title: Unraveling the mechanisms of chromatin fibril packaging.
abstract: Recent data indicate that eukaryotic chromosomes are organized into Topologically Associating Domains (TADs); however, the mechanisms underlying TAD formation remain obscure. Based on the results of Hi-C analysis performed on 4 Drosophila melanogaster cell lines, we have proposed that specific properties of nucleosomes in active and repressed chromatin play a key role in the formation of TADs. Our computer simulations showed that the ability of "inactive" nucleosomes to stick to each other and the lack of such ability in "active" nucleosomes is sufficient for spatial segregation of these types of chromatin, which is revealed in the Hi-C analysis as TAD/inter-TAD partitioning. However, some Drosophila and mammalian TADs contain both active and inactive chromatin, a fact that does not fit this model. Herein, we present additional arguments for the model by postulating that transcriptionally active chromatin is extruded on the surface of a TAD, and discuss the possible impact of this organization on the enhancer-promoter communication and on the segregation of TADs.
authors.affiliation: a Institute of Gene Biology RAS , Moscow , Russia.
authors.forename: Alexey A
authors.initials: AA
authors.lastname: Gavrilov
authors.affiliation: b Department of Molecular Genetics of Cell , Institute of Molecular Genetics RAS , Moscow , Russia.
authors.forename: Yuri Y
authors.initials: YY
authors.lastname: Shevelyov
authors.affiliation: a Institute of Gene Biology RAS , Moscow , Russia.|c Department of Molecular Biology , Lomonosov Moscow State University , Moscow , Russia.
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Ulianov
authors.affiliation: d Institute for Information Transmission Problems (The Kharkevich Institute) RAS , Moscow , Russia.
authors.forename: Ekaterina E
authors.initials: EE
authors.lastname: Khrameeva
authors.affiliation: e Physics Department , Lomonosov Moscow State University , Moscow , Russia.
authors.forename: Pavel
authors.initials: P
authors.lastname: Kos
authors.affiliation: e Physics Department , Lomonosov Moscow State University , Moscow , Russia.
authors.forename: Alexander
authors.initials: A
authors.lastname: Chertovich
authors.affiliation: a Institute of Gene Biology RAS , Moscow , Russia.|c Department of Molecular Biology , Lomonosov Moscow State University , Moscow , Russia.
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Razin
mesh_terms: D000818:Animals; D002843:Chromatin / Q000737:chemistry* / Q000378:metabolism*; D059006:Chromosomes, Insect / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics; D006801:Humans
chemical_list: D002843:Chromatin
keywords: chromatin spatial structure; nucleosome; polymer simulations; topologically associating domains; transcription