Monoallelic, antisense and total RNA transcription in an in vitro neural differentiation system based on F1 hybrid mice
Monoallelic, antisense and total RNA transcription in an in vitro neural differentiation system based on F1 hybrid mice
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DOI：
10.1242/jcs.228973
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发表时间：
2019-09-01
影响因子：
4
通讯作者：
Kiyosawa, Hidenori
中科院分区：
文献类型：
--
作者：
Kondo, Shinji;Kato, Hidemasa;Kiyosawa, Hidenori
我们建立了一个体外诱导胚胎干细胞（ESCs）向神经元分化的系统，并利用该系统研究了细胞分化不同阶段poly（A）+和总RNA的转录。通过比较从20个RNA测序数据集[2个等位基因x（2个细胞系x4个时间点+2个小鼠脑）]组装的转录物的表达谱，可以评估品系、细胞和亲本特异性对总体表达的相对影响。在神经祖细胞阶段，ESCs的不同表达谱紧密会聚。单等位基因表达的转录本和反义转录本的时间变化模式进行了定量。在poly（A）+样品内、在总RNA样品内以及在poly（A）+和总RNA样品之间比较有义和反义转录物对揭示了显示出反相关表达变化的对的不同比率。在不同的RNA种类中鉴定了共享poly（A）+和poly（A）-转录的独特模式。单等位基因表达、反义转录物和多聚腺苷酸转录的调控和功能仍然是难以捉摸的。我们证明了我们的方法捕获这些转录活性的有效性，并提供了新的资源来阐明哺乳动物发育转录组。
We developed an in vitro system to differentiate embryonic stem cells (ESCs) derived from reciprocally crossed PI hybrid mice into neurons, and used it to investigate poly(A)+ and total RNA transcription at different stages of cell differentiation. By comparing expression profiles of transcripts assembled from 20 RNA sequencing datasets [2 allelesx(2 cell linesx4 time-points+2 mouse brains)], the relative influence of strain, cell and parent specificities to overall expression could be assessed. Divergent expression profiles of ESCs converged tightly at neural progenitor stage. Patterns of temporal variation of monoallelically expressed transcripts and antisense transcripts were quantified. Comparison of sense and antisense transcript pairs within the poly(A)+ sample, within the total RNA sample, and across poly(A)+ and total RNA samples revealed distinct rates of pairs showing anti-correlated expression variation. Unique patterns of sharing of poly(A)+ and poly(A)- transcription were identified in distinct RNA species. Regulation and functionality of monoallelic expression, antisense transcripts and poly(A)- transcription remain elusive. We demonstrated the effectiveness of our approach to capture these transcriptional activities, and provided new resources to elucidate the mammalian developmental transcriptome.