From compartments to loops: understanding the unique chromatin organization in neuronal cells

Hansen AS, Cattoglio C, Darzacq X, Tjian R. Recent evidence that TADs and chromatin loops are dynamic structures. Nucleus. 2018;9(1):20–32. https://doi.org/10.1080/19491034.2017.1389365.

Article  CAS  PubMed  Google Scholar 

Cremer T, Cremer C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet. 2001;2(4):292–301. https://doi.org/10.1038/35066075.

Article  CAS  PubMed  Google Scholar 

Lieberman-Aiden E, Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326(5950):289–93. https://doi.org/10.1126/science.1181369.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bonev B, Cavalli G. Organization and function of the 3d genome. Nat Rev Genet. 2016;17(11):661–78. https://doi.org/10.1038/nrg.2016.112.

Article  CAS  PubMed  Google Scholar 

Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485(7398):376–80. https://doi.org/10.1038/nature11082.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sanborn AL, Rao SSP, Huang S-C, Durand NC, Huntley MH, Jewett AI, Bochkov ID, Chinnappan D, Cutkosky A, Li J, Geeting KP, Gnirke A, Melnikov A, McKenna D, Stamenova EK, Lander ES, Aiden EL. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proc Nat Acad Sci. 2015;112(47): e6456. https://doi.org/10.1073/pnas.1518552112.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rowley MJ, Corces VG. Organizational principles of 3d genome architecture. Nat Rev Genet. 2018;19(12):789–800. https://doi.org/10.1038/s41576-018-0060-8.

Article  CAS  PubMed  Google Scholar 

Blackledge NP, Rose NR, Klose RJ. Targeting polycomb systems to regulate gene expression: modifications to a complex story. Nat Rev Mol Cell Biol. 2015;16(11):643–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

German B, Ellis L. Polycomb directed cell fate decisions in development and cancer. Epigenomes. 2022;6(3):28.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Du Z, Zheng H, Kawamura YK, Zhang K, Gassler J, Powell S, Xu Q, Lin Z, Xu K, Zhou Q, Ozonov EA, Véron N, Huang B, Li L, Yu G, Liu L, Au Yeung WK, Wang P, Chang L, Wang Q, He A, Sun Y, Na J, Sun Q, Sasaki H, Tachibana K, Peters AHFM, Xie W. Polycomb group proteins regulate chromatin architecture in mouse oocytes and early embryos. Mol Cell. 2020;77(4):825–8397. https://doi.org/10.1016/j.molcel.2019.11.011.

Article  CAS  PubMed  Google Scholar 

Kundu S, Ji F, Sunwoo H, Jain G, Lee JT, Sadreyev RI, Dekker J, Kingston RE. Polycomb repressive complex 1 generates discrete compacted domains that change during differentiation. Mol Cell. 2017;65(3):432–46.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bantignies F, Roure V, Comet I, Leblanc B, Schuettengruber B, Bonnet J, Tixier V, Mas A, Cavalli G. Polycomb-dependent regulatory contacts between distant hox loci in drosophila. Cell. 2011;144(2):214–26.

Article  CAS  PubMed  Google Scholar 

Kraft K, Yost KE, Murphy SE, Magg A, Long Y, Corces MR, Granja JM, Wittler L, Mundlos S, Cech TR, Boettiger AN, Chang HY. Polycomb-mediated genome architecture enables long-range spreading of h3k27 methylation. Proc Nat Acad Sci. 2022;119(22):2201883119. https://doi.org/10.1073/pnas.2201883119.

Article  CAS  Google Scholar 

Bonev B, Mendelson Cohen N, Szabo Q, Fritsch L, Papadopoulos GL, Lubling Y, Xu X, Lv X, Hugnot J-P, Tanay A, Cavalli G. Multiscale 3d genome rewiring during mouse neural development. Cell. 2017;171(3):557–57224. https://doi.org/10.1016/j.cell.2017.09.043.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pletenev IA, Bazarevich M, Zagirova DR, Kononkova AD, Cherkasov AV, Efimova OI, Tiukacheva EA, Morozov KV, Ulianov KA, Komkov D, Tvorogova AV, Golimbet VE, Kondratyev NV, Razin SV, Khaitovich P, Ulianov SV, Khrameeva EE. Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3d genome. Nucleic Acids Res. 2024. https://doi.org/10.1093/nar/gkae271.

