Transcriptional landscape of the human cell cycle.
Yin LiuSujun ChenSu WangFraser SoaresMartin FischerFeilong MengZhou DuCharles LinClifford MeyerJames A DeCaprioMyles BrownX Shirley LiuHousheng Hansen HePublished in: Proceedings of the National Academy of Sciences of the United States of America (2017)
Steady-state gene expression across the cell cycle has been studied extensively. However, transcriptional gene regulation and the dynamics of histone modification at different cell-cycle stages are largely unknown. By applying a combination of global nuclear run-on sequencing (GRO-seq), RNA sequencing (RNA-seq), and histone-modification Chip sequencing (ChIP-seq), we depicted a comprehensive transcriptional landscape at the G0/G1, G1/S, and M phases of breast cancer MCF-7 cells. Importantly, GRO-seq and RNA-seq analysis identified different cell-cycle-regulated genes, suggesting a lag between transcription and steady-state expression during the cell cycle. Interestingly, we identified genes actively transcribed at early M phase that are longer in length and have low expression and are accompanied by a global increase in active histone 3 lysine 4 methylation (H3K4me2) and histone 3 lysine 27 acetylation (H3K27ac) modifications. In addition, we identified 2,440 cell-cycle-regulated enhancer RNAs (eRNAs) that are strongly associated with differential active transcription but not with stable expression levels across the cell cycle. Motif analysis of dynamic eRNAs predicted Kruppel-like factor 4 (KLF4) as a key regulator of G1/S transition, and this identification was validated experimentally. Taken together, our combined analysis characterized the transcriptional and histone-modification profile of the human cell cycle and identified dynamic transcriptional signatures across the cell cycle.
Keyphrases
- cell cycle
- single cell
- rna seq
- transcription factor
- gene expression
- cell proliferation
- dna methylation
- genome wide
- high throughput
- poor prognosis
- endothelial cells
- induced apoptosis
- circulating tumor cells
- heat shock
- oxidative stress
- signaling pathway
- multidrug resistant
- genome wide identification
- cell cycle arrest
- heat stress
- data analysis
- breast cancer cells