RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome
RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome
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DOI：
10.1016/j.isci.2018.06.005
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发表时间：
2018-06-29
期刊：
影响因子：
5.8
通讯作者：
Zhong, Sheng
中科院分区：
文献类型：
--
作者：
Chen, Weizhong;Yan, Zhangming;Zhong, Sheng
由于核斑点核心和染色质之间的物理分离，识别核斑点附近的核基因组的所有部分仍然具有挑战性。我们假设，非编码RNA，包括小核RNA（snRNA）和Malat 1，积累在核斑点的周边（nsaRNA [核斑点相关RNA]），可能会延伸到足够接近基因组。利用转录组-基因组相互作用测定（RNA-基因组相互作用图谱[MARGI]），我们鉴定了nsaRNA相互作用基因组序列簇（nsaPeaks）。转录后前mRNA也积累成核斑点，表现出与nsaPeaks接近，但很少与其他基因组区域接近。我们在182个单细胞中进行的DNA荧光原位杂交和免疫荧光分析显示，核斑点定位在nsaPeak附近的几率比其邻近的基因组序列增加了3倍。这些数据表明，nsaRNA位于足够接近核基因组的模型，并留下可识别的基因组足迹，从而揭示了基因组接近核斑点的部分。
It remains challenging to identify all parts of the nuclear genome that are in proximity to nuclear speckles, due to physical separation between the nuclear speckle cores and chromatin. We hypothesized that noncoding RNAs including small nuclear RNA (snRNAs) and Malat1, which accumulate at the periphery of nuclear speckles (nsaRNA [nuclear speckle-associated RNA]), may extend to sufficient proximity to the genome. Leveraging a transcriptome-genome interaction assay (mapping of RNA-genome interactions [MARGI]), we identified clusters of nsaRNA-interacting genomic sequences (nsaPeaks). Posttranscriptional pre-mRNAs, which also accumulate to nuclear speckles, exhibited proximity to nsaPeaks but rarely to other genomic regions. Our combined DNA fluorescence in situ hybridization and immunofluorescence analysis in 182 single cells revealed a 3-fold increase in odds for nuclear speckles to localize near an nsaPeak than its neighboring genomic sequence. These data suggest a model that nsaRNAs are located in sufficient proximity to the nuclear genome and leave identifiable genomic footprints, thus revealing the parts of genome proximal to nuclear speckles.