Article  PubMed  Google Scholar 

Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, Ye Z, Kim A, Rajagopal N, Xie W, Diao Y, Liang J, Zhao H, Lobanenkov VV, Ecker JR, Thomson JA, Ren B. Chromatin architecture reorganization during stem cell differentiation. Nature. 2015;518(7539):331–6. https://doi.org/10.1038/nature14222.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li L, Lyu X, Hou C, Takenaka N, Nguyen HQ, Ong C-T, Cubeñas-Potts C, Hu M, Lei EP, Bosco G. Widespread rearrangement of 3d chromatin organization underlies polycomb-mediated stress-induced silencing. Mol Cell. 2015;58(2):216–31.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rowley MJ, Nichols MH, Lyu X, Ando-Kuri M, Rivera ISM, Hermetz K, Wang P, Ruan Y, Corces VG. Evolutionarily conserved principles predict 3d chromatin organization. Mol Cell. 2017;67(5):837–52.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rahman S, Dong P, Apontes P, Fernando MB, Kosoy R, Townsley KG, Girdhar K, Bendl J, Shao Z, Misir R, Tsankova N, Kleopoulos SP, Brennand KJ, Fullard JF, Roussos P. Lineage specific 3D genome structure in the adult human brain and neurodevelopmental changes in the chromatin interactome. Nucleic Acids Res. 2023;51(20):11142–61.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hu B, Won H, Mah W, Park RB, Kassim B, Spiess K, Kozlenkov A, Crowley CA, Pochareddy S, The PsychENCODE Consortium, Ashley-Koch AE, Crawford GE, Garrett ME, Song L, Safi A, Johnson GD, Wray GA, Reddy TE, Goes FS, Zandi P, Bryois J, Jaffe AE, Price AJ, Ivanov NA, Collado-Torres L, Hyde TM, Burke EE, Kleiman JE, Tao R, Shin JH, Girdhar K, Jiang Y, Kundakovic M, Brown L, Wiseman JR, Zharovsky E, Jacobov R, Devillers O, Flatow E, Hoffman GE, Belmont J, Del Valle D, Francoeur N, Hadjimichael E, Pinto D, Bakel H, Roussos P, Fullard JF, Bendl J, Hauberg ME, Charney AW, Haroutunian V, Lipska BK, Lewis DA, Hahn C-G, Mangravite LM, Peters MA, Chae Y, Peng J, Niu M, Wang X, Webster MJ, Beach TG, Chen C, Jiang Y, Dai R, Wang Y, Xia Y, Shieh AW, Liu C, Grennan KS, Vadukapuram R, Giase G, Fitzgerald D, Cheng L, Brown M, Brown M, Brunetti T, Goodman T, Alsayed M, White KP, Ray M, Polioudakis D, Wamsley B, Yin J, De La Torre Ubieta L, Gandal MJ, Swarup V, Sanders SJ, State MW, Werling DM, An J-Y, Sheppard B, Willsey AJ, Kefi A, Mattei E, Purcaro M, Weng Z, Moore J, Pratt H, Huey J, Borrman T, Sullivan PF, Giusti-Rodriguez P, Kim Y, Szatkiewicz J, Rhie SK, Armoskus C, Camarena A, Farnham PJ, Spitsyna VN, Witt H, Schreiner S, Evgrafov OV, Knowles JA, Gerstein M, Liu S, Navarro FCP, Warrell J, Clarke D, Emani PS, Gu M, Shi X, Xu M, Yang YT, Kitchen RR, Gürsoy G, Zhang J, Carlyle BC, Nairn AC, Li M, Skarica M, Li Z, Sousa AMM, Santpere G, Choi J, Zhu Y, Gao T, Miller DJ, Cherskov A, Yang M, Amiri A, Coppola G, Mariani J, Scuderi S, Szekely A, Vaccarino FM, Wu F, Weissman S, Wang D, Roychowdhury T, Abyzov A, Li Y, Dracheva S, Sestan N, Akbarian S, Geschwind DH. Neuronal and glial 3d chromatin architecture informs the cellular etiology of brain disorders. Nat Commun. 12(1):3968. https://doi.org/10.1038/s41467-021-24243-0

