Coding RNAs with a non-coding function Maintenance of open chromatin structure
Coding RNAs with a non-coding function Maintenance of open chromatin structure
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DOI：
10.4161/nucl.2.5.17736
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发表时间：
2011-09-01
期刊：
影响因子：
3.7
通讯作者：
Rippe, Karsten
中科院分区：
文献类型：
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作者：
Caudron-Herger, Maiwen;Mueller-Ott, Katharina;Rippe, Karsten
基因组在称为染色质的大型核蛋白复合物中的多层组织通过建立具有不同 DNA 相关活性的子区室来调节核功能。在这里，我们证明 RNA 在维持人类和小鼠细胞系中解压缩且具有生物活性的间期染色质构象方面发挥着重要作用。如 RNase A 显微注射和荧光显微镜成像所示，单链 RNA 的消化诱导了这些解压缩区域明显的微米级染色质聚集。相比之下，中心周异染色质对 RNase A 处理更具抵抗力。我们鉴定出一类负责这种活性的编码 RNA 转录本，因此将这些“染色质互连”RNA 或 ciRNA 命名为“染色质互连”RNA 或 ciRNA。用纯化的核 RNA 片段进行 RNase A 处理后，可以恢复初始染色质分布，并通过高通量测序进行分析。它包含超过 500 个核苷酸 (nt) 的长 RNA 聚合酶 II (RNAP II) 转录物，这些转录物经过剪接、去除多聚腺苷酸化，并富含长度与 800 nt 类似的长 3'-非翻译区 (3'-UTR)。此外，RNA 耗尽或 RNAP II 抑制也会诱导染色质构象和 RNAP II 分布的类似可逆变化。基于这些结果，我们提出 ciRNA 可以充当主动转录的染色质区室的基因组组织结构因素。
The multi-layered organization of the genome in a large nucleoprotein complex termed chromatin regulates nuclear functions by establishing subcompartments with distinct DNA-associated activities. Here, we demonstrate that RNA plays an important role in maintaining a decondensed and biologically active interphase chromatin conformation in human and mouse cell lines. As shown by RNase A microinjection and fluorescence microscopy imaging, digestion of single-stranded RNAs induced a distinct micrometer scale chromatin aggregation of these decondensed regions. In contrast, pericentric heterochromatin was more resistant to RNase A treatment. We identified a class of coding RNA transcripts that are responsible for this activity, and thus termed these 'chromatin-interlinking' RNAs or ciRNAs. The initial chromatin distribution could be restored after RNase A treatment with a purified nuclear RNA fraction that was analyzed by high-throughput sequencing. It comprised long >500 nucleotides (nt) RNA polymerase II (RNAP II) transcripts that were spliced, depleted of polyadenylation and was enriched with long 3'-untranslated regions (3'-UTRs) above similar to 800 nt in length. Furthermore, similar reversible changes of the chromatin conformation and the RNAP II distribution were induced by either RNA depletion or RNAP II inhibition. Based on these results we propose that ciRNAs could act as genome organizing architectural factors of actively transcribed chromatin compartments.