Comparative sequence analysis of the MECP2-locus in human and mouse reveals new transcribed regions

Mamm Genome. 2000 Mar;11(3):182-90. doi: 10.1007/s003350010035.


Comparative sequence analysis facilitates the identification of evolutionarily conserved regions, that is, gene-regulatory elements, which can not be detected by analyzing one species only. Sequencing of a 152-kb region on human Chromosome (Chr) Xq28 and of the synthenic 123 kb on mouse Chr XC identified the MECP2/Mecp2 locus, which is flanked by the gene coding for Interleukin-1 receptor associated kinase (IRAK/Il1rak) and the red opsin gene (RCP/Rsvp). By comparative sequence analysis, we identified a previously unknown, non-coding 5' exon embedded in a CpG island associated with MECP2/Mecp2. Thus, the MECP2/Mecp2 gene is comprised of four exons instead of three. Furthermore, sequence comparison 3' to the previously reported polyadenylation signal revealed a highly conserved region of 8.5 kb terminating in an alternative polyadenylation signal. Northern blot analysis verified the existence of two main transcripts of 1.9 kb and approximately 10 kb, respectively. Both transcripts exhibit tissue-specific expression patterns and have almost identical short half-lifes. The approximately 10-kb transcript corresponds to a giant 3' UTR contained in the fourth exon of MECP2. The long 3' UTR and the newly identified first intron of MECP2/Mecp2 are highly conserved in human and mouse. Furthermore, the human MECP2 locus is heterogeneous with respect to its DNA composition. We postulate that it represents a boundary between two H3 isochores that has not been observed previously.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions / genetics
  • Alternative Splicing
  • Animals
  • Blotting, Northern
  • Chromosomal Proteins, Non-Histone*
  • Conserved Sequence
  • CpG Islands
  • DNA / chemistry
  • DNA / genetics*
  • DNA-Binding Proteins / genetics*
  • Exons
  • Female
  • Gene Expression Regulation
  • Genes / genetics
  • Half-Life
  • Humans
  • Interleukin-1 Receptor-Associated Kinases
  • Introns
  • Male
  • Methyl-CpG-Binding Protein 2
  • Mice
  • Molecular Sequence Data
  • Poly A
  • Protein Kinases / genetics
  • RNA Stability
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Repressor Proteins*
  • Rod Opsins / genetics
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Tissue Distribution
  • Transcription, Genetic
  • Tumor Cells, Cultured


  • 3' Untranslated Regions
  • Chromosomal Proteins, Non-Histone
  • DNA-Binding Proteins
  • MECP2 protein, human
  • Mecp2 protein, mouse
  • Methyl-CpG-Binding Protein 2
  • RNA, Messenger
  • Repressor Proteins
  • Rod Opsins
  • long-wavelength opsin
  • Poly A
  • DNA
  • Protein Kinases
  • Interleukin-1 Receptor-Associated Kinases

Associated data

  • GENBANK/AF030876
  • GENBANK/AF121351
  • GENBANK/AF158180
  • GENBANK/AF158181