ArticleProceedings of the National Academy of Sciences of the United States of America2017
Transcriptional landscape of the human cell cycle.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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Who cites it
78 citing papers in PubMed, 167 citations in OpenAlex.
- Lack of evidence for transcription-to-RNA maturation lags across G1-to-G2-phase boundary in fibroblasts.Life science alliance · 2026Article
- Synonymous codon usage shapes ERα function through specialized translational programs during breast cancer progression.Oncogene · 2026Article
- Nuclear Histone 3 Post-Translational Modification Profiling in Whole Cells using Spectral Flow Cytometry.bioRxiv : the preprint server for biology · 2026Article
- Aminated Quinolinequinones With EDG(s) as a Prostate Cancer Inhibitor: Mechanistic Insights and Pharmacokinetic Limitations.Chemistry & biodiversity · 2026Article
- A deep learning approach for time-consistent cell cycle phase prediction from microscopy data.PLoS computational biology · 2025Article
- Cell-cycle dynamics of nascent transcription and mature RNA accumulation are concordant in normal fibroblasts.bioRxiv : the preprint server for biology · 2025Article
- The epigenetic circle: feedback loops in the maintenance of cellular memory.Epigenetics & chromatin · 2025Review
- Subtle alteration in transcriptional memory governs the lineage-level cell cycle duration heterogeneities of mammalian cells.iScience · 2025Article
- Preliminary investigation of the epigenetic regulation of KMT2D via H3K4me1/H3K27ac in oral squamous cell carcinoma.Cellular and molecular life sciences : CMLS · 2025Article
- Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages.BMC genomics · 2025Article
- A reappraisal of cell cycle phase enrichment in synchronized estrogen receptor-positive cell models derived from breast adenocarcinomas.Scientific reports · 2025Article
- Identification of new reference genes with stable expression patterns for cell cycle experiments in human leukemia cell lines.Scientific reports · 2025Article
- Acetylation-Mediated Epigenetic Consequences for Biological Control and Cancer.Results and problems in cell differentiation · 2025Review
- Generic and queryable data integration schema for transcriptomics and epigenomics studies.Computational and structural biotechnology journal · 2024Article
- Transcriptomic landscape of quiescent and proliferating human corneal stromal fibroblasts.Experimental eye research · 2024Article
- MethylSeqLogo: DNA methylation smart sequence logos.BMC bioinformatics · 2024Article
- Human genomic DNA is widely interspersed with i-motif structures.The EMBO journal · 2024Article
- A comprehensive review of computational cell cycle models in guiding cancer treatment strategies.NPJ systems biology and applications · 2024Review
- G-quadruplex-mediated genomic instability drives SNVs in cancer.Nucleic acids research · 2024Article
- A neural network-based model framework for cell-fate decisions and development.Communications biology · 2024Article
18 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 6 institutions in 3 countries.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.