Skip to main content

Table 3 Relative allele usage in expression of genes neighboring strain-specific ZFP57 peaks

From: Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression

   Genomic DNA cDNA ES cells cDNA NS cells
Gene Zfp57 peak BC2 BC8 CB4 CB9 BC2 BC8 CB4 CB9 ANOVA BC2 BC8 CB4 CB9 ANOVA
B2_Nhlrc1 3′ intergna 38 % 35 % 32 % 38 % 28 % 21 % 38 % 39 % NS - - - - -
B3_Talpid3 Intron 51 % 52 % 51 % 50 % 51 % 51 % 51 % 51 % NS 54 % 52 % 52 % 53 % *
B4_Cmtm4 Intron 49 % 52 % 49 % 48 % 54 % 55 % 52 % 52 % * 47 % 50 % 47 % 49 % NS
B7_Efhd2 3′ intergn 52 % 53 % 59 % 56 % 37 % 37 % 40 % 38 % *** 53 % 55 % 53 % 57 % NS
B8_Arhgef10 Intron 42 % 45 % 41 % 40 % 31 % 27 % 26 % 28 % *** 40 % 39 % 39 % 40 % NS
B10_Fam89 3′ intergn 52 % 48 % 47 % 47 % 84 % 83 % 80 % 87 % *** 93 % 92 % 94 % 88 % ***
B10_Trim67 5′ intergn 45 % 48 % 45 % 46 % 64 % 75 % 84 % 84 % ** 47 % 53 % 47 % 58 % NS
B12_Nbas Intron 53 % 44 % 54 % 54 % 66 % 48 % 65 % 66 % NS 53 % 44 % 54 % 54 % NS
B13_Ankrd6 Intron 49 % 49 % 47 % 51 % 52 % 51 % 54 % 55 % NS 41 % 43 % 37 % 44 % **
B15_Btbd11 Intron 58 % 59 % 59 % 57 % 56 % 57 % 57 % 52 % NS 53 % 54 % 57 % 57 % NS
B16_Ccdc11 5′ intergn 51 % 51 % 52 % 53 % 62 % 71 % 62 % 66 % * 62 % 60 % 62 % 47 % NS
C1_Zfp553 3′ exon 36 % 35 % 36 % 34 % 73 % 78 % 73 % 75 % *** 39 % 39 % 39 % 43 % *
C2_Sdk2 Intron - - - - 12 % 11 % 20 % 20 % ** 59 % 56 % 50 % 56 % NS
C3_Qrsl1 Exon 50 % 46 % 45 % 48 % 46 % 49 % 51 % 49 % NS 47 % 48 % 50 % 49 % NS
C4_Ube2w Intron 40 % 37 % 39 % 38 % 67 % 66 % 64 % 63 % *** 66 % 66 % 64 % 66 % ***
C5_Usp14 Intron 47 % 45 % 46 % 47 % 47 % 45 % 45 % 46 % NS 43 % 42 % 43 % 43 % *
C6_4933422H20Rik Intron 50 % 48 % 46 % 49 % 21 % 28 % 32 % 36 % ** 8 % 19 % 8 % 22 % ***
C7_Tmem86a 3′ exon 52 % 49 % 52 % 52 % 52 % 41 % 51 % 59 % NS 46 % 45 % 48 % 44 % NS
C8_Atrn Intron 41 % 37 % 37 % 37 % 45 % 42 % 43 % 47 % * 36 % 38 % 40 % 46 % NS
  1. a Intergn intergenic ZFP57 binding upstream (5′) or downstream (3′) of the gene. Each row shows the gene name, position of the associated ZFP57 binding site and percentage of BL6 allelic expression ascertained by SNP pyrosequencing (i.e., 100 % = exclusively BL6, 0 % = exclusively Cast and 50 % = perfect biallelic expression). cDNA from four hybrid ES and neural stem cells was analyzed and compared with their corresponding genomic control for PCR bias (gDNA). Values in bold font emphasize significant C57BL/6 or Cast preferential allelic expression (p < 0.01, median difference greater than 15 % compared with genomic DNA control). For Sdk2, where no gDNA is available, ES cells are compared relative to neural stem cell expression. (*p < 0.05, **p < 0.01, ***p < 0.001 repeated measures ANOVA with Bonferroni’s post-test; NS not significant). See also Fig. S10 in Additional file 1 and Fig. 6 highlighting the relative expression level and allelic preference for eight highlighted genes.
Back to article page

Genome Biology

ISSN: 1474-760X

Contact us