Nat Genet Feb 2006

Nat Genet Feb 2006

• Evidence for an instructive mechanism of de novo methylation in cancer cells. Nature Genetics 38, 149 - 153 (2006) by Howard Cedar Group.

  we have adopted a new approach for detecting CpG island DNA methylation that can be used together with microarray technology. Genome-wide analysis by this technique demonstrated that tumor-specific methylated genes belong to distinct functional categories, have common sequence motifs in their promoters and are found in clusters on chromosomes.
  Their approach was to employ methyl-DNA immunoprecipitation (mDIP) assay, that used antibodies specific for 5-methyl–cytosine residues. They verified this approach by comparing tumor cell lines and normal cells. Then, they carried out genome-wide mDIP on DNA from the colon cancer cell line Caco-2. A set of 135 gene promoters that were specifically methylated in the cancer cell line

  The most interesting finding was the set of genes methylated differently in tumor cells. They also further verified the expression levels of those genes in colon cancer. This paper worthy of a further look.
  
• MKS1, encoding a component of the flagellar apparatus basal body proteome, is mutated in Meckel syndrome. Nature Genetics 38, 141 - 143 (2006)
  
• The transmembrane protein meckelin (MKS3) is mutated in Meckel-Gruber syndrome and the wpk rat. Nature Genetics 38, 191 - 196 (2006)
  
• The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nature Genetics 38, 228 - 233 (2005) by Da-zhi Wang at UNC.
  They showed miR-1 and miR-133 had distinct roles in modulating skeletal muscle proliferation and differentiation in cultured myoblasts in vitro and in Xenopus laevis embryos in vivo. Downsream pathways were also identified for those 2 miRNAs, including histone deacetylase 4 (HDAC4) and serum response factor (SRF) respectively.
  
• Cooperative and antagonistic interactions between Sall4 and Tbx5 pattern the mouse limb and heart. Nature Genetics 38, 175 - 183 (2005) Published online: 25 December 2005; by Benoit G Bruneau group at The Hospital for Sick Children/U Toronto.
  TBX5, a gene encoding a T-box transcription factor, and SALL4, a gene encoding a zinc-finger transcription factor both are critical in limb formation. They found Tbx5 regulated Sall4 expression in the developing mouse forelimb and heart.
  
• Physiogenomic resources for rat models of heart, lung and blood disorders. Nature Genetics 38, 234 - 239 (2006). By Norman H Lee at TREX Inst Genomic Res.
  

  The TIGR rodent expression web-based resource (TREX) contains over 2,200 microarray hybridizations, involving over 800 animals from 18 different rat strains.

  Interesting concept. It would become fairly useful for physiological research. Thanks to our progress in bioinformatics.