Neuron-type specific regulation of a 3'UTR through redundant and combinatorially acting cis-regulatory elements

RNA. 2010 Feb;16(2):349-63. doi: 10.1261/rna.1931510. Epub 2009 Dec 29.


3' Untranslated region (UTR)-dependent post-transcriptional regulation has emerged as a critical mechanism of controlling gene expression in various physiological contexts, including cellular differentiation events. Here, we examine the regulation of the 3'UTR of the die-1 transcription factor in a single neuron of the nematode C. elegans. This 3'UTR shows the intriguing feature of being differentially regulated across the animal's left/right axis. In the left gustatory neuron, ASEL, in which DIE-1 protein is normally expressed in adult animals, the 3'UTR confers no regulatory information, while in the right gustatory neuron, ASER, where DIE-1 is normally not expressed, this 3'UTR confers negative regulatory information. Here, we systematically analyze the cis-regulatory architecture of the die-1 3'UTR using a transgenic, in vivo assay system. Through extensive mutagenesis and sequence insertions into heterologous 3'UTR contexts, we describe three 25-base-pair (bp) sequence elements that are both required and sufficient to mediate the ASER-specific down-regulation of the die-1 3'UTR. These three 25-bp sequence elements operate in both a redundant and combinatorial manner. Moreover, there are not only redundant elements within the die-1 3'UTR regulating its left/right asymmetric activity but asymmetric 3'UTR regulation is itself redundant with other regulatory mechanisms to achieve asymmetric DIE-1 protein expression and function in ASEL versus ASER. The features of 3'UTR regulation we describe here may apply to some of the vast number of genes in animal genomes whose expression is predicted to be regulated through their 3'UTR.

Publication types

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

MeSH terms

  • 3' Untranslated Regions*
  • Animals
  • Animals, Genetically Modified
  • Base Sequence
  • Caenorhabditis / cytology
  • Caenorhabditis / genetics
  • Caenorhabditis / metabolism
  • Caenorhabditis elegans / cytology
  • Caenorhabditis elegans / genetics*
  • Caenorhabditis elegans / metabolism*
  • Caenorhabditis elegans Proteins / genetics
  • Genes, Helminth
  • Genetic Complementation Test
  • Homeodomain Proteins / genetics
  • MicroRNAs / genetics
  • Molecular Sequence Data
  • Mutation
  • Neurons / metabolism
  • RNA, Helminth / genetics*
  • Regulatory Elements, Transcriptional
  • Sequence Homology, Nucleic Acid
  • Species Specificity
  • Transcription Factors / genetics


  • 3' Untranslated Regions
  • Caenorhabditis elegans Proteins
  • DIE-1 protein, C elegans
  • Homeodomain Proteins
  • MicroRNAs
  • RNA, Helminth
  • Transcription Factors
  • cog-1 protein, C elegans