Abstract
The nuclear lamina is a meshwork of A- and B-type lamins which interact with chromatin and regulate many nuclear functions. Recent studies have reported the discovery of chromatin domains interacting with nuclear lamins by chromatin immunoprecipitation (ChIP) of lamin A/C or B1 and identification of the associated DNA sequences by microarray or high-throughput sequencing. ChIP has been used over many years to get a snapshot of interactions between DNA and proteins in cells, including modified histones, transcription factors, chromatin remodelers, and recently, structural proteins such as nuclear lamins. We describe here the procedure we have established in our laboratory for ChIP of lamin A/C and lamin B1 from human cultured cells. The protocol is compatible with polymerase chain reaction and high-throughput sequencing analysis of the co-immunoprecipitated DNA.
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References
Burke B, Stewart CL (2013) The nuclear lamins: flexibility in function. Nat Rev Mol Cell Biol 14:13–24
Li Z, Zhu Y, Zhai Y, Castroagudin R, Bao Y, White TE, Glavy JS (2013) Werner complex deficiency in cells disrupts the nuclear pore complex and the distribution of lamin B1. Biochim Biophys Acta 1833:3338–3345
Sadaie M, Salama R, Carroll T, Tomimatsu K, Chandra T, Young AR, Narita M, Perez-Mancera PA, Bennett DC, Chong H, Kimura H, Narita M (2013) Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence. Genes Dev 27:1800–1808
Shah PP, Donahue G, Otte GL, Capell BC, Nelson DM, Cao K, Aggarwala V, Cruickshanks HA, Rai TS, McBryan T, Gregory BD, Adams PD, Berger SL (2013) Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape. Genes Dev 27:1787–1799
Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de Laat W, van Steensel B (2008) Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453:948–951
Kind J, Pagie L, Ortabozkoyun H, Boyle S, de Vries SS, Janssen H, Amendola M, Nolen LD, Bickmore WA, van Steensel B (2013) Single-cell dynamics of genome-nuclear lamina interactions. Cell 153:178–192
Meuleman W, Peric-Hupkes D, Kind J, Beaudry JB, Pagie L, Kellis M, Reinders M, Wessels L, van Steensel B (2013) Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence. Genome Res 23:270–280
Collas P, Lund EG, Oldenburg AR (2014) Closing the (nuclear) envelope on the genome: how nuclear lamins interact with promoters and modulate gene expression. BioEssays 36:75–83
Lund EG, Oldenburg A, Delbarre E, Freberg C, Duband-Goulet I, Eskeland R, Buendia B, Collas P (2013) Lamin A/C-promoter interactions specify chromatin state-dependent transcription outcomes. Genome Res 23:1580–1589
Lund EG, Oldenburg A, Collas P (2014) Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations. Nucleic Acids Res 42:e92
Lund EG, Duband-Goulet I, Oldenburg A, Buendia B, Collas P (2015) Distinct features of lamin A-interacting chromatin domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin. Nucleus 6:30–38
Dechat T, Gesson K, Foisner R (2010) Lamina-independent lamins in the nuclear interior serve important functions. Cold Spring Harb Symp Quant Biol 75:533–543
Kolb T, Maass K, Hergt M, Aebi U, Herrmann H (2011) 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 2:425–433
Collas P (2009) The state-of-the-art of chromatin immunoprecipitation. Methods Mol Biol 567:1–25
Acknowledgments
Our work is supported by the Norwegian Research Council, the University of Oslo and the Norwegian Center for Stem Cell Research (P.C.), and by South East Health Norway (A.R.O.).
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Oldenburg, A.R., Collas, P. (2016). Mapping Nuclear Lamin-Genome Interactions by Chromatin Immunoprecipitation of Nuclear Lamins. In: Shackleton, S., Collas, P., Schirmer, E. (eds) The Nuclear Envelope. Methods in Molecular Biology, vol 1411. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3530-7_20
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DOI: https://doi.org/10.1007/978-1-4939-3530-7_20
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Publisher Name: Humana Press, New York, NY
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Online ISBN: 978-1-4939-3530-7
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