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Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters

Nature Genetics volume 43, pages 621–629 (2011)Cite this article

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Abstract

Transcription of long noncoding RNAs (lncRNAs) within gene regulatory elements can modulate gene activity in response to external stimuli, but the scope and functions of such activity are not known. Here we use an ultrahigh-density array that tiles the promoters of 56 cell-cycle genes to interrogate 108 samples representing diverse perturbations. We identify 216 transcribed regions that encode putative lncRNAs, many with RT-PCR–validated periodic expression during the cell cycle, show altered expression in human cancers and are regulated in expression by specific oncogenic stimuli, stem cell differentiation or DNA damage. DNA damage induces five lncRNAs from the CDKN1A promoter, and one such lncRNA, named PANDA, is induced in a p53-dependent manner. PANDA interacts with the transcription factor NF-YA to limit expression of pro-apoptotic genes; PANDA depletion markedly sensitized human fibroblasts to apoptosis by doxorubicin. These findings suggest potentially widespread roles for promoter lncRNAs in cell-growth control.

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Figure 1: Identification of ncRNAs near and within cell-cycle genes.
Figure 2: ncRNA expression across diverse cell cycle perturbations.
Figure 3: Functional associations of ncRNAs.
Figure 4: Validated expression of ncRNAs in cell cycle progression, ESC differentiation and human cancers.
Figure 5: ncRNAs at the CDKN1A locus are induced by DNA damage.
Figure 6: PANDA lncRNA regulates the apoptotic response to DNA damage.
Figure 7: PANDA regulates transcription factor NF-YA.
Figure 8: Model of coding and noncoding transcripts at the CDKN1A locus coordinating the DNA damage response.

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Acknowledgements

We thank J. Rinn, M. Guttman and A. Regev for discussions, L. Attardi for careful reading of the manuscript and P. Khavari for reagents. Y.W., B.K. and Yu Wang are employees of Life Technologies. This work was supported by grants from the US National Institutes of Health (NIH)/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) (K08-AR054615 to D.J.W.), NIH/National Cancer Institute (NCI) (R01-CA118750 to H.Y.C.and R01-CA130795 to M.L.W.), the Juvenile Diabetes Research Foundation (S.K.K. and H.Y.C.) and the American Cancer Society (H.Y.C.). H.Y.C. is an Early Career Scientist of the Howard Hughes Medical Institute. T.H. is supported by the Stanford Graduate Fellowship, the National Science Foundation (NSF) Graduate Research Fellowship and the Department of Defense (DoD) National Defense Science & Engineering Graduate Fellowship (NDSEG).

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Author notes

  1. David J Wong and Howard Y Chang: These authors contributed equally to this work.

Authors and Affiliations

  1. Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA

    Tiffany Hung, Ashley K Koegel, David J Wong & Howard Y Chang

  2. Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA

    Tiffany Hung, Ashley K Koegel, Seung K Kim & Howard Y Chang

  3. Life Technologies, Foster City, California, USA

    Yulei Wang, Yu Wang & Benjamin Kong

  4. The Broad Institute, Cambridge, Massachusetts, USA

    Michael F Lin & Manolis Kellis

  5. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Michael F Lin & Manolis Kellis

  6. Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA

    Yojiro Kotake & Yue Xiong

  7. Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA

    Yojiro Kotake

  8. Department of Biochemistry 1, Hamamatsu University School of Medicine, Higashi-ku, Hamamatsu, Japan

    Yojiro Kotake

  9. Department of Genetics, Dartmouth Medical School, Hanover, New Hampshire, USA

    Gavin D Grant & Michael L Whitfield

  10. Department of Pathology, Academic Medical Center, Amsterdam, The Netherlands

    Hugo M Horlings & Marc van de Vijver

  11. Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Nilay Shah & Saraswati Sukumar

  12. Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Christopher Umbricht

  13. Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA

    Pei Wang & Seung K Kim

  14. Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Montebello, Oslo, Norway

    Anita Langerød & Anne-Lise Børresen-Dale

  15. Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway

    Anne-Lise Børresen-Dale

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Contributions

H.Y.C. and D.J.W. initiated the project. H.Y.C., D.J.W. and T.H. designed the experiments. T.H. performed the experiments and the computational analysis. Yulei Wang, Yu Wang and B.K. conducted high-throughput TaqMan RT-PCRs. M.F.L. and M.K. contributed CSF analysis. The following authors contributed samples or reagents: A.K.K., Y.K., G.D.G., H.M.H., N.S., C.U., P.W., A.L., S.K.K., M.v.d.V., A.-L.B.-D., S.S., M.L.W. and Y.X. The manuscript was prepared by H.Y.C., T.H. and D.J.W. with input from all co-authors.

Corresponding authors

Correspondence to David J Wong or Howard Y Chang.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–11 and Supplementary Tables 1, 2 and 5. (PDF 1466 kb)

Supplementary Table 3

List of cell cycle promoter transcripts (XLSX 25 kb)

Supplementary Table 4

Combined expression of all transcripts across all tiling arrays (XLSX 107 kb)

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Hung, T., Wang, Y., Lin, M. et al. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet 43, 621–629 (2011). https://doi.org/10.1038/ng.848

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