Distinct features of lamin A-interacting chromatin domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin

References

• Burke B, Stewart CL. The nuclear lamins: flexibility in function. Nat Rev Mol Cell Biol 2013; 14:13-24; PMID:23212477; http://dx.doi.org/10.1038/nrm3488
   PubMed Web of Science ®Google Scholar
• Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de KA, Wessels L, de Laat W, et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 2008; 453:948-951; PMID:18463634; http://dx.doi.org/10.1038/nature06947
   PubMed Web of Science ®Google Scholar
• Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Graf S, Flicek P, Kerkhoven RM, van Lohuizen M, et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell 2010; 38:603-613; PMID:20513434; http://dx.doi.org/10.1016/j.molcel.2010.03.016
   PubMed Web of Science ®Google Scholar
• Meuleman W, Peric-Hupkes D, Kind J, Beaudry JB, Pagie L, Kellis M, Reinders M, Wessels L, van Steensel B. Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence. Genome Res 2013; 23:270-280; PMID:23124521; http://dx.doi.org/10.1101/gr.141028.112
   PubMed Web of Science ®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; 153:178-192; PMID:23523135; http://dx.doi.org/10.1016/j.cell.2013.02.028
   PubMed Web of Science ®Google Scholar
• Kind J, van Steensel B. Genome-nuclear lamina interactions and gene regulation. Curr Opin Cell Biol 2010; 22:320-325; PMID:20444586; http://dx.doi.org/10.1016/j.ceb.2010.04.002
   PubMed Web of Science ®Google Scholar
• Zuleger N, Robson MI, Schirmer EC. The nuclear envelope as a chromatin organizer. Nucleus 2011; 2:339-349; PMID:21970986; http://dx.doi.org/10.4161/nucl.2.5.17846
   PubMed Web of Science ®Google Scholar
• Collas P, Lund EG, Oldenburg AR. Closing the (nuclear) envelope on the genome: how nuclear lamins interact with promoters and modulate gene expression. BioEssays 2014; 36:75-83; PMID:24272858; http://dx.doi.org/10.1002/bies.201300138
   PubMed Web of Science ®Google Scholar
• Reddy KL, Zullo JM, Bertolino E, Singh H. Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 2008; 452:243-247; PMID:18272965; http://dx.doi.org/10.1038/nature06727
   PubMed Web of Science ®Google Scholar
• Mattout A, Pike BL, Towbin BD, Bank EM, Gonzalez-Sandoval A, Stadler MB, Meister P, Gruenbaum Y, Gasser SM. An EDMD mutation in C. elegans lamin blocks muscle-specific gene relocation and compromises muscle integrity. Curr Biol 2011; 21:1603-1614; PMID:21962710; http://dx.doi.org/10.1016/j.cub.2011.08.030
   PubMed Web of Science ®Google Scholar
• Towbin BD, Gonzalez-Aguilera C, Sack R, Gaidatzis D, Kalck V, Meister P, Askjaer P, Gasser SM. Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery. Cell 2012; 150:934-947; PMID:22939621; http://dx.doi.org/10.1016/j.cell.2012.06.051
   PubMed Web of Science ®Google Scholar
• Lund E, Oldenburg A, Delbarre E, Freberg C, Duband-Goulet I, Eskeland R, Buendia B, Collas P. Lamin A/C-promoter interactions specify chromatin state-dependent transcription outcomes. Genome Res 2013; 23:1580-1589; PMID:23861385; http://dx.doi.org/10.1101/gr.159400.113
   PubMed Web of Science ®Google Scholar
• Sadaie M, Salama R, Carroll T, Tomimatsu K, Chandra T, Young AR, Narita M, Perez-Mancera PA, Bennett DC, Chong H, et al. Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence. Genes Dev 2013; 27:1800-1808; PMID:23964094; http://dx.doi.org/10.1101/gad.217281.113
   PubMed Web of Science ®Google Scholar
• Shah PP, Donahue G, Otte GL, Capell BC, Nelson DM, Cao K, Aggarwala V, Cruickshanks HA, Rai TS, McBryan T, et al. Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape. Genes Dev 2013; 27:1787-1799; PMID:23934658; http://dx.doi.org/10.1101/gad.223834.113
   PubMed Web of Science ®Google Scholar
• Lund EG, Oldenburg AR, Collas P. Enriched Domain Detector: a program for detection of wide genomic enrichment domains robust against local variations. Nucleic Acids Res 2014; 42:e92; PMID:24782521; http://dx.doi.org/10.1093/nar/gku324
   PubMed Web of Science ®Google Scholar
