Evaluation of the RET regulatory landscape reveals the biological relevance of a HSCR-implicated enhancer

Hum Mol Genet. 2005 Dec 15;14(24):3837-45. doi: 10.1093/hmg/ddi408. Epub 2005 Nov 3.


Evolutionary sequence conservation is now a relatively common approach for the prediction of functional DNA sequences. However, the fraction of conserved non-coding sequences with regulatory potential is still unknown. In this study, we focus on elucidating the regulatory landscape of RET, a crucial developmental gene within which we have recently identified a regulatory Hirschsprung disease (HSCR) susceptibility variant. We report a systematic examination of conserved non-coding sequences (n=45) identified in a 220 kb interval encompassing RET. We demonstrate that most of these conserved elements are capable of enhancer or suppressor activity in vitro, and the majority of the elements exert cell type-dependent control. We show that discrete sequences within regulatory elements can bind nuclear protein in a cell type-dependent manner that is consistent with their identified in vitro regulatory control. Finally, we focused our attention on the enhancer implicated in HSCR to demonstrate that this element drives reporter expression in cell populations of the excretory system and central nervous system (CNS) and peripheral nervous system (PNS), consistent with expression of the endogenous RET protein. Importantly, this sequence also modulates expression in the enteric nervous system consistent with its proposed role in HSCR.

Publication types

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

MeSH terms

  • Animals
  • Base Sequence
  • Binding Sites
  • Cells, Cultured
  • Central Nervous System / cytology
  • Central Nervous System / metabolism
  • Conserved Sequence
  • Enhancer Elements, Genetic / genetics*
  • Gene Expression Regulation, Developmental
  • Hirschsprung Disease / genetics*
  • Humans
  • Mice
  • Mice, Transgenic
  • Nuclear Proteins / metabolism
  • Peripheral Nervous System / cytology
  • Peripheral Nervous System / metabolism
  • Proto-Oncogene Proteins c-ret / genetics*
  • Proto-Oncogene Proteins c-ret / metabolism


  • Nuclear Proteins
  • Proto-Oncogene Proteins c-ret