Long nuclear-retained non-coding RNAs and allele-specific higher-order chromatin organization at imprinted snoRNA gene arrays

Abstract

SummaryThe imprinted Snurf-Snrpn domain, also referred to as the Prader-Willi syndrome region, contains two ~100-200 kb arrays of repeated small nucleolar (sno)RNAs processed from introns of long, paternally expressed non-protein-coding RNAs whose biogenesis and functions are poorly understood. We provide evidence that C/D snoRNAs do not derive from a single transcript as previously envisaged, but rather from (at least) two independent transcription units. We show that spliced snoRNA host-gene transcripts accumulate near their transcription sites as structurally constrained RNA species that are prevented from diffusing, as well as multiple stable nucleoplasmic RNA foci dispersed in the entire nucleus but not in the nucleolus. Chromatin structure at these repeated arrays displays an outstanding parent-of-origin-specific higher-order organization: the transcriptionally active allele is revealed as extended DNA FISH signals whereas the genetically identical, silent allele is visualized as singlet DNA FISH signals. A similar allele-specific chromatin organization is documented for snoRNA gene arrays at the imprinted Dlk1-Dio3 domain. Our findings have repercussions for understanding the spatial organization of gene expression and the intra-nuclear fate of non-coding RNAs in the context of nuclear architecture.

Microprocessor dynamics and interactions at endogenous imprinted C19MC microRNA genes

“…1D, bottom) that presumably reflect specific higher-order chromatin organization at highly expressed, tandemly repeated arrays of non-coding DNA in decondensed chromatin. Indeed, they recall DNA FISH patterns recently documented at three other imprinted repeated small RNA gene clusters that, notably, also give rise to huge amounts of nuclear-retained repeated non-coding RNA species (Leung et al, 2009;Vitali et al, 2010). Whether high expression of imprinted non-coding RNA genes plays a role in chromatin structure is an appealing hypothesis that needs to be tested experimentally.…”

“…This does not imply that post-transcriptional pri-miRNA processing occurs systematically at other mammalian miRNA gene loci but suggests that it might be more prevalent than previously thought, particularly when numerous highly expressed hairpins are generated. The highly compartmentalized C19MC pri-miRNA species recall post-transcriptional 'RNA tracks' documented at several gene loci, including repeated small RNA-gene clusters (Lawrence et al, 1989;Royo et al, 2007;Shopland et al, 2002;Smith et al, 1999;Vitali et al, 2010), emphasizing the notion that RNA flow from its gene to the surrounding nucleoplasm is likely to be much more complex than generally assumed (see Smith et al, 1999). Defects in posttranscriptional RNA processing impair the full release and perturb the intranuclear fate of newly made RNA species (Custódio et al, 1999;Johnson et al, 2000).…”

Highly restricted deletion of the SNORD116 region is implicated in Prader–Willi Syndrome

“…14,16 This case therefore strengthens an evidence for the role of the SNORD116 region that has recently been highlighted in the molecular pathophysiology of PWS, [6][7][8] either as fully processed box C/D snoRNA species or as long non-coding host transcripts (116HG). [16][17][18][19] Next step will be to investigate the functions of these RNAs and their role in the pathogenesis of PWS. More distant genes potentially implicated in PWS syndrome as NDN and MAGEL2, 2 which were not deleted, were normally expressed in the fibroblasts of the proband (Supplementary Figure 4Sb).…”

R-loop formation at Snord116 mediates topotecan inhibition of Ube3a-antisense and allele-specific chromatin decondensation

“…Maternal mutations in UBE3A/Ube3a in humans and mice have identified the loss of function of this ubiquitin E3 ligase encoding gene as the cause of AS (3, 4). For PWS, small deletions of the HBII-85/ SNORD116 locus (5-7) and two mouse models of Snord116 deletions (8, 9) have identified the minimal causative deficiency to be the paternally expressed, highly repetitive, long noncoding RNA (lncRNA) that is processed into multiple small nucleolar RNAs (snoRNAs) and spliced nuclear retained host genes (116HG and 115HG) (10,11).A recent drug screen discovered that topoisomerase inhibitors, including topotecan, reduce Ube3a-ATS by an unknown mechanism to reverse the silencing of paternal Ube3a in mouse neurons and brain (12). Topotecan activates paternal Ube3a by reducing the abundance of an antisense transcript, Ube3a-ATS, at the 3′ end of a 1-Mb paternal transcript originating at the PWS imprinting control region (PWS-ICR; Fig.…”

“…Maternal mutations in UBE3A/Ube3a in humans and mice have identified the loss of function of this ubiquitin E3 ligase encoding gene as the cause of AS (3, 4). For PWS, small deletions of the HBII-85/ SNORD116 locus (5-7) and two mouse models of Snord116 deletions (8, 9) have identified the minimal causative deficiency to be the paternally expressed, highly repetitive, long noncoding RNA (lncRNA) that is processed into multiple small nucleolar RNAs (snoRNAs) and spliced nuclear retained host genes (116HG and 115HG) (10,11).…”