PubMed Central Google Scholar Mao, A., Chen, C., Portillo-Ledesma, S. & Schlick, T. Effect of single-residue mutations on CTCF binding to DNA: insights from molecular dynamics simulations. Int. J. Mol. Sci. 24, 6395 (2023).Article CAS PubMed PubMed Central Google Scholar Parenteau, J. et al. Introns are mediators of cell response to starvation. Nature 565, 612–617 (2019).Article CAS PubMed Google Scholar Pellicer, J., Hidalgo, O., Dodsworth, S. & Leitch, I. J. Genome size diversity and its impact on the evolution of land plants. Genes 9, 88 (2018).Article PubMed PubMed Central Google Scholar Borsari, B. et al. Enhancers with tissue-specific activity are enriched in intronic regions. Genome Res. 31, 1325–1336 (2021).Article CAS PubMed PubMed Central Google Scholar He, B. et al. Evolution of plant genome size and composition. Genomics Proteom. Bioinforma. 22, qzae078 (2024).Article Google Scholar Wells, J. N. & Feschotte, C. A field guide to eukaryotic transposable elements. Annu. Rev. Genet. 54, 539–561 (2020).Article CAS PubMed PubMed Central Google Scholar Elbarbary, R. A., Lucas, B. A. & Maquat, L. E. Retrotransposons as regulators of gene expression. Science 351, aac7247 (2016).Article PubMed PubMed Central Google Scholar Sibley, C. R. et al. Recursive splicing in long vertebrate genes. Nature 521, 371–375 (2015).Article CAS PubMed PubMed Central Google Scholar Duff, M. O. et al. Genome-wide identification of zero nucleotide recursive splicing in Drosophila. Nature 521, 376–379 (2015).Article CAS PubMed PubMed Central Google Scholar Cai, Y. et al. Du13 encodes a C2H2 zinc-finger protein that regulates pre-mRNA splicing and microRNA biogenesis in rice endosperm. Plant Biotechnol. J. 20, 1387–1401 (2022).Article CAS PubMed PubMed Central Google Scholar Chen, S., Zhou, Y., Chen, Y. & Gu, J. Fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).Article PubMed PubMed Central Google Scholar Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).Article CAS PubMed PubMed Central Google Scholar Zhang, Y. et al. Model-based analysis of ChIP-seq (MACS). Genome Biol. 9, R137 (2008).Article PubMed PubMed Central Google Scholar Ma, W., Noble, W. S. & Bailey, T. L. Motif-based analysis of large nucleotide data sets using MEME-ChIP. Nat. Protoc. 9, 1428–1450 (2014).Article CAS PubMed PubMed Central Google Scholar Sati, S. et al. HiCuT: an efficient and low input method to identify protein-directed chromatin interactions. PLoS Genet. 18, e1010121 (2022).Article CAS PubMed PubMed Central Google Scholar Bhattacharyya, S., Chandra, V., Vijayanand, P. & Ay, F. Identification of significant chromatin contacts from HiChIP data by FitHiChIP. Nat. Commun. 10, 4221 (2019).Article PubMed PubMed Central Google Scholar Krijger, P. H. L., Geeven, G., Bianchi, V., Hilvering, C. R. E. & de Laat, W. 4C-seq from beginning to end: a detailed protocol for sample preparation and data analysis. Methods 170, 17–32 (2020).Article CAS PubMed Google Scholar Geeven, G., Teunissen, H., de Laat, W. & de Wit, E. peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data. Nucleic Acids Res. 46, e91 (2018).Article PubMed PubMed Central Google Scholar Yu, G., Wang, L. G. & He, Q. Y. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 31, 2382–2383 (2015).Article CAS PubMed Google Scholar Ramírez, F. et al. High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nat. Commun. 9, 189 (2018).Article PubMed PubMed Central Google Scholar Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014).Article CAS PubMed PubMed Central Google Scholar Mifsud, B. et al. Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat. Genet. 47, 598–606 (2015).Article CAS PubMed Google Scholar Cairns, J. et al. CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data. Genome Biol. 17, 127 (2016).Article PubMed PubMed Central Google Scholar Kaya-Okur, H. S. et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat. Commun. 10, 1930 (2019).Article PubMed PubMed Central Google Scholar Young, M. D., Wakefield, M. J., Smyth, G. K. & Oshlack, A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 11, R14 (2010).Article PubMed PubMed Central Google Scholar Krueger, F. & Andrews, S. R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571–1572 (2011).Article CAS PubMed PubMed Central Google Scholar Ou, S. et al. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol. 20, 275 (2019).Article CAS PubMed PubMed Central Google Scholar Xu, Z. & Wang, H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 35, W265–W268 (2007).Article PubMed PubMed Central Google Scholar Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015).Article PubMed PubMed Central Google Scholar Mokhtaridoost, M. et al. Chromosomal contacts demarcate genome topology along a spatial gradient. Nat. Commun. 15, 9813 (2024).Article CAS PubMed PubMed Central Google Scholar Chowdhury, H. M. A. M., Boult, T. & Oluwadare, O. Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness. BMC Bioinforma. 25, 123 (2024).Article CAS Google Scholar Finn, R. D., Clements, J. & Eddy, S. R. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39, W29–W37 (2011).Article CAS PubMed PubMed Central Google Scholar Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015).Article CAS PubMed PubMed Central Google Scholar Goodstein, D. M. et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40, D1178–D1186 (2012).Article CAS PubMed Google Scholar Sneddon, T. P., Li, P. & Edmunds, S. C. GigaDB: announcing the GigaScience database. Gigascience 1, 11 (2012).Article PubMed PubMed Central Google Scholar Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).Article CAS PubMed Google Scholar