title: New insights into gene positional clustering and its properties supported by large-scale analysis of various differentiation pathways.
abstract: To understand how genes are distributed on chromosomes we bring new insights into gene positional clustering and its properties. We have made a large-scale analysis of three types of differentiation and we observed that genes that subsequently enter into different cell processes are positionally clustered on chromosomes. Genes from the clusters are transcribed subsequently with respect to time kinetics and also to position. This means that the genes related to a cellular process are clustered together, independent of the period of time during which they are active and important for the process. Our results also demonstrate not only that there are general regions of increased or decreased levels of gene expression, but also that, in fact, in some chromosome regions we can find clustering of genes related to specific cell processes. The results provided in this paper also support the theory of "transcription factories" and show that transcription of genes from the clusters is managed by softer epigenetic mechanisms.
authors.affiliation: Center for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Botanická 68a, 602 00 Brno, Czech Republic. qkoutna@fi.muni.cz
authors.forename: Irena
authors.initials: I
authors.lastname: Koutná
authors.forename: Petr
authors.initials: P
authors.lastname: Krontorád
authors.forename: Zbynek
authors.initials: Z
authors.lastname: Svoboda
authors.forename: Eva
authors.initials: E
authors.lastname: Bártová
authors.forename: Michal
authors.initials: M
authors.lastname: Kozubek
authors.forename: Stanislav
authors.initials: S
authors.lastname: Kozubek
mesh_terms: D001483:Base Sequence; D002454:Cell Differentiation / Q000235:genetics*; D017931:DNA Primers / Q000235:genetics; D020869:Gene Expression Profiling; D006098:Granulocytes / Q000166:cytology / Q000378:metabolism; D018922:HL-60 Cells; D006801:Humans; D020014:K562 Cells; D008533:Megakaryocytes / Q000166:cytology / Q000378:metabolism; D009000:Monocytes / Q000166:cytology / Q000378:metabolism; D005810:Multigene Family; D038042:Myelopoiesis / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D034061:Thrombopoiesis / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D017931:DNA Primers