Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

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

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

Subjects

This article has been updated

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

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.

Similar content being viewed by others

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.

References

  1. Mercer, T. R., Dinger, M. E. & Mattick, J. S. Long non-coding RNAs: insights into functions. Nature Rev. Genet. 10, 155–159 (2009)

    Article  CAS  Google Scholar 

  2. Ponting, C. P., Oliver, P. L. & Reik, W. Evolution and functions of long noncoding RNAs. Cell 136, 629–641 (2009)

    Article  CAS  Google Scholar 

  3. Sanchez-Elsner, T., Gou, D., Kremmer, E. & Sauer, F. Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax . Science 311, 1118–1123 (2006)

    Article  ADS  CAS  Google Scholar 

  4. Petruk, S. et al. Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in cis by transcriptional interference. Cell 127, 1209–1221 (2006)

    Article  CAS  Google Scholar 

  5. Dinger, M. E. et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res. 18, 1433–1445 (2008)

    Article  CAS  Google Scholar 

  6. Dean, A. On a chromosome far, far away: LCRs and gene expression. Trends Genet. 22, 38–45 (2006)

    Article  CAS  Google Scholar 

  7. Ashe, H. L., Monks, J., Wijgerde, M., Fraser, P. & Proudfoot, N. J. Intergenic transcription and transinduction of the human β-globin locus. Genes Dev. 11, 2494–2509 (1997)

    Article  CAS  Google Scholar 

  8. De Santa, F. et al. A large fraction of extragenic RNA Pol II transcription sites overlap enhancers. PLoS Biol. 8, e1000384 (2010)

    Article  Google Scholar 

  9. Kim, T. K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182–187 (2010)

    Article  ADS  CAS  Google Scholar 

  10. Ørom, U. A. et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 143, 46–58 (2010)

    Article  Google Scholar 

  11. Chang, H. Y. Anatomic demarcation of cells: genes to patterns. Science 326, 1206–1207 (2009)

    Article  ADS  CAS  Google Scholar 

  12. Rinn, J. L. et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, 1311–1323 (2007)

    Article  CAS  Google Scholar 

  13. Dostie, J. et al. Chromosome conformation capture carbon copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 16, 1299–1309 (2006)

    Article  CAS  Google Scholar 

  14. Schuettengruber, B., Chourrout, D., Vervoort, M., Leblanc, B. & Cavalli, G. Genome regulation by polycomb and trithorax proteins. Cell 128, 735–745 (2007)

    Article  CAS  Google Scholar 

  15. Zhang, X. et al. A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood 113, 2526–2534 (2009)

    Article  ADS  CAS  Google Scholar 

  16. Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006)

    Article  CAS  Google Scholar 

  17. Kmita, M., Fraudeau, N., Herault, Y. & Duboule, D. Serial deletions and duplications suggest a mechanism for the collinearity of Hoxd genes in limbs. Nature 420, 145–150 (2002)

    Article  ADS  CAS  Google Scholar 

  18. Harpavat, S. & Cepko, C. L. RCAS-RNAi: a loss-of-function method for the developing chick retina. BMC Dev. Biol. 6, 2 (2006)

    Article  Google Scholar 

  19. Nelson, C. E. et al. Analysis of Hox gene expression in the chick limb bud. Development 122, 1449–1466 (1996)

    CAS  PubMed  Google Scholar 

  20. Kmita, M. et al. Early developmental arrest of mammalian limbs lacking HoxA/HoxD gene function. Nature 435, 1113–1116 (2005)

    Article  ADS  CAS  Google Scholar 

  21. Small, K. M. & Potter, S. S. Homeotic transformations and limb defects in Hox A11 mutant mice. Genes Dev. 7, 2318–2328 (1993)

    Article  CAS  Google Scholar 

  22. Davis, A. P., Witte, D. P., Hsieh-Li, H. M., Potter, S. S. & Capecchi, M. R. Absence of radius and ulna in mice lacking hoxa-11 and hoxd-11 . Nature 375, 791–795 (1995)

    Article  ADS  CAS  Google Scholar 

  23. Fromental-Ramain, C. et al. Hoxa-13 and Hoxd-13 play a crucial role in the patterning of the limb autopod. Development 122, 2997–3011 (1996)

    CAS  PubMed  Google Scholar 

  24. Ruthenburg, A. J., Allis, C. D. & Wysocka, J. Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol. Cell 25, 15–30 (2007)

