Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells

Abstract

The eukaryotic genome is folded into higher-order conformation accompanied with constrained dynamics for coordinated genome functions. However, the molecular machinery underlying these hierarchically organized three-dimensional (3D) chromatin architecture and dynamics remains poorly understood. Here by combining imaging and sequencing, we studied the role of lamin B1 in chromatin architecture and dynamics. We found that lamin B1 depletion leads to detachment of lamina-associated domains (LADs) from the nuclear periphery accompanied with global chromatin redistribution and decompaction. Consequently, the interchromosomal as well as inter-compartment interactions are increased, but the structure of topologically associating domains (TADs) is not affected. Using live-cell genomic loci tracking, we further proved that depletion of lamin B1 leads to increased chromatin dynamics, owing to chromatin decompaction and redistribution toward nucleoplasm. Taken together, our data suggest that lamin B1 and chromatin interactions at the nuclear periphery promote LAD maintenance, chromatin compaction, genomic compartmentalization into chromosome territories and A/B compartments and confine chromatin dynamics, supporting their crucial roles in chromatin higher-order structure and chromatin dynamics.

Key words： lamin B1; 3D genome; Hi-C; chromatin dynamics; chromosome territories; A/B compartments; livecell imaging; super-resolution imaging

References

1 Ai S, Peng Y, Li C, Gu F, Yu X, Yue Y, Ma Q, Chen J, Lin Z, Zhou P (2017) EED orchestration of heart maturation through interaction with HDACs is H3K27me3-independent. eLife 6: e24570

2 Akhtar J,More P, Albrecht S, Marini F, Kaiser W,Kulkarni A, Wojnowski L, Fontaine J-F,Andrade-Navarro MA, Silies M (2019) TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assay. Life science alliance 2: e201900318

3 Albert B, Mathon J, Shukla A, Saad H, Normand C, Leger-Silvestre I, Villa D, Kamgoue A, Mozziconacci J, Wong H (2013) Systematic characterization of the conformation and dynamics of budding yeast chromosome XII. J Cell Biol 202:201–210

4 Amendola M, Steensel BV (2015) Nuclear lamins are not required for lamina-associated domain organization in mouse embryonic stem cells. EMBO Rep 16:610–617

5 Barton LJ, Soshnev AA, Geyer PK (2015) Networking in the nucleus: a spotlight on LEM-domain proteins. Curr Opin Cell Biol 34:1–8

6 Bintu B, Mateo LJ, Su J-H, Sinnott-Armstrong NA, Parker M, Kinrot S, Yamaya K, Boettiger AN, Zhuang X (2018) Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science 362:eaau1783

7 Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu CT, Zhuang X (2016) Superresolution imaging reveals distinct chromatin folding for different epigenetic states. Nature 529:418–422

8 Brakemann T, Stiel AC, Weber G, Andresen M, Testa I, Grotjohann T, Leutenegger M, Plessmann U, Urlaub H, Eggeling C (2011) A reversibly photoswitchable GFP-like protein with fluorescence excitation decoupled from switching. Nat Biotechnol 29:942–947

9 Briand N, Collas P (2018) Laminopathy-causing lamin A mutations reconfigure lamina-associated domains and local spatial chromatin conformation. Nucleus 9:216–226

10 Briand N, Collas P (2020) Lamina-associated domains: peripheral matters and internal affairs. Genome Biol 21:85–85

11 Bronshtein I, Kepten E, Kanter I, Berezin S, Lindner M, Redwood AB, Mai S, Gonzalo S, Foisner R, Shav-Tal Y (2015) Loss of lamin A function increases chromatin dynamics in the nuclear interior. Nat Commun 6:8044

12 Camps J, Wangsa D, Falke M, Brown M, Case CM, Erdos MR, Ried T (2014) Loss of lamin B1 results in prolongation of S phase and decondensation of chromosome territories. FASEB J 28:3423–3434

13 Cho NW, Dilley RL, Lampson MA, Greenberg RA (2014) Interchromosomal homology searches drive directional ALT telomere movement and synapsis. Cell 159:108–121

