Short interspersed element (SINE) depletion and long interspersed element (LINE) abundance are not features universally required for imprinting - PubMed (original) (raw)
Short interspersed element (SINE) depletion and long interspersed element (LINE) abundance are not features universally required for imprinting
Michael Cowley et al. PLoS One. 2011.
Abstract
Genomic imprinting is a form of gene dosage regulation in which a gene is expressed from only one of the alleles, in a manner dependent on the parent of origin. The mechanisms governing imprinted gene expression have been investigated in detail and have greatly contributed to our understanding of genome regulation in general. Both DNA sequence features, such as CpG islands, and epigenetic features, such as DNA methylation and non-coding RNAs, play important roles in achieving imprinted expression. However, the relative importance of these factors varies depending on the locus in question. Defining the minimal features that are absolutely required for imprinting would help us to understand how imprinting has evolved mechanistically. Imprinted retrogenes are a subset of imprinted loci that are relatively simple in their genomic organisation, being distinct from large imprinting clusters, and have the potential to be used as tools to address this question. Here, we compare the repeat element content of imprinted retrogene loci with non-imprinted controls that have a similar locus organisation. We observe no significant differences that are conserved between mouse and human, suggesting that the paucity of SINEs and relative abundance of LINEs at imprinted loci reported by others is not a sequence feature universally required for imprinting.
Conflict of interest statement
Competing Interests: The authors have declared that no competing interests exist.
Figures
Figure 1. Imprinted and non-imprinted murine retrogenes.
(A) Four retrogenes expressed from the paternally-derived copy in newborn mouse brain (blue text) share three common features: location within the intron of a host gene, a 5′ CpG island and derivation from a parent gene on Chr X. A further three retrogenes sharing these features are biallelically expressed (black text). Further in silico analyses identified additional retrogenes that share two of the three features. The number of genes is indicated at each intersection of the Venn diagram. All were shown to be biallelically expressed (Figure 1b and data not shown). (B) Example sequence traces using gene specific primers amplifying from gDNA and newborn brain cDNA over SNPs between Bl6 and another strain (strain B). For Mcts2, 4933416C03Rik and Klhl9, strain B is cast. For Chmp1b and Galnt4, strain B is JF1. For the crosses, the maternal strain is presented first. Mcts2 is imprinted while the others are biallelically expressed. 4933416C03Rik and Chmp1b share all three of the common features, while Galnt4 and Klhl9 share only two of the three features (see Table S2).
Figure 2. Abundance of SINEs and LINEs at murine retrogene loci.
The five imprinted genes were compared with eighteen non-imprinted control retrogenes. The abundance of SINEs (A) and LINEs (B) is expressed per kb for each nested window. (C) – (G) The abundance of SINE subfamily elements. *p<0.05 by Student's T-test.
Figure 3. Abundance of L1 subfamilies at murine retrogene loci.
The abundance of V (A), F (B), Tf (C) and A (D) L1 subfamilies is expressed per kb for each nested window.
Figure 4. Abundance of SINEs and LINEs at human retrogene loci.
The three imprinted retrogenes and one imprinted processed pseudogene were compared with ten controls. (A) and (B) As for Figure 2. (C) The abundance of MIR elements.
Figure 5. Mean hot score of L1 elements at human retrogene loci.
Scores were assigned for L1 elements flanking the analysed genes according to their similarity to the hot L1 consensus sequence . Mean hot scores are presented from the three imprinted retrogenes and one imprinted processed pseudogene compared with ten non-imprinted controls.
References
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