Hug, C. B. & Vaquerizas, J. M. The birth of the 3D genome during early embryonic development. Trends Genet. 34, 903–914 (2018).
Du, Z., Zhang, K. & Xie, W. Epigenetic reprogramming in early animal development. Cold Spring Harb. Perspect. Biol. 14, a039677 (2022).
Bonev, B. & Cavalli, G. Organization and function of the 3D genome. Nat. Rev. Genet. 17, 661–678 (2016).
Dekker, J. & Misteli, T. Long-range chromatin interactions. Cold Spring Harb. Perspect. Biol. 7, a019356 (2015).
Van Bortle, K. & Corces, V. G. Nuclear organization and genome function. Annu. Rev. Cell Dev. Biol. 28, 163–187 (2012).
Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).
Dixon, J. R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380 (2012).
Davidson, I. F. & Peters, J. M. Genome folding through loop extrusion by SMC complexes. Nat. Rev. Mol. Cell Biol. 22, 445–464 (2021).
Banigan, E. J. & Mirny, L. A. Loop extrusion: theory meets single-molecule experiments. Curr. Opin. Cell Biol. 64, 124–138 (2020).
Nasmyth, K. & Haering, C. H. Cohesin: its roles and mechanisms. Annu. Rev. Genet. 43, 525–558 (2009).
Rao, S. S. P. et al. Cohesin loss eliminates all loop domains. Cell 171, 305–320 (2017).
Nora, E. P. et al. Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization. Cell 169, 930–944 (2017).
Busslinger, G. A. et al. Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl. Nature 544, 503–507 (2017).
Davidson, I. F. et al. Rapid movement and transcriptional re-localization of human cohesin on DNA. EMBO J. 35, 2671–2685 (2016).
Banigan, E. J. et al. Transcription shapes 3D chromatin organization by interacting with loop extrusion. Proc. Natl Acad. Sci. USA 120, e2210480120 (2023).
Lengronne, A. et al. Cohesin relocation from sites of chromosomal loading to places of convergent transcription. Nature 430, 573–578 (2004).
Olan, I. et al. Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence. Nat. Commun. 11, 6049 (2020).
Heinz, S. et al. Transcription elongation can affect genome 3D structure. Cell 174, 1522–1536 (2018).
Du, Z. et al. Allelic reprogramming of 3D chromatin architecture during early mammalian development. Nature 547, 232–235 (2017).
Ke, Y. et al. 3D chromatin structures of mature gametes and structural reprogramming during mammalian embryogenesis. Cell 170, 367–381 (2017).
Jiang, Y. et al. Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III. Genome Biol. 21, 158 (2020).
Hug, C. B., Grimaldi, A. G., Kruse, K. & Vaquerizas, J. M. Chromatin architecture emerges during zygotic genome activation independent of transcription. Cell 169, 216–228 (2017).
Nagano, T. et al. Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature 547, 61–67 (2017).
Zhang, H. Y. et al. Chromatin structure dynamics during the mitosis-to-G1 phase transition. Nature 576, 158–162 (2019).
Skene, P. J. & Henikoff, S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. Elife 6, e21856 (2017).
Chen, X. et al. Key role for CTCF in establishing chromatin structure in human embryos. Nature 576, 306–310 (2019).
Consortium, E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
Wu, J. et al. The landscape of accessible chromatin in mammalian preimplantation embryos. Nature 534, 652–657 (2016).
Kaaij, L. J. T., Mohn, F., van der Weide, R. H., de Wit, E. & Buhler, M. The ChAHP complex counteracts chromatin looping at CTCF sites that emerged from SINE expansions in mouse. Cell 178, 1437–1451 (2019).
Wang, W. et al. ADNP modulates SINE B2-derived CTCF-binding sites during blastocyst formation in mice. Genes Dev. 38, 168–188 (2024).
Xiong, Z. et al. Ultrasensitive Ribo-seq reveals translational landscapes during mammalian oocyte-to-embryo transition and pre-implantation development. Nat. Cell Biol. 24, 968–980 (2022).
Gassler, J. et al. A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture. EMBO J. 36, 3600–3618 (2017).
Liu, B. et al. The landscape of RNA Pol II binding reveals a stepwise transition during ZGA. Nature 587, 139–144 (2020).
Jia, Y. W., Hartshorn, C., Hartung, O. & Wangh, L. J. Heat shock memory in preimplantation mouse embryos. Fertil. Steril. 93, 2760–2763 (2010).
