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Cell Res. 2016 Aug;26(8):946-62. doi: 10.1038/cr.2016.84. Epub 2016 Jul 1.

A high-resolution transcriptome map of cell cycle reveals novel connections between periodic genes and cancer.

Dominguez D1,2, Tsai YH1,3, Gomez N2,4, Jha DK5, Davis I2,6,7,8, Wang Z1,2,9.

Author information

1
Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
2
Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
3
Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
4
Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
5
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
6
Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
7
Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
8
Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
9
Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Science, Shanghai, China.

Abstract

Progression through the cell cycle is largely dependent on waves of periodic gene expression, and the regulatory networks for these transcriptome dynamics have emerged as critical points of vulnerability in various aspects of tumor biology. Through RNA-sequencing of human cells during two continuous cell cycles (>2.3 billion paired reads), we identified over 1 000 mRNAs, non-coding RNAs and pseudogenes with periodic expression. Periodic transcripts are enriched in functions related to DNA metabolism, mitosis, and DNA damage response, indicating these genes likely represent putative cell cycle regulators. Using our set of periodic genes, we developed a new approach termed "mitotic trait" that can classify primary tumors and normal tissues by their transcriptome similarity to different cell cycle stages. By analyzing >4 000 tumor samples in The Cancer Genome Atlas (TCGA) and other expression data sets, we found that mitotic trait significantly correlates with genetic alterations, tumor subtype and, notably, patient survival. We further defined a core set of 67 genes with robust periodic expression in multiple cell types. Proteins encoded by these genes function as major hubs of protein-protein interaction and are mostly required for cell cycle progression. The core genes also have unique chromatin features including increased levels of CTCF/RAD21 binding and H3K36me3. Loss of these features in uterine and kidney cancers is associated with altered expression of the core 67 genes. Our study suggests new chromatin-associated mechanisms for periodic gene regulation and offers a predictor of cancer patient outcomes.

PMID:
27364684
PMCID:
PMC4973334
DOI:
10.1038/cr.2016.84
[Indexed for MEDLINE]
Free PMC Article

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