Transcriptional kinetics and molecular functions of long noncoding RNAs

• Published in: Nature genetics Vol. 54; no. 3; pp. 306 - 317
• Main Authors: Johnsson, Per, Ziegenhain, Christoph, Hartmanis, Leonard, Hendriks, Gert-Jan, Hagemann-Jensen, Michael, Reinius, Björn, Sandberg, Rickard
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.03.2022; Nature Publishing Group
• Subjects: 631/208/191/2018; 631/208/200; 631/208/212; Actinomycin; Agriculture; Animal Genetics and Genomics; Biomedical and Life Sciences; Biomedicine; Burst size; Cancer Research; Cell cycle; Decay rate; Fibroblasts; Frequency analysis; Gene expression; Gene Expression Regulation - genetics; Gene Function; Genes; Human Genetics; Kinetics; Non-coding RNA; Proteins; Ribonucleic acid; RNA; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; Stem cells; Transcription; Transcription, Genetic - genetics
• ISSN: 1061-4036; 1546-1718; 1546-1718
• DOI: 10.1038/s41588-022-01014-1

An increasing number of long noncoding RNAs (lncRNAs) have experimentally confirmed functions, yet little is known about their transcriptional dynamics and it is challenging to determine their regulatory effects. Here, we used allele-sensitive single-cell RNA sequencing to demonstrate that, compared to messenger RNAs, lncRNAs have twice as long duration between two transcriptional bursts. Additionally, we observed increased cell-to-cell variability in lncRNA expression due to lower frequency bursting producing larger numbers of RNA molecules. Exploiting heterogeneity in asynchronously growing cells, we identified and experimentally validated lncRNAs with cell state-specific functions involved in cell cycle progression and apoptosis. Finally, we identified cis -functioning lncRNAs and showed that knockdown of these lncRNAs modulated the nearby protein-coding gene’s transcriptional burst frequency or size. In summary, we identified distinct transcriptional regulation of lncRNAs and demonstrated a role for lncRNAs in the regulation of mRNA transcriptional bursting. Allele-sensitive single-cell RNA sequencing analysis of long noncoding RNA (lncRNA) transcriptional kinetics shows that their lower expression compared to mRNA is due to lower burst frequencies and highlights cell-state-specific functions for several lncRNAs.