title: Epigenetics of eu- and heterochromatin in inverted and conventional nuclei from mouse retina.
abstract: To improve light propagation through the retina, the rod nuclei of nocturnal mammals are uniquely changed compared to the nuclei of other cells. In particular, the main classes of chromatin are segregated in them and form regular concentric shells in order; inverted in comparison to conventional nuclei. A broad study of the epigenetic landscape of the inverted and conventional mouse retinal nuclei indicated several differences between them and several features of general interest for the organization of the mammalian nuclei. In difference to nuclei with conventional architecture, the packing density of pericentromeric satellites and LINE-rich chromatin is similar in inverted rod nuclei; euchromatin has a lower packing density in both cases. A high global chromatin condensation in rod nuclei minimizes the structural difference between active and inactive X chromosome homologues. DNA methylation is observed primarily in the chromocenter, Dnmt1 is primarily associated with the euchromatic shell. Heterochromatin proteins HP1-alpha and HP1-beta localize in heterochromatic shells, whereas HP1-gamma is associated with euchromatin. For most of the 25 studied histone modifications, we observed predominant colocalization with a certain main chromatin class. Both inversions in rod nuclei and maintenance of peripheral heterochromatin in conventional nuclei are not affected by a loss or depletion of the major silencing core histone modifications in respective knock-out mice, but for different reasons. Maintenance of peripheral heterochromatin appears to be ensured by redundancy both at the level of enzymes setting the epigenetic code (writers) and the code itself, whereas inversion in rods rely on the absence of the peripheral heterochromatin tethers (absence of code readers).
authors.affiliation: Department of Biology II, Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilian University Munich, Grosshadernerstrasse 2, Planegg-Martinsried, 82152, Munich, Germany.
authors.forename: Anja
authors.initials: A
authors.lastname: Eberhart
authors.forename: Yana
authors.initials: Y
authors.lastname: Feodorova
authors.forename: Congdi
authors.initials: C
authors.lastname: Song
authors.forename: Gerhard
authors.initials: G
authors.lastname: Wanner
authors.forename: Elena
authors.initials: E
authors.lastname: Kiseleva
authors.forename: Takahisa
authors.initials: T
authors.lastname: Furukawa
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Kimura
authors.forename: Gunnar
authors.initials: G
authors.lastname: Schotta
authors.forename: Heinrich
authors.initials: H
authors.lastname: Leonhardt
authors.forename: Boris
authors.initials: B
authors.lastname: Joffe
authors.forename: Irina
authors.initials: I
authors.lastname: Solovei
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000235:genetics* / Q000378:metabolism / Q000648:ultrastructure; D002868:Chromosomal Proteins, Non-Histone / Q000378:metabolism; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000378:metabolism; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D057890:Epigenomics; D022041:Euchromatin / Q000235:genetics* / Q000378:metabolism / Q000648:ultrastructure; D006570:Heterochromatin / Q000235:genetics* / Q000378:metabolism / Q000648:ultrastructure; D006657:Histones / Q000378:metabolism; D051379:Mice; D018345:Mice, Knockout; D012160:Retina / Q000378:metabolism*; D017948:Retinal Rod Photoreceptor Cells / Q000378:metabolism / Q000648:ultrastructure; D012728:Sex Chromatin; D014960:X Chromosome; D049951:X Chromosome Inactivation
chemical_list: D002868:Chromosomal Proteins, Non-Histone; D022041:Euchromatin; D006570:Heterochromatin; D006657:Histones; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases; C000619381:Dnmt1 protein, mouse