14 Chuang CH, Carpenter AE, Fuchsova B, Johnson T, de Lanerolle P, Belmont AS (2006) Long-range directional movement of an interphase chromosome site. Curr Biol 16:825–831

15 Chubb JR, Boyle S, Perry P, Bickmore WA (2002) Chromatin motion is constrained by association with nuclear compartments in human cells. Curr Biol 12:439–445

16 Crane E,Bian Q, McCord RP, Lajoie BR, Wheeler BS, Ralston EJ, Uzawa S, Dekker J,Meyer BJ (2015) Condensin-driven remodelling of X chromosome topology during dosage compensation. Nature 523:240–244

17 Cremer M, Küpper K, Wagler B, Wizelman L, Hase JV, Weiland Y, Kreja L, Diebold J, Speicher MR, Cremer T (2003) Inheritance of gene density-related higher order chromatin arrangements in normal and tumor cell nuclei. J Cell Biol 162:809–820

18 Croft JA, Bridger JM, Boyle S, Perry P, Teague P, Bickmore WA (1999) Differences in the localization and morphology of chromosomes in the human nucleus . J Cell Biol 145:1119–1131

19 Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295:1306–1311

20 Dimitrova N, Chen Y-CM, Spector DL, de Lange T (2008) 53BP1 promotes non-homologous end joining of telomeres by increasing chromatin mobility. Nature 456:524–528

21 Dixon CR, Platani M, Makarov AA, Schirmer EC (2017) Microinjection of antibodies targeting the lamin A/C histone-binding site blocks mitotic entry and reveals separate chromatin interactions with HP1, CenpB and PML. Cells 6:9

22 Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485:376–380

23 Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C (2006) Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 16:1299–1309

24 Du Z, Zheng H, Huang B, Ma R, Wu J, Zhang X, He J, Xiang Y, Wang Q, Li Y (2017) Allelic reprogramming of 3D chromatin architecture during early mammalian development. Nature 547:232–235

25 Falk M, Feodorova Y, Naumova N, Imakaev M, Lajoie BR, Leonhardt H, Joffe B, Dekker J,Fudenberg G, Solovei I (2019) Heterochromatin drives compartmentalization of inverted and conventional nuclei. Nature 570:395–399

26 Fan H, Lv P, Huo X, Wu J, Wang Q, Cheng L, Liu Y, Tang QQ, Zhang L, Zhang F (2018) The nuclear matrix protein HNRNPU maintains 3D genome architecture globally in mouse hepatocytes. Genome Res 28:192–202

27 Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH (2009) An oestrogen-receptor-α-bound human chromatin interactome. Nature 462:58–64

28 Gesson K, Rescheneder P,Skoruppa MP, von Haeseler A, Dechat T, Foisner R (2016) A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2 alpha. Genome Res 26:462–473

29 Goto C, Tamura K, Fukao Y, Shimada T,Hara-Nishimura I(2014) The novel nuclear envelope protein KAKU4 modulates nuclear morphology in arabidopsis. Plant Cell 26:2143–2155

30 Gruenbaum Y,Foisner R (2015) Lamins: nuclear intermediate filament proteins with fundamental functions in nuclear mechanics and genome regulation. Annu Rev Biochem 84:131–164

31 Gu B, Swigut T, Spencley A, Bauer MR, Chung M, Meyer T, Wysocka J (2018) Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements. Science 359:1050–1055

32 Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de Laat W (2008) Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453:948–951

33 Haarhuis JHI, van der Weide RH, Blomen VA, Yanez-Cuna JO, Amendola M, van Ruiten MS, Krijger PHL, Teunissen H, Medema RH, Steensel BV (2017) The cohesin release factor WAPL restricts chromatin loop extension. Cell 169(693–707):e614

34 Hajjoul H, Mathon J, Ranchon H, Goiffon I, Mozziconacci J, Albert B, Carrivain P, Victor JM, Gadal O, Bystricky K (2013) Highthroughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome. Genome Res 23:1829–1838

35 Ho CY, Lammerding J (2012) Lamins at a glance. J Cell Sci 125:2087–2093

36 Hu B, Wang N, Bi X, Karaaslan ES, Weber A-L, Zhu W, Berendzen KW, Liu C (2019) Plant lamin-like proteins mediate chromatin tethering at the nuclear periphery. Genome Biol 20:87

