Cell-Size-Dependent Transcription of FLC and Its Antisense Long Non-coding RNA COOLAIR Explain Cell-to-Cell Expression Variation
- 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-sizedependent, Poissonian FLC mRNA production, but not by large transcriptional bursts. In COOLAIRexpressing cells, however, antisense transcription increases with cell size and contributes to FLC transcription decreasing with cell size. OurSingle-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-sizedependent, Poissonian FLC mRNA production, but not by large transcriptional bursts. In COOLAIRexpressing 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.…
| Author details: | Robert Ietswaart, Stefanie RosaGND, Zhe Wu, Caroline DeanORCiD, Martin HowardORCiD |
|---|---|
| DOI: | https://doi.org/10.1016/j.cels.2017.05.010 |
| ISSN: | 2405-4712 |
| ISSN: | 2405-4720 |
| Pubmed ID: | https://pubmed.ncbi.nlm.nih.gov/28624615 |
| Title of parent work (English): | Cell systems |
| Publisher: | Cell Press |
| Place of publishing: | Cambridge |
| Publication type: | Article |
| Language: | English |
| Date of first publication: | 2017/06/28 |
| Publication year: | 2017 |
| Release date: | 2022/04/19 |
| Volume: | 4 |
| Number of pages: | 23 |
| First page: | 622 |
| Last Page: | 635 |
| Funding institution: | BBSRC grant [BB/K007203/1]; BBSRC Institute Strategic Program GRO [BB/J004588/1]; BBSRC studentship; EMBO Fellowship [ALTF 422-2016]; European Research Council Advanced grant MEXTIM |
| Organizational units: | Mathematisch-Naturwissenschaftliche Fakultät / Institut für Biochemie und Biologie |
| DDC classification: | 5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie |
| Peer review: | Referiert |
| Publishing method: | Open Access / Hybrid Open-Access |
| License (German): |  CC-BY - Namensnennung 4.0 International |
