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An Inducible DamID System for Profiling Interactions of Nuclear Lamina Protein Component Lamin B1 with Chromosomes in Mouse Cells

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Abstract

At the level of DNA organization into chromatin, there are mechanisms that define gene expression profiles in specialized cell types. Genes within chromatin regions that are located at the nuclear periphery are generally expressed at lower levels; however, the nature of this phenomenon remains unclear. These parts of chromatin interact with nuclear lamina proteins like Lamin B1 and, therefore, can be identified in a given cell type by chromatin profiling of these proteins. In this study, we created and tested a Dam Identification (DamID) system induced by Cre recombinase using Lamin B1 and mouse embryonic fibroblasts. This inducible system will help to generate genome-wide profiles of chromatin proteins in given cell types and tissues with no need to dissect tissues from organs or separate cells from tissues, which is achieved by using specific regulatory DNA elements and due to the high sensitivity of the method.

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Abbreviations

Amp[r] :

ampicillin resistance gene

CMV:

cytomegalovirus

Dam:

DNA adenine methyltransferase

DamID:

DNA adenine methyltransferase identification

gDNA:

genomic DNA

mePCR:

methyl PCR (amplification of Dam-methylated genome fragments)

ori:

replication origin

RLA:

Rosa Left Arm

RRA:

Rosa Right Arm

STOP:

transcription terminator

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Authors and Affiliations

  1. Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia

    E. N. Kozhevnikova, A. E. Leshchenko & A. V. Pindyurin

  2. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia

    E. N. Kozhevnikova & A. V. Pindyurin

Authors
  1. E. N. Kozhevnikova
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  2. A. E. Leshchenko
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  3. A. V. Pindyurin
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Correspondence to E. N. Kozhevnikova.

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Original Russian Text © E. N. Kozhevnikova, A. E. Leshchenko, A. V. Pindyurin, 2018, published in Biokhimiya, 2018, Vol. 83, No. 5, pp. 763–773.

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Kozhevnikova, E.N., Leshchenko, A.E. & Pindyurin, A.V. An Inducible DamID System for Profiling Interactions of Nuclear Lamina Protein Component Lamin B1 with Chromosomes in Mouse Cells. Biochemistry Moscow 83, 586–594 (2018). https://doi.org/10.1134/S0006297918050115

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  • DOI: https://doi.org/10.1134/S0006297918050115

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