37 Hubner MR, Spector DL (2010) Chromatin dynamics. Annu Rev Biophys 39:471–489

38 Huo X, Ji L, Zhang Y, Lv P, Cao X, Wang Q, Yan Z, Dong S, Du D, Zhang F (2020) The nuclear matrix protein SAFB cooperates with major satellite RNAs to stabilize heterochromatin architecture partially through phase separation. Mol Cell 77:368–383

39 Imakaev M, Fudenberg G,McCord RP, Naumova N, Goloborodko A, Lajoie BR, Dekker J, Mirny LA (2012) Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods 9:999–1003

40 Izumi M, Vaughan OA, Hutchison CJ, Gilbert DM (2000) Head and/or CaaX domain deletions of lamin proteins disrupt preformed lamin A and C but not lamin B structure in mammalian cells. Mol Biol Cell 11:4323–4337

41 Jaqaman K, Loerke D, Mettlen M, Kuwata H, Grinstein S, Schmid SL, Danuser G (2008) Robust single-particle tracking in live-cell time-lapse sequences. Nat Methods 5:695–702

42 Javer A, Long Z, Nugent E, Grisi M, Siriwatwetchakul K, Dorfman KD, Cicuta P, Cosentino-Lagomarsino M (2013) Short-time movement of E. coli chromosomal loci depends on coordinate and subcellular localization. Nat Commun 4:3003

43 Ji L, Huo X, Zhang Y, Yan Z, Wang Q, Wen B (2020) TOPORS, a tumor suppressor protein, contributes to the maintenance of higher-order chromatin architecture. Biochim Biophys Acta 1863:194518

44 Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360

45 Kim KD, Tanizawa H,Iwasaki O, Corcoran CJ, Capizzi JR, Hayden JE, Noma K (2013) Centromeric motion facilitates the mobility of interphase genomic regions in fission yeast. JCellSci 126:5271–5283

46 Kind J, Pagie L, de Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, de Graaf CA, Amendola M (2015) Genome-wide maps of nuclear lamina interactions in single human cells. Cell 163:134–147

47 Kind J,Pagie L, Ortabozkoyun H, Boyle S, de Vries SS, Janssen H,Amendola M, Nolen LD, Bickmore WA, Steensel BV (2013) Single-cell dynamics of genome-nuclear lamina interactions. Cell 153:178–192

48 Kind J,Steensel BV (2014) Stochastic genome-nuclear lamina interactions: modulating roles of Lamin A and BAF. Nucleus 5:124–130

49 Korfali N, Wilkie GS, Swanson SK, Srsen V, Heras JDL, Batrakou DG, Malik P, Zuleger N, Kerr ARW, Florens L (2012) The nuclear envelope proteome differs notably between tissues. Nucleus 3:552–564

50 Krishan A (1975) Rapid flow cytofluorometric analysis of mammalian cell cycle by propidium iodide staining. J Cell Biol 66:188–193

51 Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A (2016) Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res 44:W90

52 Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

53 Lawrence MF, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, Morgan MT, Carey VJ (2013) Software for computing and annotating genomic ranges. PLoS Comput Biol 9:e1003118

54 Lerner J, Gomez-Garcia PA, McCarthy RL, Liu Z, Lakadamyali M, Zaret KS (2020) Two-parameter mobility assessments discriminate diverse regulatory factor behaviors in chromatin. Mol Cell 79:677

55 Li M, Gan J, Sun Y, Xu Z, Yang J,Sun Y,Li C (2020) Architectural proteins for the formation and maintenance of the 3D genome. Sci China Life Sci 63:795–810

56 Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–293

57 Liu L, Shi G, Thirumalai D, Hyeon C (2018) Chain organization of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci. PLoS Comput Biol 14:e1006617

58 Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550–550

59 Lund E, Oldenburg AR, Collas P (2014) Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations. Nucleic Acids Res 42:e92

