Coiled bodies preferentially associate with U4, U11, and U12 small nuclearRNA genes in interphase HeLa cells but not with U6 and U7 genes

Coiled bodies (CBs) are nuclear organelles involved in the metabolism of sm all nuclear RNAs (snRNAs) and histone messages. Their structural morphology and molecular composition have been conserved from plants to animals. CBs preferentially and specifically associate with genes that encode U1, U2, an d U3 snRNAs as well as the cell cycle-regulated histone loci. A common link among these previously identified CB-associated genes is that they are eit her clustered or tandemly repeated in the human genome. Ln an effort to ide ntify additional loci that associate with CBs, we have isolated and mapped the chromosomal locations of genomic clones corresponding to bona fide U4, U6, U7, U11, and U12 snRNA loci. Unlike the clustered U1 and U2 genes, each of these loci encode a single gene, with the exception of the U4 clone, wh ich contains two genes. We next examined the association of these snRNA gen es with CBs and found that they colocalized less frequently than their mult icopy counterparts. To differentiate a lower level of preferential associat ion from random colocalization, we developed a theoretical model of random colocalization, which yielded expected values for chi(2) tests against the experimental data. Certain single-copy snRNA genes (U4, U11, and U12) but n ot controls were found to significantly (p < 0.000001) associate with CBs. Recent evidence indicates that the interactions between CBs and genes are m ediated by nascent transcripts. Taken together, these new results suggest t hat CB association may be substantially augmented by the increased transcri ptional capacity of clustered genes. Possible functional roles for the obse rved interactions of CBs with snRNA genes are discussed.