Vilborg, A. et al. Comparative analysis reveals genomic features of stress-induced transcriptional readthrough. Proc. Natl Acad. Sci. USA 114, E8362–E8371 (2017).
Mahat, D. B., Salamanca, H. H., Duarte, F. M., Danko, C. G. & Lis, J. T. Mammalian heat shock response and mechanisms underlying its genome-wide transcriptional regulation. Mol. Cell 62, 63–78 (2016).
Gao, Y. et al. Protein expression landscape of mouse embryos during pre-implantation development. Cell Rep. 21, 3957–3969 (2017).
Benayoun, B. A. et al. H3K4me3 breadth is linked to cell identity and transcriptional consistency. Cell 158, 673–688 (2014).
Chen, K. et al. Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes. Nat. Genet. 47, 1149–1157 (2015).
Dall’Agnese, A. & Young, R. Regulatory architecture of cell identity genes and housekeeping genes. Trends Cell Biol. 33, 1010–1013 (2023).
Ji, S. et al. OBOX regulates mouse zygotic genome activation and early development. Nature 620, 1047–1053 (2023).
Lai, F. et al. NR5A2 connects zygotic genome activation to the first lineage segregation in totipotent embryos. Cell Res. 33, 952–966 (2023).
Li, L. et al. Lineage regulators TFAP2C and NR5A2 function as bipotency activators in totipotent embryos. Nat. Struct. Mol. Biol. 31, 950–963 (2024).
Kim, E., Barth, R. & Dekker, C. Looping the genome with SMC complexes. Annu. Rev. Biochem. 92, 15–41 (2023).
Sanborn, A. L. et al. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proc. Natl Acad. Sci. USA 112, E6456–E6465 (2015).
Hsieh, T. H. S. et al. Resolving the 3D landscape of transcription-linked mammalian chromatin folding. Mol. Cell 78, 539–553 (2020).
Krietenstein, N. et al. Ultrastructural details of mammalian chromosome architecture. Mol. Cell 78, 554–565 (2020).
Meier, M. et al. Cohesin facilitates zygotic genome activation in zebrafish. Development 145, dev156521 (2018).
Wike, C. L. et al. Chromatin architecture transitions from zebrafish sperm through early embryogenesis. Genome Res. 31, 981–994 (2021).
Nakamura, R. et al. CTCF looping is established during gastrulation in medaka embryos. Genome Res. 31, 968–980 (2021).
Andreu, M. J. et al. Establishment of 3D chromatin structure after fertilization and the metabolic switch at the morula-to-blastocyst transition require CTCF. Cell Rep. 41, 111501 (2022).
Gabriele, M. et al. Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging. Science 376, 496–501 (2022).
Zhang, Y. et al. Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells. Nat. Genet. 51, 1380–1388 (2019).
Kruse, K. et al. Transposable elements drive reorganisation of 3D chromatin during early embryogenesis. Preprint at bioRxiv https://doi.org/10.1101/523712 (2019).
Niu, L. et al. Three-dimensional folding dynamics of the Xenopus tropicalis genome. Nat. Genet. 53, 1075–1087 (2021).
Sun, X. M. et al. Size-dependent increase in RNA polymerase II initiation rates mediates gene expression scaling with cell size. Curr. Biol. 30, 1217–1230 (2020).
Swaffer, M. P. et al. RNA polymerase II dynamics and mRNA stability feedback scale mRNA amounts with cell size. Cell 186, 5254–5268 (2023).
Boskovic, A. et al. Higher chromatin mobility supports totipotency and precedes pluripotency in vivo. Genes Dev. 28, 1042–1047 (2014).
Burton, A. et al. Heterochromatin establishment during early mammalian development is regulated by pericentromeric RNA and characterized by non-repressive H3K9me3. Nat. Cell Biol. 22, 767–778 (2020).
Arias, A. M. & Hayward, P. Filtering transcriptional noise during development: concepts and mechanisms. Nat. Rev. Genet. 7, 34–44 (2006).
Zhang, B. et al. Allelic reprogramming of the histone modification H3K4me3 in early mammalian development. Nature 537, 553–557 (2016).
Wang, Q. et al. Imprecise DNMT1 activity coupled with neighbor-guided correction enables robust yet flexible epigenetic inheritance. Nat. Genet. 52, 828–839 (2020).
