linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis

Genes Dev. 2013 Jun 1;27(11):1260-71. doi: 10.1101/gad.217018.113. Epub 2013 May 30.


Recently, researchers have uncovered the presence of many long noncoding RNAs (lncRNAs) in embryonic stem cells and believe they are important regulators of the differentiation process. However, there are only a few examples explicitly linking lncRNA activity to transcriptional regulation. Here, we used transcript counting and spatial localization to characterize a lncRNA (dubbed linc-HOXA1) located ∼50 kb from the Hoxa gene cluster in mouse embryonic stem cells. Single-cell transcript counting revealed that linc-HOXA1 and Hoxa1 RNA are highly variable at the single-cell level and that whenever linc-HOXA1 RNA abundance was high, Hoxa1 mRNA abundance was low and vice versa. Knockdown analysis revealed that depletion of linc-HOXA1 RNA at its site of transcription increased transcription of the Hoxa1 gene cis to the chromosome and that exposure of cells to retinoic acid can disrupt this interaction. We further showed that linc-HOXA1 RNA represses Hoxa1 by recruiting the protein PURB as a transcriptional cofactor. Our results highlight the power of transcript visualization to characterize lncRNA function and also suggest that PURB can facilitate lncRNA-mediated transcriptional regulation.

Keywords: gene regulation; noncoding RNA; single molecule.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Line
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Embryonic Stem Cells / metabolism
  • Gene Expression
  • Gene Knockdown Techniques
  • Gene Silencing*
  • Genes, Homeobox / genetics*
  • Homeodomain Proteins / genetics*
  • Mice
  • Multigene Family / genetics
  • RNA Isoforms / analysis
  • RNA Isoforms / biosynthesis
  • RNA Isoforms / genetics
  • RNA, Long Noncoding / analysis
  • RNA, Long Noncoding / biosynthesis
  • RNA, Long Noncoding / genetics*
  • Single-Cell Analysis
  • Transcription Factors / genetics*
  • Transcription, Genetic / genetics*
  • Tretinoin


  • DNA-Binding Proteins
  • Homeodomain Proteins
  • Purb protein, mouse
  • RNA Isoforms
  • RNA, Long Noncoding
  • Transcription Factors
  • homeobox A1 protein
  • Tretinoin