• Greil F, Moorman C, van Steensel B. DamID: mapping of in vivo protein-genome interactions using tethered DNA adenine methyltransferase. Methods Enzymol 2006; 410:342-359; PMID:16938559; http://dx.doi.org/10.1016/S0076-6879(06)10016-6
   PubMedGoogle Scholar
• Collas P. The state-of-the-art of chromatin immunoprecipitation. Methods Mol Biol 2009; 567:1-25; PMID:19588082; http://dx.doi.org/10.1007/978-1-60327-414-2_1
   PubMedGoogle Scholar
• Dahl JA, Collas P. A rapid micro chromatin immunoprecipitation assay (mChIP). Nat Protoc 2008; 3:1032-1045; PMID:18536650; http://dx.doi.org/10.1038/nprot.2008.68
   PubMed Web of Science ®Google Scholar
• O'Neill LP, Turner BM. Histone H4 acetylation distinguishes coding regions of the human genome from heterochromatin in a differentiation-dependent but transcription- independent manner. EMBO J 1995; 14:3946-3957; PMID:7664735
   PubMed Web of Science ®Google Scholar
• Kouskouti A, Talianidis I. Histone modifications defining active genes persist after transcriptional and mitotic inactivation. EMBO J 2005; 24:347-357; PMID:15616580; http://dx.doi.org/10.1038/sj.emboj.7600516
   PubMed Web of Science ®Google Scholar
• Comelli L, Marchetti L, Arosio D, Riva S, Abdurashidova G, Beltram F, Falaschi A. The homeotic protein HOXC13 is a member of human DNA replication complexes. Cell Cycle 2009; 8:454-459; PMID:19182517; http://dx.doi.org/10.4161/cc.8.3.7649
   PubMed Web of Science ®Google Scholar
• Hirano Y, Hizume K, Kimura H, Takeyasu K, Haraguchi T, Hiraoka Y. Lamin B receptor recognizes specific modifications of histone H4 in heterochromatin formation. J Biol Chem 2012; 287(51):42654-63; PMID:23100253; http://dx.doi.org/10.1074/jbc.M112.397950
   PubMedGoogle Scholar
• Wal M, Pugh BF. Genome-wide mapping of nucleosome positions in yeast using high-resolution MNase ChIP-Seq. Methods Enzymol 2012; 513:233-250; PMID:22929772; http://dx.doi.org/10.1016/B978-0-12-391938-0.00010-0
   PubMed Web of Science ®Google Scholar
• McGhee JD, Felsenfeld G. Another potential artifact in the study of nucleosome phasing by chromatin digestion with micrococcal nuclease. Cell 1983; 32:1205-1215; PMID:6301684; http://dx.doi.org/10.1016/0092-8674(83)90303-3
   PubMed Web of Science ®Google Scholar
• Cockell M, Rhodes D, Klug A. Location of the primary sites of micrococcal nuclease cleavage on the nucleosome core. J Mol Biol 1983; 170:423-446; PMID:6631965; http://dx.doi.org/10.1016/S0022-2836(83)80156-9
   PubMed Web of Science ®Google Scholar
• Noll M, Kornberg RD. Action of micrococcal nuclease on chromatin and the location of histone H1. J Mol Biol 1977; 109:393-404; PMID:833849; http://dx.doi.org/10.1016/S0022-2836(77)80019-3
   PubMed Web of Science ®Google Scholar
• Dechat T, Korbei B, Vaughan OA, Vlcek S, Hutchison CJ, Foisner R. Lamina-associated polypeptide 2alpha binds intranuclear A-type lamins. J Cell Sci 2000; 113:3473-3484; PMID:10984438
   PubMed Web of Science ®Google Scholar
• Dechat T, Gesson K, Foisner R. Lamina-independent lamins in the nuclear interior serve important functions. Cold Spring Harb Symp Quant Biol 2010; 75:533-543; PMID:21209392; http://dx.doi.org/10.1101/sqb.2010.75.018
   PubMedGoogle Scholar
• Sarcinella E, Zuzarte PC, Lau PN, Draker R, Cheung P. Monoubiquitylation of H2A.Z distinguishes its association with euchromatin or facultative heterochromatin. Mol Cell Biol 2007; 27:6457-6468; PMID:17636032; http://dx.doi.org/10.1128/MCB.00241-07
   PubMed Web of Science ®Google Scholar
• Weber CM, Henikoff JG, Henikoff S. H2A.Z nucleosomes enriched over active genes are homotypic. Nat Struct Mol Biol 2010; 17:1500-1507; PMID:21057526; http://dx.doi.org/10.1038/nsmb.1926
   PubMedGoogle Scholar
• Weber CM, Ramachandran S, Henikoff S. Nucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase. Mol Cell 2014; 53:819-830; PMID:24606920; http://dx.doi.org/10.1016/j.molcel.2014.02.014
   PubMed Web of Science ®Google Scholar
