The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies

van Steensel B, Furlong EEM. The role of transcription in shaping the spatial organization of the genome. Nature Rev Mol Cell Biol. 2019;20:327–37. https://doi.org/10.1038/s41580-019-0114-6.

Article  CAS  Google Scholar 

Hafner A, Boettiger A. The spatial organization of transcriptional control. Nature Rev Genet. 2023;24:53–68. https://doi.org/10.1038/s41576-022-00526-0.

Article  CAS  PubMed  Google Scholar 

Lupiáñez DG, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E, Horn D, Kayserili H, Opitz JM, Laxova R, Santos-Simarro F, Gilbert-Dussardier B, Wittler L, Borschiwer M, Haas SA, Osterwalder M, Franke M, Timmermann B, Hecht J, Spielmann M, Visel A, Mundlos S. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell. 2015;161(5):1012–25. https://doi.org/10.1016/j.cell.2015.04.004.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ibn-Salem J, Köhler S, Love MI, Chung H-R, Huang N, Hurles ME, Haendel M, Washington NL, Smedley D, Mungall CJ, Lewis SE, Ott C-E, Bauer S, Schofield PN, Mundlos S, Spielmann M, Robinson PN. Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biol. 2014. https://doi.org/10.1186/s13059-014-0423-1.

Article  PubMed  PubMed Central  Google Scholar 

Spielmann M, Lupiáñez DG, Mundlos S. Structural variation in the 3d genome. Nature Rev Genet. 2018;19(7):453–67. https://doi.org/10.1038/s41576-018-0007-0.

Article  CAS  PubMed  Google Scholar 

Morgan SL, Mariano NC, Bermudez A, Arruda NL, Wu F, Luo Y, Shankar G, Jia L, Chen H, Hu J-F, Hoffman AR, Huang C-C, Pitteri SJ, Wang KC. Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping. Nature Commun. 2017. https://doi.org/10.1038/ncomms1599.

Article  Google Scholar 

Oudelaar AM, Beagrie RA, Gosden M, de Ornellas S, Georgiades E, Kerry J, Hidalgo D, Carrelha J, Shivalingam A, El-Sagheer AH, Telenius JM, Brown T, Buckle VJ, Socolovsky M, Higgs DR, Hughes JR. Dynamics of the 4d genome during in vivo lineage specification and differentiation. Nature Commun. 2020. https://doi.org/10.1038/s41467-020-16598-7.

Article  Google Scholar 

Ing-Simmons E, Vaid R, Bing XY, Levine M, Mannervik M, Vaquerizas JM. Independence of chromatin conformation and gene regulation during drosophila dorsoventral patterning. Nature Genet. 2021;53(4):487–99. https://doi.org/10.1038/s41588-021-00799-x.

Article  CAS  PubMed  Google Scholar 

Heist T, Fukaya T, Levine M. Large distances separate coregulated genes in living drosophila embryos. Proc Natl Acad Sci. 2019;116(30):15062–7. https://doi.org/10.1073/pnas.1908962116.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen H, Levo M, Barinov L, Fujioka M, Jaynes JB, Gregor T. Dynamic interplay between enhancer–promoter topology and gene activity. Nature Genet. 2018;50(9):1296–303. https://doi.org/10.1038/s41588-018-0175-z.

Article  CAS  PubMed  Google Scholar 

Nora EP, Goloborodko A, Valton A-L, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG. Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization. Cell. 2017;169(5):930–94422. https://doi.org/10.1016/j.cell.2017.05.004.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rao SSP, Huang S-C, Hilaire BGS, Engreitz JM, Perez EM, Kieffer-Kwon K-R, Sanborn AL, Johnstone SE, Bascom GD, Bochkov ID, Huang X, Shamim MS, Shin J, Turner D, Ye Z, Omer AD, Robinson JT, Schlick T, Bernstein BE, Casellas R, Lander ES, Aiden EL. Cohesin loss eliminates all loop domains. Cell. 2017;171(2):305–32024. https://doi.org/10.1016/j.cell.2017.09.026.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stadler MR, Haines JE, Eisen MB. Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early drosophila melanogaster embryo. eLife. 2017. https://doi.org/10.7554/elife.29550.

Article  PubMed  PubMed Central  Google Scholar 

Rooijers K, Markodimitraki CM, Rang FJ, de Vries SS, Chialastri A, de Luca KL, Mooijman D, Dey SS, Kind J. Simultaneous quantification of protein–DNA contacts and transcriptomes in single cells. Nature Biotechnol. 2019;37(7):766–72. https://doi.org/10.1038/s41587-019-0150-y.

Article  CAS  Google Scholar 

Das P, Martin RS, McCord RP. Differential contributions of nuclear lamina association and genome compartmentalization to gene regulation. Nucleus. 2023. https://doi.org/10.1080/19491034.2023.2197693.