60 Luo YB, Mastaglia FL, Wilton SD (2014) Normal and aberrant splicing of LMNA. J Med Genet 51:215–223

61 Luperchio TR, Sauria ME, Wong X, Gaillard M-C, Tsang P, Pekrun K, Ach RA, Yamada NA, Taylor J, Reddy K (2017) Chromosome conformation paints reveal the role of lamina association in genome organization and regulation. bioRxiv

62 Ma H, Naseri A, Reyes-Gutierrez P, Wolfe SA, Zhang S, Pederson T (2015) Multicolor CRISPR labeling of chromosomal loci in human cells. Proc Natl Acad Sci USA 112:3002–3007

63 Maass PG, Barutcu AR, Weiner CL, Rinn JL (2018) Inter-chromosomal contact properties in live-cell imaging and in Hi-C. Mol Cell 69:1039–1045

64 Meuleman W, Peric-Hupkes D, Kind J, Beaudry J-B,Pagie L, Kellis M, Reinders M, Wessels L, Steensel BV (2013) Constitutive nuclear lamina–genome interactions are highly conserved and associated with A/T-rich sequence. Genome Res 23:270–280

65 Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, Laue ED, Tanay A, Fraser P (2013) Single-cell Hi-C reveals cellto-cell variability in chromosome structure. Nature 502:59–64

66 Nora EP, Goloborodko A, Valton AL, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG (2017) Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization. Cell 169:930–944

67 Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum NL, Meisig J,Sedat J (2012) Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485:381–385

68 Nozaki T, Imai R, Tanbo M, Nagashima R, Tamura S, Tani T, Joti Y, Tomita M, Hibino K,Kanemaki MT (2017) Dynamic organization of chromatin domains revealed by super-resolution live-cell imaging. Mol Cell 67:282–293

69 Nuebler J, Fudenberg G,Imakaev M, Abdennur N, Mirny LA(2018) Chromatin organization by an interplay of loop extrusion and compartmental segregation. Proc Natl Acad Sci USA 115:E6697–E6706

70 Ochiai H, Sugawara T, Yamamoto T (2015) Simultaneous live imaging of the transcription and nuclear position of specific genes. Nucleic Acids Res 43:e127

71 Pierro MD, Potoyan DA, Wolynes PG, Onuchic JN (2018) Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes. Proc Natl Acad Sci USA 115:7753–7758

72 Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159:1665–1680

73 Rao SSP, Huang SC, Glenn StHilaire B, Engreitz JM, Perez EM, Kieffer-Kwon KR, Sanborn AL, Johnstone SE, Bascom GD, Bochkov ID (2017) Cohesin loss eliminates all loop domains. Cell 171:305–320

74 Ricci MA, Manzo C, Garcia-Parajo MF, Lakadamyali M, Cosma MP (2015) Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo. Cell 160:1145–1158

75 Ruan J, Xu C, Bian C,Lam R,Wang JP, Kania J, Min J, Zang J (2012) Crystal structures of the coil 2B fragment and the globular tail domain of human lamin B1. FEBS Lett 586:314–318

76 Rust MJ, Bates M, Zhuang X (2006) Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 3:793–795

77 Sawh AN, Shafer MER, Su J-H, Zhuang X, Wang S, Mango SE (2020) Lamina-dependent stretching and unconventional chromosome compartments in early C. elegans embryos. Mol Cell 78:96–111

78 Schirmer EC, Guan T, Gerace L (2001) Involvement of the lamin rod domain in heterotypic lamin interactions important for nuclear organization. J Cell Biol 153:479–490

79 Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, Haering CH, Mirny L (2017) Two independent modes of chromatin organization revealed by cohesin removal. Nature 551:51–56

80 Servant N, Lajoie BR, Nora EP, Giorgetti L, Chen CJ, Heard E, Dekker J, Barillot E (2012) HiTC: exploration of high-throughput ‘C’ experiments. Bioinformatics 28:2843–2844

81 Servant N,Varoquaux N, Lajoie BR, Viara E, Chen C-J, Vert J-P, Heard E, Dekker J, Barillot E (2015) HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol 16:259

