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Table 1 Gene-specific repair in low, medium, and high expression genes in young and aging adult glp-1 nematodes

From: Decline of nucleotide excision repair capacity in aging Caenorhabditis elegans

   Measuredb expression Percentage repair after 24 hours
Genomic target Estimateda transcription in adults young adult glp-1s aging adult glp-1s young adult glp-1s aging adult glp-1s
Low transcription genes
   par-2 (ubiquitin ligase; F58B6.3b) None/low 10a 12a 61 ± 2 33 ± 10
   pax-3 (homeodomain transcription factor; F27E5.2) Low 2a 3a 49 ± 1 25 ± 4
   lin-39 (HOX domain transcription factor; C07H6.7) None/low 22a 48a 55 ± 1 30 ± 2
   nob-1 (HOX domain transcription factor; Y75B8A.2) None/low 12a 13a 60 ± 3 22 ± 2
   Average     56 ± 3 28 ± 2
Medium transcription genes
   unc-2 (calcium channel α subunit; T02C5.5a) Medium 19 42 55 ± 1 29 ± 8
   polymerase epsilon (F33H2.5), F33H2.6, and part of dog-1 Medium 54 288 63 ± 5 32 ± 4
   atl-1 (ATM-like protein kinase; T06E4.3) Medium 88 146 70 ± 1 32 ± 1
   Average     63 ± 4 31 ± 2
High transcription genes
   act-1, act-2, act-3 (T04C12.6, T04C12.5, T04C12.4), and about 3 kb noncoding High 7,541 6,881 66 ± 2 39 ± 5
   unc-44 (ankyrin; B0350.2a.1) High 501 765 66 ± 4 48 ± 5
   act-4 (M03F4.2), M03F4.6, and M03F4.7 High 4,018 3,946 63 ± 5 41 ± 3
   Average     65 ± 1 42 ± 3
  1. Shown are gene-specific repair in low, medium, and high expression genes in young (1 day after L4) and aging (6 days after L4) adult glp-1 nematodes. The decrease in repair with age is very highly significant when all genes are analyzed individually (effect of age across all genes, P < 0.0001). Different genes are repaired at different rates when analyzed individually (effect of gene analyzed, irrespective of age; P = 0.003; two-factor analysis of variance on effects of age and Affymetrix-derived expression level). When genes were grouped qualitatively for statistical analysis as 'low', 'medium', and 'high' transcription, the level of expression had a significant effect on repair rate in young (P = 0.001) and aging (P = 0.005) nematodes. In young adults, repair of 'low' expression genes was significantly different than 'medium' and 'high' expression genes by Fisher's protected least significant difference (FPLSD; P = 0.01 and 0.0006, respectively), but repair of 'medium' and 'high' expression genes was not different (P = 0.28). In aging adults, repair of 'high' expression genes was significantly different than 'medium' and 'low' expression genes by FPLSD (P = 0.02 and 0.001, respectively), but repair of 'medium' and 'low' expression genes was not different (P = 0.37). Percentage repair data are presented as mean ± standard error (n = 3-4 per gene per time point). Initial damage was comparable in 1-day and 6-day adults: 2.1 ± 0.25 lesions/10 kilobases (kb) in 1-day adults, and 2.0 ± 0.20 lesions/10 kb in 6-day adults. aEstimated transcription levels were based on literature review. bMeasured expression data are average raw fluorescence values obtained from gene expression analysis in this study. cValues flagged as 'absent' (below reliable detection). The variability in raw scores flagged as absent is due to variability in the measurements made from different chips. Raw data presented in this table were averaged when multiple probes were present for a specific mRNA, and weighted averages were used when more than one gene is included in the amplified target.