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A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

Nature volume 472, pages 120–124 (2011)Cite this article

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Abstract

The genome is extensively transcribed into long intergenic noncoding RNAs (lincRNAs), many of which are implicated in gene silencing1,2. Potential roles of lincRNAs in gene activation are much less understood3,4,5. Development and homeostasis require coordinate regulation of neighbouring genes through a process termed locus control6. Some locus control elements and enhancers transcribe lincRNAs7,8,9,10, hinting at possible roles in long-range control. In vertebrates, 39 Hox genes, encoding homeodomain transcription factors critical for positional identity, are clustered in four chromosomal loci; the Hox genes are expressed in nested anterior-posterior and proximal-distal patterns colinear with their genomic position from 3′ to 5′of the cluster11. Here we identify HOTTIP, a lincRNA transcribed from the 5′ tip of the HOXA locus that coordinates the activation of several 5′ HOXA genes in vivo. Chromosomal looping brings HOTTIP into close proximity to its target genes. HOTTIP RNA binds the adaptor protein WDR5 directly and targets WDR5/MLL complexes across HOXA, driving histone H3 lysine 4 trimethylation and gene transcription. Induced proximity is necessary and sufficient for HOTTIP RNA activation of its target genes. Thus, by serving as key intermediates that transmit information from higher order chromosomal looping into chromatin modifications, lincRNAs may organize chromatin domains to coordinate long-range gene activation.

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Figure 1: HOTTIP is a lincRNA transcribed in distal anatomic sites.
Figure 2: HOTTIP is required for coordinate activation of 5′ HOXA genes.
Figure 3: HOTTIP RNA is required for the active chromatin state of 5′ HOXA cluster.
Figure 4: HOTTIP RNA programs active chromatin via WDR5.

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Accession codes

Primary accessions

GenBank/EMBL/DDBJ

Gene Expression Omnibus

Data deposits

Sequence for human HOTTIP RNA has been deposited with GenBank under the accession number GU724873. Microarray data are deposited in Gene Expression Omnibus (GEO) under accession number GSE26540.

Change history

  • 07 April 2011

    The labelling of Fig. 4 was corrected.

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Acknowledgements

We thank C. Tabin for chick Hox gene probes, M. Scott and members of our labs for input, and M. Lin for use of the confocal microscope and imaging expertise. Supported by grants from the California Institute for Regenerative Medicine (H.Y.C., J.W.), the National Institutes of Health (HG003143 to J.D.), and the Scleroderma Research Foundation (H.Y.C.). K.C.W. is a recipient of a Dermatology Foundation Career Development Award. J.D. is a recipient of the W. M. Keck Foundation Distinguished Young Scholar Award. H.Y.C. and M.L. are Early Career Scientists of the Howard Hughes Medical Institute.

Author information

Author notes

  1. Yul W. Yang and Bo Liu: These authors contributed equally to this work.

Authors and Affiliations

  1. Howard Hughes Medical Institute, Program in Epithelial Biology, Stanford University School of Medicine, Stanford, 94305, California, USA

    Kevin C. Wang, Yul W. Yang, Ryan Corces-Zimmerman, Angeline Protacio, Ryan A. Flynn, Rajnish A. Gupta & Howard Y. Chang

  2. Department of Dermatology, University of California San Francisco (UCSF), San Francisco, 94115, California, USA

    Kevin C. Wang

  3. Department of Surgery, Stanford University School of Medicine, Stanford, 94305, California, USA

    Bo Liu & Jill A. Helms

  4. Program in Gene Function and Expression, Dept. of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, 01605, Massachusetts, USA

    Amartya Sanyal, Bryan R. Lajoie & Job Dekker

  5. Department of Biological Chemistry, Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, 48109, Michigan, USA

    Yong Chen & Ming Lei

  6. Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, 94305, California

    Joanna Wysocka

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Contributions

K.C.W., R.A.G. and H.Y.C. initiated the project; K.C.W. and H.Y.C. designed the experiments; K.C.W., Y.W.Y., B.L., A.S., R.C.-Z., B.R.L., A.P., R.A.F., J.D. and J.A.H. conducted the experiments and analysed the data; Y.C. and M.L. purified the recombinant proteins; J.W. provided antibodies and cell lines; K.C.W. and H.Y.C. prepared the manuscript with inputs from all co-authors.

Corresponding author

Correspondence to Howard Y. Chang.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains Supplementary Figures 1-13 with legends, legends for Supplementary Data 1 and Supplementary Tables 1-3 and additional references. (PDF 7723 kb)

Supplementary Data 1

The file shows 5C data. Binned data sets for the 5C experiments in Figures 1A and S6. (XLS 77 kb)

Supplementary Table 1

The table shows 5C primers used for the interrogation of the HoxA locus (ENm010). Primer sequences used in the 5C experiments. (XLS 67 kb)

Supplementary Table 2

The table shows a data summary of all of the 5C experiments. (XLS 29 kb)

Supplementary Table 3

The table shows sequences of quantitative PCR (qPCR) primers and siRNA against intronic HOTTIP (siIntronic 1 through 10). (XLS 29 kb)

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Wang, K., Yang, Y., Liu, B. et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472, 120–124 (2011). https://doi.org/10.1038/nature09819

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