Table 1

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

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


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.

Meyer et al. Genome Biology 2007 8:R70   doi:10.1186/gb-2007-8-5-r70

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