Tian W, Zhou J, Bartlett A, Zeng Q, Liu H, Castanon RG, Kenworthy M, Altshul J, Valadon C, Aldridge A, Nery JR, Chen H, Xu J, Johnson ND, Lucero J, Osteen JK, Emerson N, Rink J, Lee J, Li YE, Siletti K, Liem M, Claffey N, O’Connor C, Yanny AM, Nyhus J, Dee N, Casper T, Shapovalova N, Hirschstein D, Ding S-L, Hodge R, Levi BP, Keene CD, Linnarsson S, Lein E, Ren B, Behrens MM, Ecker JR. Single-cell DNA methylation and 3D genome architecture in the human brain. Science. 2023;382(6667):5357.

Article  Google Scholar 

Chandrasekaran S, Espeso-Gil S, Loh Y-HE, Javidfar B, Kassim B, Zhu Y, Zhang Y, Dong Y, Bicks LK, Li H, Rajarajan P, Peter CJ, Sun D, Agullo-Pascual E, Iskhakova M, Estill M, Lesch BJ, Shen L, Jiang Y, Akbarian S. Neuron-specific chromosomal megadomain organization is adaptive to recent retrotransposon expansions. Nat Commun. 2021;12(1):7243.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liu H, Zeng Q, Zhou J, Bartlett A, Wang B-A, Berube P, Tian W, Kenworthy M, Altshul J, Nery JR, Chen H, Castanon RG, Zu S, Li YE, Lucero J, Osteen JK, Pinto-Duarte A, Lee J, Rink J, Cho S, Emerson N, Nunn M, O’Connor C, Yao Z, Smith KA, Tasic B, Zeng H, Luo C, Dixon JR, Ren B, Behrens MM, Ecker JR. Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain. Nature. 2023;624:366.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kojic A, Cuadrado A, De Koninck M, Giménez-Llorente D, Rodríguez-Corsino M, Gómez-López G, Le Dily F, Marti-Renom MA, Losada A. Distinct roles of cohesin-SA1 and cohesin-SA2 in 3d chromosome organization. Nat Struct Mol Biol. 2018;25(6):496–504. https://doi.org/10.1038/s41594-018-0070-4.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, Haering CH, Mirny L, Spitz F. Two independent modes of chromatin organization revealed by cohesin removal. Nature. 2017;551(7678):51–6.

Article  PubMed  PubMed Central  Google Scholar 

Closser M, Guo Y, Wang P, Patel T, Jang S, Hammelman J, De Nooij JC, Kopunova R, Mazzoni EO, Ruan Y, Gifford DK, Wichterle H. An expansion of the non-coding genome and its regulatory potential underlies vertebrate neuronal diversity. Neuron. 2022;110(1):70–856.

Article  CAS  PubMed  Google Scholar 

Jaura R, Yeh S-Y, Montanera KN, Ialongo A, Anwar Z, Lu Y, Puwakdandawa K, Rhee HS. Extended intergenic DNA contributes to neuron-specific expression of neighboring genes in the mammalian nervous system. Nat Commun. 2022;13(1):2733.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sun Y, Xu X, Zhao W, Zhang Y, Chen K, Li Y, Wang X, Zhang M, Xue B, Yu W, Hou Y, Wang C, Xie W, Li C, Kong D, Wang S, Sun Y. RAD21 is the core subunit of the cohesin complex involved in directing genome organization. Genome Biol. 2023;24(1):155.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lupiáñez D, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E, Horn D, Kayserili H, Opitz J, Laxova R, Santos-Simarro F, Gilbert-Dussardier B, Wittler L, Borschiwer M, Haas S, 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 

留言 (0)

沒有登入
gif