Article  PubMed  PubMed Central  Google Scholar 

Nakayama K, Shachar S, Finn EH, Sato H, Hirakawa A, Misteli T. Large-scale mapping of positional changes of hypoxia-responsive genes upon activation. Mol Biol Cell. 2022. https://doi.org/10.1091/mbc.e21-11-0593.

Article  PubMed  PubMed Central  Google Scholar 

Shah PP, Keough KC, Gjoni K, Santini GT, Abdill RJ, Wickramasinghe NM, Dundes CE, Karnay A, Chen A, Salomon REA, Walsh PJ, Nguyen SC, Whalen S, Joyce EF, Loh KM, Dubois N, Pollard KS, Jain R. An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype. Genome Biol. 2023. https://doi.org/10.1186/s13059-023-02849-5.

Article  PubMed  PubMed Central  Google Scholar 

van Steensel B, Belmont A. Lamina-associated domains: links with chromosome architecture, heterochromatin, and gene repression. Cell. 2017;169:780–91. https://doi.org/10.1016/j.cell.2017.04.022.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Buchwalter A, Kaneshiro JM, Hetzer MW. Coaching from the sidelines: the nuclear periphery in genome regulation. Nature Rev Genet. 2018;20(1):39–50. https://doi.org/10.1038/s41576-018-0063-5.

Article  CAS  Google Scholar 

Briand N, Collas P. Lamina-associated domains: peripheral matters and internal affairs. Genome Biol. 2020. https://doi.org/10.1186/s13059-020-02003-5.

Article  PubMed  PubMed Central  Google Scholar 

Rullens PMJ, Kind J. Attach and stretch: emerging roles for genome-lamina contacts in shaping the 3d genome. Current Opin Cell Biol. 2021;70:51–7. https://doi.org/10.1016/j.ceb.2020.11.006.

Article  CAS  Google Scholar 

Guerreiro I, Kind J. Spatial chromatin organization and gene regulation at the nuclear lamina. Current Opin Genet & Develop. 2019;55:19–25. https://doi.org/10.1016/j.gde.2019.04.008.

Article  CAS  Google Scholar 

Martino S, Carollo PS, Barra V. A glimpse into chromatin organization and nuclear lamina contribution in neuronal differentiation. Genes. 2023;14(5):1046. https://doi.org/10.3390/genes14051046.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kind J, Pagie L, Ortabozkoyun H, Boyle S, de Vries SS, Janssen H, Amendola M, Nolen LD, Bickmore WA, van Steensel B. Single-cell dynamics of genome-nuclear lamina interactions. Cell. 2013;153(1):178–92. https://doi.org/10.1016/j.cell.2013.02.028.

Article  CAS  PubMed  Google Scholar 

Kind J, Pagie L, de Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, de Graaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny LA, Jalink K, Dekker J, van Oudenaarden A, van Steensel B. Genome-wide maps of nuclear lamina interactions in single human cells. Cell. 2015;163(1):134–47. https://doi.org/10.1016/j.cell.2015.08.040.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dietzel S, Zolghadr K, Hepperger C, Belmont AS. Differential large-scale chromatin compaction and intranuclear positioning of transcribed versus non-transcribed transgene arrays containing \(\beta\) - globin regulatory sequences. J Cell Sci. 2004;117(19):4603–14. https://doi.org/10.1242/jcs.01330.

Article  CAS  PubMed  Google Scholar 

Misteli T. Beyond the sequence: cellular organization of genome function. Cell. 2007;128(4):787–800. https://doi.org/10.1016/j.cell.2007.01.028.

Article  CAS  PubMed  Google Scholar 

Kosak ST, Medina JASKL, Riblet R, Beau MML, Fisher AG, Singh H. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science. 2002;296:158–62. https://doi.org/10.1126/science.1068768.

Article  CAS  PubMed  Google Scholar 

Hewitt SL, High FA, Reiner SL, Fisher AG, Merkenschlager M. Nuclear repositioning marks the selective exclusion of lineage-inappropriate transcription factor loci during t helper cell differentiation. Eur J Immunol. 2004;34:3604–13. https://doi.org/10.1002/eji.200425469.

Article  CAS  PubMed  Google Scholar 

Zink D, Amaral MD, Englmann A, Lang S, Clarke LA, Rudolph C, Alt F, Luther K, Braz C, Sadoni N, Rosenecker J, Schindelhauer D. Transcription-dependent spatial arrangements of CFTR and adjacent genes in human cell nuclei. J Cell Biol. 2004;166(6):815–25. https://doi.org/10.1083/jcb.200404107.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Williams RRE, Azuara V, Perry P, Sauer S, Dvorkina M, Jørgensen H, Roix J, McQueen P, Misteli T, Merkenschlager M, Fisher AG. Neural induction promotes large-scale chromatin reorganisation of the mash1 locus. J Cell Biol. 2006;119:132–40. https://doi.org/10.1242/jcs.02727.

Article  CAS  Google Scholar 

Gonzalez-Sandoval A, Gasser SM. On TADs and LADs: spatial control over gene expression. Trends Genet. 2016;32(8):485–95.

留言 (0)

沒有登入
gif