Imprinted genes: identification by chromosome rearrangements and post-genomic strategies

Abstract

Imprinted genes are differentially expressed from the maternally and paternally inherited alleles. Accordingly, inheritance of both copies of an imprinted chromosome or region from a single parent leads to the mis-expression of the imprinted genes present in the selected region. Strains of mice with reciprocal and Robertsonian chromosomal translocations or mice with engineered chromosomal rearrangements can be used to produce progeny where both copies of a chromosomal region are inherited from one parent. In combination with systematic differential expression and methylation-based approaches, these mice can be used to identify novel imprinted genes. Advances in genome sequencing and computer-based technologies have facilitated this approach to finding imprinted genes.

Fig. I

Fig. I

Distal chromosome 7 imprinting cluster. (a) Red boxes show maternally expressed genes and blue boxes show paternally expressed genes. (b) LoxP sites were inserted between Kcnq1 and Cdkn1c on the distal end of chromosome 7, and the distal end of chromosome 11 to generate a reciprocal translocation between chromosomes 7 and 11 in an embryonic stem cell. Adapted from Ref. [b].

Fig. I

Map of chromosomes 2, 6, 7 and 9. Yellow regions have abnormal imprinting phenotypes with maternal (Mat) or paternal (Pat) duplication. Imprinted genes in blue are paternally expressed. Imprinted genes in red are maternally expressed. Imprinted genes within clusters are not necessarily in correct order Asterisks show paternally expressed small nucleolar RNAs.

Fig. 1

Methylation RDA (Me-RDA) can be used to compare gene expression between normal (fertilized) and parthenogenetic embryos. Genomic DNA is digested with HpaII and adapters are ligated before PCR. Rounds of subtractive hybridization remove DNA species in common between the embryos and enrich for differentially methylated products, which are recovered by PCR.