    Article  CAS  Google Scholar 

  25. Wang, P. et al. Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II. Mol. Cell. Biol. 29, 6074–6085 (2009)

    Article  CAS  Google Scholar 

  26. Guenther, M. G. et al. Global and Hox-specific roles for the MLL1 methyltransferase. Proc. Natl Acad. Sci. USA 102, 8603–8608 (2005)

    Article  ADS  CAS  Google Scholar 

  27. Krajewski, W. A., Nakamura, T., Mazo, A. & Canaani, E. A motif within SET-domain proteins binds single-stranded nucleic acids and transcribed and supercoiled DNAs and can interfere with assembly of nucleosomes. Mol. Cell. Biol. 25, 1891–1899 (2005)

    Article  CAS  Google Scholar 

  28. Wysocka, J. et al. WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell 121, 859–872 (2005)

    Article  CAS  Google Scholar 

  29. Baron-Benhamou, J., Gehring, N. H., Kulozik, A. E. & Hentze, M. W. Using the λN peptide to tether proteins to RNAs. Methods Mol. Biol. 257, 135–154 (2004)

    CAS  PubMed  Google Scholar 

  30. Lajoie, B. R., van Berkum, N. L., Sanyal, A. & Dekker, J. My5C: web tools for chromosome conformation capture studies. Nature Methods 6, 690–691 (2009)

    Article  CAS  Google Scholar 

  31. Chang, H. Y. et al. Diversity, topographic differentiation, and positional memory in human fibroblasts. Proc. Natl Acad. Sci. USA 99, 12877–12882 (2002)

    Article  ADS  CAS  Google Scholar 

  32. Chang, H. Y. et al. Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol. 2, 206–214 (2004)

    Article  CAS  Google Scholar 

  33. Bernstein, B. E. et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120, 169–181 (2005)

    Article  CAS  Google Scholar 

  34. Rinn, J. L., Bondre, C., Gladstone, H. B., Brown, P. O. & Chang, H. Y. Anatomic demarcation by positional variation in fibroblast gene expression programs. PLoS Genet. 2, e119 (2006)

    Article  Google Scholar 

  35. Rinn, J. L. et al. A dermal HOX transcriptional program regulates site-specific epidermal fate. Genes Dev. 22, 303–307 (2008)

    Article  CAS  Google Scholar 

  36. Rinn, J. L. et al. A systems biology approach to anatomic diversity of skin. J. Invest. Dermatol. 128, 776–782 (2008)

    Article  CAS  Google Scholar 

  37. Soshnikova, N. & Duboule, D. Epigenetic temporal control of mouse Hox genes in vivo. Science 324, 1320–1323 (2009)

    Article  ADS  CAS  Google Scholar 

  38. Harrow, J. et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 7, (Suppl 1)S4 (2006)

    Article  Google Scholar 

  39. Birney, E. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007)

    Article  ADS  CAS  Google Scholar 

  40. Dostie, J. & Dekker, J. Mapping networks of physical interactions between genomic elements using 5C technology. Nature Protocols 2, 988–1002 (2007)

    Article  CAS  Google Scholar 

  41. Sasaki, Y. T., Sano, M., Kin, T., Asai, K. & Hirose, T. Coordinated expression of ncRNAs and HOX mRNAs in the human HOXA locus. Biochem. Biophys. Res. Commun. 357, 724–730 (2007)

    Article  CAS  Google Scholar 

  42. Raj, A., van den Bogaard, P., Rifkin, S. A., van Oudenaarden, A. & Tyagi, S. Imaging individual mRNA molecules using multiple singly labeled probes. Nature Methods 5, 877–879 (2008)

    Article  CAS  Google Scholar 

  43. Smith, D. B. & Johnson, K. S. Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase. Gene 67, 31–40 (1988)

    Article  CAS  Google Scholar 

  44. Dignam, J. D., Lebovitz, R. M. & Roeder, R. G. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11, 1475–1489 (1983)

    Article  CAS  Google Scholar 

  45. Michlewski, G. & Caceres, J. F. RNase-assisted RNA chromatography. RNA 16, 1673–1678 (2010).

Download references

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

Authors
  1. Kevin C. Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yul W. Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Bo Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Amartya Sanyal
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ryan Corces-Zimmerman
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yong Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Bryan R. Lajoie
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Angeline Protacio
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Ryan A. Flynn
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Rajnish A. Gupta
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Joanna Wysocka
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Ming Lei
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Job Dekker
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Jill A. Helms
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Howard Y. Chang
    View author publications

    You can also search for this author in PubMed Google Scholar

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.

Ethics declarations

Competing interests

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)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature09819

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing