Cell-Size-Dependent Transcription of FLC and Its Antisense Long Non-coding RNA COOLAIR Explain Cell-to-Cell Expression Variation.
Cell-Size-Dependent Transcription of FLC and Its Antisense Long Non-coding RNA COOLAIR Explain Cell-to-Cell Expression Variation.
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DOI：
10.1016/j.cels.2017.05.010
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发表时间：
2017-06-28
期刊：
影响因子：
9.3
通讯作者：
Howard M
中科院分区：
文献类型：
--
作者：
Ietswaart R;Rosa S;Wu Z;Dean C;Howard M
单细胞转录动力学和变异的量化促进了对基因调控的机制理解。本文利用单分子RNA荧光原位杂交技术和数学模型，研究了拟南芥开花位点C （FLC）的细胞RNA动力学。FLC的表达量决定开花时间，并受反义（COOLAIR）转录调控。在没有观察到COOLAIR表达的细胞中，我们量化了FLC转录起始、延伸、内含子加工和lariat降解，以及mRNA从位点和降解的释放。在这些大小不一的细胞中，FLC mRNA数量随细胞大小线性增加，导致转录水平在细胞间存在很大的差异。这种变异是由细胞大小依赖的泊松FLC mRNA产生引起的，而不是由大的转录爆发引起的。然而，在表达coolair的细胞中，反义转录随细胞大小而增加，并导致FLC转录随细胞大小而减少。因此，我们的分析揭示了反义转录在调节细胞大小的转录比例中意想不到的作用。在没有反义转录的单细胞中，FLC mRNA的表达动力学和变异性被量化，FLC mRNA的产生随细胞大小的变化而变化。在转录反义RNA COOLAIR的细胞中，FLC的大小变化被改变。他们揭示，虽然FLC的表达在细胞之间是可变的，但这不是由于噪声。相反，变异来自FLC mRNA数量和细胞大小之间的线性缩放。FLC表达的大小可通过其反义长链非编码RNA COOLAIR的转录来调节。
Single-cell quantification of transcription kinetics and variability promotes a mechanistic understanding of gene regulation. Here, using single-molecule RNA fluorescence in situ hybridization and mathematical modeling, we dissect cellular RNA dynamics for Arabidopsis FLOWERING LOCUS C (FLC). FLC expression quantitatively determines flowering time and is regulated by antisense (COOLAIR) transcription. In cells without observable COOLAIR expression, we quantify FLC transcription initiation, elongation, intron processing, and lariat degradation, as well as mRNA release from the locus and degradation. In these heterogeneously sized cells, FLC mRNA number increases linearly with cell size, resulting in a large cell-to-cell variability in transcript level. This variation is accounted for by cell-size-dependent, Poissonian FLC mRNA production, but not by large transcriptional bursts. In COOLAIR-expressing cells, however, antisense transcription increases with cell size and contributes to FLC transcription decreasing with cell size. Our analysis therefore reveals an unexpected role for antisense transcription in modulating the scaling of transcription with cell size. The kinetics and variability of FLC expression are quantified in single cells Without antisense transcription, FLC mRNA production scales with cell size FLC transcription shows minimal stochasticity and no large bursts In cells transcribing the antisense RNA COOLAIR, size scaling of FLC is altered Ietswaart et al. quantify the kinetics of Arabidopsis FLOWERING LOCUS C (FLC) expression on the single-cell level. They reveal that while FLC expression is variable from cell to cell, this is not due to noise. Instead, variability arises from a linear scaling between FLC mRNA number and cell size. The size scaling of FLC expression can be modulated by transcription of its antisense long non-coding RNA, COOLAIR.