title: A top-down analysis of Xa- and Xi-territories reveals differences of higher order structure at ≥ 20 Mb genomic length scales.
abstract: The active and inactive X (Xa;Xi) territory with its seemingly highly compacted Barr body in nuclei of female mammalian cells provide a key example for studies of structure/function relationships in homologous chromosomes with different functional properties. Here we used about 300 human X-specific large insert clones to generate probe sets, which target physically or functionally defined sub-chromosomal segments. We combined 3D multicolor FISH with quantitative 3D image analysis in order to compare the higher order organization in Xi-and Xa-territories in human diploid fibroblasts (HDFs) at various length scales ranging from about 50 Mb down to 1 Mb. Xi-territories were characterized by a rounder shape as compared to the flatter and more extended shape of Xa-territories. The overall compaction of the entire Xi-territory, including the Barr body, was only 1.2-fold higher than the Xa-territory. Significant differences, however, were noted between distinct subchromosomal segments: At 20 Mb length scales higher compaction in Xi-territories was restricted to specific segments, but higher compaction in these segments was not correlated with gene density, transcriptional activity, LINE content or histone markers locally enriched in Xi-territories. Notably, higher compaction in Xi-territories observed for 20 Mb segments was not reflected accordingly by inclosed segments of 1-4 Mb. We conclude that compaction differences result mainly from a regrouping of ~1 Mb chromatin domains rather than from an increased condensation of individual domains. In contrast to a previous report, genes subject to inactivation as well as escaping from inactivation were not excluded from the interior of the Barr body.
authors.affiliation: Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany.
authors.forename: Kathrin
authors.initials: K
authors.lastname: Teller
authors.forename: Doris
authors.initials: D
authors.lastname: Illner
authors.forename: Stefanie
authors.initials: S
authors.lastname: Thamm
authors.forename: Corella S
authors.initials: CS
authors.lastname: Casas-Delucchi
authors.forename: Rogier
authors.initials: R
authors.lastname: Versteeg
authors.forename: Mireille
authors.initials: M
authors.lastname: Indemans
authors.forename: Thomas
authors.initials: T
authors.lastname: Cremer
authors.forename: Marion
authors.initials: M
authors.lastname: Cremer
mesh_terms: D002467:Cell Nucleus / Q000648:ultrastructure; D002478:Cells, Cultured; D002874:Chromosome Mapping; D041321:Chromosomes, Human, X / Q000648:ultrastructure*; D015342:DNA Probes / Q000737:chemistry; D005260:Female; D006801:Humans; D007091:Image Processing, Computer-Assisted; D017404:In Situ Hybridization, Fluorescence; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated / Q000032:analysis / Q000648:ultrastructure*; D012728:Sex Chromatin / Q000648:ultrastructure
chemical_list: D015342:DNA Probes; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated; C077885:XIST non-coding RNA