Abstract
The mechanisms underlying nuclear body (NB) formation and their contribution to genome function are unknown. Here we examined the non-random positioning of Cajal bodies (CBs), major NBs involved in spliceosomal snRNP assembly and their role in genome organization. CBs are predominantly located at the periphery of chromosome territories at a multi-chromosome interface. Genome-wide chromosome conformation capture analysis (4C-seq) using CB-interacting loci revealed that CB-associated regions are enriched with highly expressed histone genes and U small nuclear or nucleolar RNA (sn/snoRNA) loci that form intra- and inter-chromosomal clusters. In particular, we observed a number of CB-dependent gene-positioning events on chromosome 1. RNAi-mediated disassembly of CBs disrupts the CB-targeting gene clusters and suppresses the expression of U sn/snoRNA and histone genes. This loss of spliceosomal snRNP production results in increased splicing noise, even in CB-distal regions. Therefore, we conclude that CBs contribute to genome organization with global effects on gene expression and RNA splicing fidelity.
Highlights
The mechanisms underlying nuclear body (NB) formation and their contribution to genome function are unknown
To increase the number of putative Cajal bodies (CBs)-associating gene loci that can be examined by microscopy, we developed a six-colour DNA FISH mapping technique to simultaneously visualize five different gene loci of interest along with coilin, the major CB marker protein, in cells using spectral imaging and linear unmixing
The majority of CBs were frequently located at the periphery of chromosome territories (CTs), where two or more chromosomes interact with each other (Fig. 1b,e,f)
Summary
The mechanisms underlying nuclear body (NB) formation and their contribution to genome function are unknown. Our integrative analysis reveals CB-dependent looping of all categories of sn/snoRNA, small CB-specific RNA (scaRNA) and histone gene loci across the genome into transcriptionally highly active intra- and inter-chromosomal regions These interactions are greatly reduced in cells where CBs are absent or have been disassembled by specific depletions of essential CB components by RNAi. Small-and total-RNA-seq analyses show critical roles of CBs for the global maintenance of elevated sn/snoRNA expression in CB-containing aneuploidy cells, RNA pol II-driven transcription and splicing that are not limited to CB-proximal genomic regions. Our study demonstrates that CBs contribute to topological chromosome organization and affect the gene expression of target RNAs through proximal association with specific sn/snoRNA gene loci This influences RNA maturation processes and splicing fidelity
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