Opposing Roles for the lncRNA Haunt and Its Genomic Locus in Regulating HOXA Gene Activation during Embryonic Stem Cell Differentiation

Cell Stem Cell. 2015 May 7;16(5):504-16. doi: 10.1016/j.stem.2015.03.007. Epub 2015 Apr 16.


Long noncoding RNAs (lncRNAs) have been implicated in controlling various aspects of embryonic stem cell (ESC) biology, although the functions of specific lncRNAs, and the molecular mechanisms through which they act, remain unclear. Here, we demonstrate discrete and opposing roles for the lncRNA transcript Haunt and its genomic locus in regulating the HOXA gene cluster during ESC differentiation. Reducing or enhancing Haunt expression, with minimal disruption of the Haunt locus, led to upregulation or downregulation of HOXA genes, respectively. In contrast, increasingly large genomic deletions within the Haunt locus attenuated HOXA activation. The Haunt DNA locus contains potential enhancers of HOXA activation, whereas Haunt RNA acts to prevent aberrant HOXA expression. This work reveals a multifaceted model of lncRNA-mediated transcriptional regulation of the HOXA cluster, with distinct roles for a lncRNA transcript and its genomic locus, while illustrating the power of rapid CRISPR/Cas9-based genome editing for assigning lncRNA functions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • CRISPR-Cas Systems
  • Cell Differentiation / genetics
  • Cell Line
  • Chromatin Assembly and Disassembly
  • DNA / genetics
  • Embryonic Stem Cells / physiology*
  • Enhancer Elements, Genetic / genetics
  • Gene Expression Regulation
  • Genetic Loci / genetics
  • Genome
  • Homeodomain Proteins / genetics
  • Homeodomain Proteins / metabolism*
  • Mice
  • RNA, Long Noncoding / genetics
  • RNA, Long Noncoding / metabolism*
  • Transcriptional Activation


  • Homeodomain Proteins
  • RNA, Long Noncoding
  • HoxA protein
  • DNA

Associated data

  • GEO/GSE58514