Cajal bodies are linked to genome conformation

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.

SMN - A chaperone for nuclear RNP social occasions?

“…90,91,95,100 Cajal bodies consistently associate with specific loci on multiple chromosomes, many of which include snRNA gene arrays, snoRNAs, as well as other small U RNA and histone gene clusters. 11,12,[118][119][120] Following siRNA knockdown of essential Cajal body components, WDR79/WRAP53 or USPL1, these chromosomal regions were no longer clustered, and the expression of many of the associated small U RNA loci were significantly reduced. Thus, disruption of Cajal bodies leads to a loss of genome conformation and this may lead to inefficient expression of snRNAs.…”

Spectral imaging to visualize higher-order genomic organization

“…Intriguingly, several sequencing-based studies have recently indicated that NBs assemble as a direct consequence of specific gene expression activity and form characteristic long-lived contact interactions with a defined cohort of genomic loci and CTs. [19][20][21] Nonetheless, the limitations of these populationbased studies using millions of mostly asynchronous cells are becoming apparent. Despite indications that genomic domains are known to form and maintain numerous spatial associations with both near (kBp) and distant (MBp) genomic locations, 22 it is unknown how many physical gene pairing events occur simultaneously.…”

“…Great strides have been made in the realm of high-content DNA FISH microscopy approaches (hiFISH), which utilize automated image acquisition and analysis tools to interrogate DNA probe libraries. 21,29,30 Potentially, this approach can accurately quantify gene pairing events that occur across larger linear genomic distances and between chromosomes at high-resolution but current highcontent microscopy experiments are still limited to only 4 distinct fluorophores for visualization (one of which must be dedicated to a nuclear stain for automated image analysis). Therefore, current methods are inadequate for the co-visualization of multiple genes in conjunction with co-detection of chromosome territories, sub-nuclear structures and/ or distinct epigenetic marks.…”

“…We have implemented this method, which we have named spectraFISH, for the study of 5 distinct genes or CTs with the CB, a major NB involved in spliceosomal snRNP biogenesis [31][32][33] and found frequently in cancer cells. 21 This nuclear structure actively coordinates 34 a network of gene pairing interactions with major and minor spliceosome U snRNA genes, [12][13][14]35 and other highly active intron-encoded U snoRNA/scaRNA genes, 21,36 but also histone gene clusters (e.g. HIST1) via the physically-associated histone locus body.…”

“…In the data presented below, we have visualized the genomic context where CBs are localized and the frequency of association between these CB-dependent genes are clustered. We achieved this by selecting genes of interest from a circular chromosome conformation capture (4C)-seq dataset 21 (using the RNU1 gene as a bait region) and co-visualized with up to 5 of these genes (or 4 CTs) with the CB marker protein, coilin. Alternatively, spectraFISH could also be modified to assess colocalization of DNA FISH foci with NBs or other nuclear structures.…”