82 Shao S, Xue B, Sun Y (2018) Intranucleus single-molecule imaging in living cells. Biophys J 115:181–189

83 Shimi T,Pfleghaar K,Kojima S, Pack CG, Solovei I, Goldman AE, Adam SA, Shumaker DK, Kinjo M, Cremer T (2008) The A- and B-type nuclear lamin networks: microdomains involved in chromatin organization and transcription. Genes Dev 22:3409–3421

84 Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, Steensel BV, de Laat W (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38:1348–1354

85 Solovei I, Thanisch K, Feodorova Y(2016) How to rule the nucleus: divide et impera. Curr Opin Cell Biol 40:47–59

86 Solovei I, Wang AS, Thanisch K, Schmidt CS, Krebs S, Zwerger M, Cohen TV, Devys D, Foisner R, Peichl L (2013) LBR and lamin A/C sequentially tether peripheral heterochromatin and inversely regulate differentiation. Cell 152:584–598

87 Steensel BV, Belmont AS (2017) Lamina-associated domains: links with chromosome architecture, heterochromatin, and gene repression. Cell 169:780–791

88 Sun HB, Shen J, Yokota H (2000) Size-dependent positioning of human chromosomes in interphase nuclei. Biophys J 79:184–190

89 Tajik A, Zhang Y, Wei F, Sun J, Jia Q, Zhou W, Singh R, Khanna N, Belmont AS, Wang N (2016) Transcription upregulation via forceinduced direct stretching of chromatin. Nat Mater 15:1287–1296

90 Tanenbaum ME, Gilbert LA, Qi LS, Weissman JS, Vale RD (2014) A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159:635–646

91 Towbin BD, González-Aguilera C, Sack R, Gaidatzis D, Kalck V, Meister P, Askjaer P, Gasser SM (2012) Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery. Cell 150:934–947

92 Ulianov SV, Doronin SA, Khrameeva EE, Kos PI, Luzhin AV, Starikov SS, Galitsyna AA, Nenasheva VV, Ilyin AA, Flyamer IM (2019) Nuclear lamina integrity is required for proper spatial organization of chromatin in Drosophila. Nat Commun 10:1176

93 Verboon JM, Rincon-Arano H, Werwie TR, Delrow JJ, Scalzo D, Nandakumar V, Groudine M, Parkhurst SM (2015) Wash interacts with lamin and affects global nuclear organization. Curr Biol 25:804–810

94 Verdaasdonk JS, Vasquez PA, Barry RM, Barry T, Goodwin S, Forest MG, Bloom K (2013) Centromere tethering confines chromosome domains. Mol Cell 52:819–831

95 Viollier PH, Thanbichler M, McGrath PT, West L, Meewan M, McAdams HH, Shapiro L (2004) Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication. Proc Natl Acad Sci USA 101:9257–9262

96 Vivante A, Brozgol E, Bronshtein I, Levi V, Garini Y(2018) Chromatin dynamics governed by a set of nuclear structural proteins. Genes Chromos Cancer 58:437

97 Wagner N, Krohne G (2007) LEM-domain proteins: new insights into lamin-interacting proteins. Int Rev Cytol Surv Cell Biol 261:1–46

98 Wang S, Su JH, Beliveau BJ, Bintu B, Moffitt JR, Wu CT, Zhuang X (2016) Spatial organization of chromatin domains and compartments in single chromosomes. Science 353:598–602

99 Wutz G,Várnai C, Nagasaka K, Cisneros DA, Stocsits RR, Tang W, Schoenfelder S,Jessberger G, Muhar M, Hossain MJ (2017) Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins. EMBO J 36:3573–3599

100 Zheng X, Hu J, Yue S, Kristiani L, Kim M, Sauria M, Taylor J, Kim Y, Zheng Y (2018) Lamins organize the global three-dimensional genome from the nuclear periphery. Mol Cell 71:802–815

101 Zidovska A, Weitz DA, Mitchison TJ (2013) Micron-scale coherence in interphase chromatin dynamics. Proc Natl Acad Sci USA 110:15555–15560

102 Zwerger M, Roschitzki-Voser H, Zbinden R, Denais C, Herrmann H, Lammerding J, Grütter MG, Medalia O (2015) Altering lamina assembly reveals lamina-dependent and-independent functions for A-type lamins. J Cell Sci 128:3607–3620