The mouse alpha-globin cluster: a paradigm for studying genome regulation and organization
Tài liệu tham khảo
Furlong, 2018, Developmental enhancers and chromosome topology, Science, 361, 1341, 10.1126/science.aau0320
Rowley, 2018, Organizational principles of 3D genome architecture, Nat Rev Genet, 19, 789, 10.1038/s41576-018-0060-8
Harteveld, 2010, α-Thalassaemia, Orphanet J Rare Dis, 5, 13, 10.1186/1750-1172-5-13
Hay, 2016, Genetic dissection of the α-globin super-enhancer in vivo, Nat Genet, 48, 895, 10.1038/ng.3605
Popescu, 2019, Decoding human fetal liver haematopoiesis, Nature, 574, 365, 10.1038/s41586-019-1652-y
Pijuan-Sala, 2019, A single-cell molecular map of mouse gastrulation and early organogenesis, Nature, 566, 490, 10.1038/s41586-019-0933-9
Pop, 2010, A key commitment step in erythropoiesis is synchronized with the cell cycle clock through mutual inhibition between PU.1 and S-phase progression, PLoS Biol, 8, 10.1371/journal.pbio.1000484
Tusi, 2018, Population snapshots predict early haematopoietic and erythroid hierarchies, Nature, 555, 54, 10.1038/nature25741
Oudelaar, 2020, Dynamics of the 4D genome during in vivo lineage specification and differentiation, Nat Commun, 11, 10.1038/s41467-020-16598-7
Whyte, 2013, Master transcription factors and mediator establish super-enhancers at key cell identity genes, Cell, 153, 307, 10.1016/j.cell.2013.03.035
Hanssen, 2017, Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo, Nat Cell Biol, 19, 952, 10.1038/ncb3573
Hughes, 2005, Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences, Proc Natl Acad Sci U S A, 102, 9830, 10.1073/pnas.0503401102
Anguita, 2004, Globin gene activation during haemopoiesis is driven by protein complexes nucleated by GATA-1 and GATA-2, EMBO J, 23, 2841, 10.1038/sj.emboj.7600274
Nora, 2012, Spatial partitioning of the regulatory landscape of the X-inactivation centre, Nature, 485, 381, 10.1038/nature11049
Dixon, 2012, Topological domains in mammalian genomes identified by analysis of chromatin interactions, Nature, 485, 376, 10.1038/nature11082
Fudenberg, 2016, Formation of chromosomal domains by loop extrusion, Cell Rep, 15, 2038, 10.1016/j.celrep.2016.04.085
Sanborn, 2015, Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes, Proc Natl Acad Sci U S A, 112, E6456, 10.1073/pnas.1518552112
Li, 2020, The structural basis for cohesin–CTCF-anchored loops, Nature, 578, 472, 10.1038/s41586-019-1910-z
Yin, 2017, Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites, Cell Res, 27, 1365, 10.1038/cr.2017.131
Pugacheva, 2020, CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention, Proc Natl Acad Sci U S A, 117, 2020, 10.1073/pnas.1911708117
Brown, 2018, A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions, Nat Commun, 9, 10.1038/s41467-018-06248-4
Chiariello, 2020, A dynamic folded hairpin conformation is associated with α-globin activation in erythroid cells, Cell Rep, 30, 2125, 10.1016/j.celrep.2020.01.044
Palstra, 2003, The beta-globin nuclear compartment in development and erythroid differentiation, Nat Genet, 35, 190, 10.1038/ng1244
Hnisz, 2017, A phase separation model for transcriptional control, Cell, 169, 13, 10.1016/j.cell.2017.02.007
Davies, 2015, Multiplexed analysis of chromosome conformation at vastly improved sensitivity, Nat Methods, 86, 1202
Oudelaar, 2018, Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains, Nat Genet, 50, 1744, 10.1038/s41588-018-0253-2
Oudelaar, 2019, A revised model for promoter competition based on multi-way chromatin interactions at the α-globin locus, Nat Commun, 10, 1, 10.1038/s41467-019-13404-x
Harrold, 2020, A functional overlap between actively transcribed genes and chromatin boundary elements, bioRxiv
Ghavi-Helm, 2014, Enhancer loops appear stable during development and are associated with paused polymerase, Nature, 513, 89
Vernimmen, 2007, Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression, EMBO J, 26, 2041, 10.1038/sj.emboj.7601654
Larke, 2019, Enhancers predominantly regulate gene expression in vivo via transcription initiation, bioRxiv
Sankaran, 2008, Human fetal hemoglobin expression is regulated by the developmental stage-specific repressor BCL11A, Science, 322, 1839, 10.1126/science.1165409
Mettananda, 2017, Editing an α-globin enhancer in primary human hematopoietic stem cells as a treatment for β-thalassemia, Nat Commun, 8, 10.1038/s41467-017-00479-7
Zhu, 2020, Single-cell multimodal omics: the power of many, Nat Methods, 17, 11, 10.1038/s41592-019-0691-5
Cramer, 2019, Organization and regulation of gene transcription, Nature, 573, 45, 10.1038/s41586-019-1517-4
Germier, 2017, Real-time imaging of a single gene reveals transcription-initiated local confinement, Biophys J, 113, 1383, 10.1016/j.bpj.2017.08.014
Bintu, 2018, Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells, Science, 362, 10.1126/science.aau1783
Gu, 2018, Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements, Science, 359, 1050, 10.1126/science.aao3136