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).
Google Scholar
Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).
Google Scholar
Hsieh, T. S., Fudenberg, G., Goloborodko, A. & Rando, O. J. Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome. Nat. Methods 13, 1009–1011 (2016).
Google Scholar
Krietenstein, N. et al. Ultrastructural details of mammalian chromosome architecture. Mol. Cell 78, 554–565.e7 (2020).
Google Scholar
Hsieh, T. S. et al. Resolving the 3D landscape of transcription-linked mammalian chromatin folding. Mol. Cell 78, 539–553.e8 (2020).
Google Scholar
Schoenfelder, S. et al. The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. Genome Res. 25, 582–597 (2015).
Google Scholar
van de Werken, H. J. et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat. Methods 9, 969–972 (2012).
Google Scholar
Davies, J. O. et al. Multiplexed analysis of chromosome conformation at vastly improved sensitivity. Nat. Methods 13, 74–80 (2016).
Google Scholar
Davies, J. O., Oudelaar, A. M., Higgs, D. R. & Hughes, J. R. How best to identify chromosomal interactions: a comparison of approaches. Nat. Methods 14, 125–134 (2017).
Google Scholar
Kornberg, R. D. Chromatin structure: a repeating unit of histones and DNA. Science 184, 868–871 (1974).
Google Scholar
Neph, S. et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489, 83–90 (2012).
Google Scholar
Hughes, J. R. et al. Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat. Genet. 46, 205–212 (2014).
Google Scholar
Tan-Wong, S. M. et al. Gene loops enhance transcriptional directionality. Science 338, 671–675 (2012).
Google Scholar
Hanssen, L. L. P. et al. Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo. Nat. Cell Biol. 19, 952–961 (2017).
Google Scholar
.Hentges, L. D., Sergeant, M. J., Downes, D. J., Hughes, J. R. & Taylor, S. LanceOtron: a deep learning peak caller for ATAC-seq, ChIP-seq, and DNase-seq. Preprint at https://doi.org/10.1101/2021.01.25.428108 (2021).
He, Q., Johnston, J. & Zeitlinger, J. ChIP-nexus enables improved detection of in vivo transcription factor binding footprints. Nat. Biotechnol. 33, 395–401 (2015).
Google Scholar
Oudelaar, A. M. et al. Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains. Nat. Genet. 50, 1744–1751 (2018).
Google Scholar
Whyte, W. A. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307–319 (2013).
Google Scholar
Hay, D. et al. Genetic dissection of the α-globin super-enhancer in vivo. Nat. Genet. 48, 895–903 (2016).
Google Scholar
Canver, M. C. et al. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature 527, 192–197 (2015).
Google Scholar
Ran, F. A. et al. Genome engineering using the CRISPR–Cas9 system. Nat. Protocols 8, 2281–2308 (2013).
Google Scholar
Trakarnsanga, K. et al. An immortalized adult human erythroid line facilitates sustainable and scalable generation of functional red cells. Nat. Commun. 8, 14750 (2017).
Google Scholar
Mettananda, S. et al. Editing an α-globin enhancer in primary human hematopoietic stem cells as a treatment for β-thalassemia. Nat. Commun. 8, 424 (2017).
Google Scholar
Bak, R. O., Dever, D. P. & Porteus, M. H. CRISPR/Cas9 genome editing in human hematopoietic stem cells. Nat. Protocols 13, 358–376 (2018).
Google Scholar
Scott, C. et al. Recapitulation of erythropoiesis in congenital dyserythropoietic anaemia type I (CDA-I) identifies defects in differentiation and nucleolar abnormalities. Haematologica https://doi.org/10.3324/haematol.2020.260158 (2020).
Magoč, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).
Google Scholar
Kent, W. J. BLAT—the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002).
Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Google Scholar
Fornes, O. et al. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 48, D87–D92 (2020).
Google Scholar
Khan, A. et al. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 46, D260–D266 (2018).
Google Scholar
Telenius, J. & Hughes, J. R. NGseqBasic – a single-command UNIX tool for ATAC-seq, DNaseI-seq, Cut-and-Run, and ChIP-seq data mapping, high-resolution visualisation, and quality control. Preprint at https://doi.org/10.1101/393413 (2018).
Feng, J., Liu, T., Qin, B., Zhang, Y. & Liu, X. S. Identifying ChIP-seq enrichment using MACS. Nat. Protocols 7, 1728–1740 (2012).
Google Scholar
Zacher, B. et al. Accurate promoter and enhancer identification in 127 ENCODE and Roadmap Epigenomics cell types and tissues by GenoSTAN. PLoS ONE 12, e0169249 (2017).
Google Scholar
Fisher, R. A. Statistical Methods for Research Workers 5th edn (Oliver and Boyd, 1932).
Kent, W. J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002).
Google Scholar
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
Google Scholar
Kowalczyk, M. S. et al. Intragenic enhancers act as alternative promoters. Mol. Cell 45, 447–458 (2012).
Google Scholar
Stadler, M. B. et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480, 490–495 (2011).
Google Scholar
Pope, B. D. et al. Topologically associating domains are stable units of replication-timing regulation. Nature 515, 402–405 (2014).
Google Scholar
Hosseini, M. et al. Causes and consequences of chromatin variation between inbred mice. PLoS Genet. 9, e1003570 (2013).
Google Scholar
The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
Google Scholar