Xia, W. et al. Resetting histone modifications during human parental-to-zygotic transition. Science 365, 353–360 (2019).
Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 9, 171–181 (2014).
Brind’Amour, J. et al. LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation. Nat. Commun. 9, 3331 (2018).
Hagemann-Jensen, M. et al. Single-cell RNA counting at allele and isoform resolution using Smart-seq3. Nat. Biotechnol. 38, 708–714 (2020).
Clift, D. et al. A method for the acute and rapid degradation of endogenous proteins. Cell 171, 1692–1706 (2017).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562–578 (2012).
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).
Korotkevich, G. et al. Fast gene set enrichment analysis. Preprint at bioRxiv https://doi.org/10.1101/060012 (2021).
Percharde, M., Wong, P. & Ramalho-Santos, M. Global hypertranscription in the mouse embryonic germline. Cell Rep. 19, 1987–1996 (2017).
Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).
Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015).
Abdennur, N. & Mirny, L. A. Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics 36, 311–316 (2020).
Open2C et al. Cooltools: enabling high-resolution Hi-C analysis in Python. PLoS Comput. Biol. 20, e1012067 (2024).
Flyamer, I. M., Illingworth, R. S. & Bickmore, W. A. Coolpup.py: versatile pile-up analysis of Hi-C data. Bioinformatics 36, 2980–2985 (2020).
Zhou, Y. Y. et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10, 1523 (2019).
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
Tu, S. Q. et al. MAnorm2 for quantitatively comparing groups of ChIP-seq samples. Genome Res. 31, 131–145 (2021).
Bailey, T. L., Johnson, J., Grant, C. E. & Noble, W. S. The MEME Suite. Nucleic Acids Res. 43, W39–W49 (2015).
Kagey, M. H. et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 467, 430–435 (2010).
Zheng, H. et al. Resetting epigenetic memory by reprogramming of histone modifications in mammals. Mol. Cell 63, 1066–1079 (2016).
Hounkpe, B. W., Chenou, F., de Lima, F. & De Paula, E. V. HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets. Nucleic Acids Res. 49, D947–D955 (2021).
Xu, S. L. Y., Grullon, S., Ge, K. & Peng, W. Q. Spatial Clustering for Identification of ChIP-Enriched Regions (SICER) to map regions of histone methylation patterns in embryonic stem cells. Methods Mol. Biol. 1150, 97–111 (2014).
Stovner, E. B. & Saetrom, P. epic2 efficiently finds diffuse domains in ChIP-seq data. Bioinformatics 35, 4392–4393 (2019).
Xia, B. et al. Machine learning uncovers cell identity regulator by histone code. Nat. Commun. 11, 2696 (2020).
Dahl, J. A. et al. Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition. Nature 537, 548–552 (2016).
Liu, B. et al. Mapping putative enhancers in mouse oocytes and early embryos reveals TCF3/12 as key folliculogenesis regulators. Nat. Cell Biol. 26, 962–974 (2024).
Chen, K. et al. DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res. 23, 341–351 (2013).
Zhang, X. O., Gingeras, T. R. & Weng, Z. Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function. Genome Res. 29, 1402–1414 (2019).
Hammal, F., de Langen, P., Bergon, A., Lopez, F. & Ballester, B. ReMap 2022: a database of human, mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments. Nucleic Acids Res. 50, D316–D325 (2022).
Parekh, S., Ziegenhain, C., Vieth, B., Enard, W. & Hellmann, I. zUMIs – a fast and flexible pipeline to process RNA sequencing data with UMIs. Gigascience 7, giy059 (2018).
Choudhary, S. & Satija, R. Comparison and evaluation of statistical error models for scRNA-seq. Genome Biol. 23, 27 (2022).
Hoetker, M. S. et al. H3K36 methylation maintains cell identity by regulating opposing lineage programmes. Nat. Cell Biol. 25, 1121–1134 (2023).
Meir, Z., Mukamel, Z., Chomsky, E., Lifshitz, A. & Tanay, A. Single-cell analysis of clonal maintenance of transcriptional and epigenetic states in cancer cells. Nat. Genet. 52, 709–718 (2020).
Guang, Y. Custom scripts in “Interplay between hyper transcription and de novo establishment of 3D chromatin architecture in early mammalian embryos”. Zenodo https://doi.org/10.5281/zenodo.13753153 (2024).