title: Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains: evidence for local euchromatic neighborhoods.
abstract: Typically, eukaryotic nuclei contain 10-30 prominent domains (referred to here as SC-35 domains) that are concentrated in mRNA metabolic factors. Here, we show that multiple specific genes cluster around a common SC-35 domain, which contains multiple mRNAs. Nonsyntenic genes are capable of associating with a common domain, but domain "choice" appears random, even for two coordinately expressed genes. Active genes widely separated on different chromosome arms associate with the same domain frequently, assorting randomly into the 3-4 subregions of the chromosome periphery that contact a domain. Most importantly, visualization of six individual chromosome bands showed that large genomic segments ( approximately 5 Mb) have striking differences in organization relative to domains. Certain bands showed extensive contact, often aligning with or encircling an SC-35 domain, whereas others did not. All three gene-rich reverse bands showed this more than the gene-poor Giemsa dark bands, and morphometric analyses demonstrated statistically significant differences. Similarly, late-replicating DNA generally avoids SC-35 domains. These findings suggest a functional rationale for gene clustering in chromosomal bands, which relates to nuclear clustering of genes with SC-35 domains. Rather than random reservoirs of splicing factors, or factors accumulated on an individual highly active gene, we propose a model of SC-35 domains as functional centers for a multitude of clustered genes, forming local euchromatic "neighborhoods."
authors.affiliation: Department of Cell Biology, University of Massachusetts Medical Center, Worcester, MA 01655, USA.
authors.forename: Lindsay S
authors.initials: LS
authors.lastname: Shopland
authors.forename: Carol V
authors.initials: CV
authors.lastname: Johnson
authors.forename: Meg
authors.initials: M
authors.lastname: Byron
authors.forename: John
authors.initials: J
authors.lastname: McNeil
authors.forename: Jeanne B
authors.initials: JB
authors.lastname: Lawrence
mesh_terms: D002460:Cell Line; D002467:Cell Nucleus / Q000235:genetics*; D002871:Chromosome Banding; D022004:Chromosome Structures / Q000235:genetics*; D024042:Collagen Type I / Q000096:biosynthesis / Q000235:genetics; D004261:DNA Replication / Q000235:genetics; D022041:Euchromatin / Q000235:genetics*; D005057:Eukaryotic Cells / Q000166:cytology / Q000378:metabolism; D005455:Fluorescent Antibody Technique; D005786:Gene Expression Regulation / Q000235:genetics; D006801:Humans; D005810:Multigene Family / Q000235:genetics*; D009687:Nuclear Proteins / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D012261:Ribonucleoproteins; D000068103:Serine-Arginine Splicing Factors
chemical_list: D024042:Collagen Type I; D022041:Euchromatin; D009687:Nuclear Proteins; D012333:RNA, Messenger; D012261:Ribonucleoproteins; C073288:SRSF2 protein, human; D000068103:Serine-Arginine Splicing Factors