• Kolb T, Maass K, Hergt M, Aebi U, Herrmann H. Lamin A and lamin C form homodimers and coexist in higher complex forms both in the nucleoplasmic fraction and in the lamina of cultured human cells. Nucleus 2011; 2:425-433; PMID:22033280; http://dx.doi.org/10.4161/nucl.2.5.17765
   PubMed Web of Science ®Google Scholar
• Kubben N, Voncken JW, Misteli T. Mapping of protein- and chromatin-interactions at the nuclear lamina. Nucleus 2010; 1:460-471; PMID:21327087; http://dx.doi.org/10.4161/nucl.1.6.13513
   PubMed Web of Science ®Google Scholar
• Dechat T, Gotzmann J, Stockinger A, Harris CA, Talle MA, Siekierka JJ, Foisner R. Detergent-salt resistance of LAP2a in interphase nuclei and phosphorylation-dependent association with chromosomes early in nuclear assembly implies functions in nuclear structure dynamics. EMBO J 1998; 17:4887-4902; PMID:9707448; http://dx.doi.org/10.1093/emboj/17.16.4887
   PubMed Web of Science ®Google Scholar
• Zhang S, Schones DE, Malicet C, Rochman M, Zhou M, Foisner R, Bustin M. High Mobility Group Protein N5 (HMGN5) and Lamina Associated Polypeptide 2 alpha (LAP2alpha) Interact and Reciprocally Affect Their Genome-wide Chromatin Organization. J Biol Chem 2013; 288:18104-18109; PMID:23673662; http://dx.doi.org/10.1074/jbc.C113.469544
   PubMedGoogle Scholar
• Fan JY, Gordon F, Luger K, Hansen JC, Tremethick DJ. The essential histone variant H2A.Z regulates the equilibrium between different chromatin conformational states. Nat Struct Biol 2002; 9:172-176; PMID:11850638; http://dx.doi.org/10.1038/nsb0402-316b
   PubMedGoogle Scholar
• Bonisch C, Hake SB. Histone H2A variants in nucleosomes and chromatin: more or less stable? Nucleic Acids Res 2012; 40:10719-10741; PMID:23002134; http://dx.doi.org/10.1093/nar/gks865
   PubMed Web of Science ®Google Scholar
• Weber CM, Henikoff S. Histone variants: dynamic punctuation in transcription. Genes Dev 2014; 28:672-682; PMID:24696452; http://dx.doi.org/10.1101/gad.238873.114
   PubMed Web of Science ®Google Scholar
• Nekrasov M, Amrichova J, Parker BJ, Soboleva TA, Jack C, Williams R, Huttley GA, Tremethick DJ. Histone H2A.Z inheritance during the cell cycle and its impact on promoter organization and dynamics. Nat Struct Mol Biol 2012; 19:1076-1083; PMID:23085713; http://dx.doi.org/10.1038/nsmb.2424
   PubMed Web of Science ®Google Scholar
• Santisteban MS, Hang M, Smith MM. Histone variant H2A.Z and RNA polymerase II transcription elongation. Mol Cell Biol 2011; 31:1848-1860; PMID:21357739; http://dx.doi.org/10.1128/MCB.01346-10
   PubMed Web of Science ®Google Scholar
• Creyghton MP, Markoulaki S, Levine SS, Hanna J, Lodato MA, Sha K, Young RA, Jaenisch R, Boyer LA. H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment. Cell 2008; 135:649-661; PMID:18992931; http://dx.doi.org/10.1016/j.cell.2008.09.056
   PubMed Web of Science ®Google Scholar
• Illingworth RS, Botting CH, Grimes GR, Bickmore WA, Eskeland R. PRC1 and PRC2 are not required for targeting of H2A.Z to developmental genes in embryonic stem cells. PLoS One 2012; 7:e34848; PMID:22496869
   PubMed Web of Science ®Google Scholar
• Wu R, Terry AV, Singh PB, Gilbert DM. Differential subnuclear localization and replication timing of histone H3 lysine 9 methylation states. Mol Biol Cell 2005; 16:2872-2881; PMID:15788566; http://dx.doi.org/10.1091/mbc.E04-11-0997
   PubMed Web of Science ®Google Scholar
• Duband-Goulet I, Woerner S, Gasparini S, Attanda W, Konde E, Tellier-Lebegue C, Craescu CT, Gombault A, Roussel P, Vadrot N, et al. Subcellular localization of SREBP1 depends on its interaction with the C-terminal region of wild-type and disease related A-type lamins. Exp Cell Res 2011; 317:2800-2813; PMID:21993218; http://dx.doi.org/10.1016/j.yexcr.2011.09.012
   PubMed Web of Science ®Google Scholar
• Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009; 10:R25; PMID:19261174; http://dx.doi.org/10.1186/gb-2009-10-3-r25
   PubMed Web of Science ®Google Scholar
• Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer. Nat Biotechnol 2011; 29:24-26; PMID:21221095; http://dx.doi.org/10.1038/nbt.1754
   PubMed Web of Science ®Google Scholar