* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Supplementary Information (doc 63K)
Ridge (biology) wikipedia , lookup
Gene therapy wikipedia , lookup
Bisulfite sequencing wikipedia , lookup
Nucleic acid double helix wikipedia , lookup
Epigenetics in learning and memory wikipedia , lookup
Minimal genome wikipedia , lookup
Biology and consumer behaviour wikipedia , lookup
No-SCAR (Scarless Cas9 Assisted Recombineering) Genome Editing wikipedia , lookup
Genomic imprinting wikipedia , lookup
Epigenetic clock wikipedia , lookup
Genealogical DNA test wikipedia , lookup
Oncogenomics wikipedia , lookup
Zinc finger nuclease wikipedia , lookup
DNA supercoil wikipedia , lookup
Gene expression programming wikipedia , lookup
Genome (book) wikipedia , lookup
Point mutation wikipedia , lookup
Genetic engineering wikipedia , lookup
DNA vaccination wikipedia , lookup
Molecular cloning wikipedia , lookup
Primary transcript wikipedia , lookup
Genome evolution wikipedia , lookup
Cell-free fetal DNA wikipedia , lookup
Epigenetics of diabetes Type 2 wikipedia , lookup
Extrachromosomal DNA wikipedia , lookup
Epigenomics wikipedia , lookup
Cre-Lox recombination wikipedia , lookup
Epigenetics of human development wikipedia , lookup
Metagenomics wikipedia , lookup
Deoxyribozyme wikipedia , lookup
Non-coding DNA wikipedia , lookup
DNA damage theory of aging wikipedia , lookup
Cancer epigenetics wikipedia , lookup
Genome editing wikipedia , lookup
Vectors in gene therapy wikipedia , lookup
Site-specific recombinase technology wikipedia , lookup
History of genetic engineering wikipedia , lookup
Gene expression profiling wikipedia , lookup
Designer baby wikipedia , lookup
Therapeutic gene modulation wikipedia , lookup
Helitron (biology) wikipedia , lookup
Microevolution wikipedia , lookup
Supplementary discussion Human aging is associated with a functional decline in both replicating and nonreplicating tissues. The transgenerational functional decline in replicative capacity of DNA repair mutants that we report here is reminiscent of that observed in germ cells of telomere replication defective C. elegans mutants(1). One such mutant, trt-1, which has lost functional telomerase reverse transcriptase, shows a decline in transgenerational replicative capacity but not in post-mitotic lifespan(2). Although this appears similar to DNA repair mutants, the phenotypes associated with shortened replicative lifespan due to DNA repair deficiency are different. Decline of DNA repair mutants is not only caused by sterility, as in telomerase mutants, but also by embryonic and larval arrest. Furthermore, DNA repair-deficiency does not necessarily lead to a progressive drop in brood size as observed when telomeres shorten. This makes it unlikely that telomere shortening is the main cause of the functional decline in DNA repair mutants. There is the possibility that changes in gene expression in the ercc-1 mutant, including regulation of growth and development, are influenced by its developmental and growth defects. To avoid such bias, transcriptomic analysis was performed on ‘mixed-stage’ populations of four biological replicates grown on multiple plates. Importantly, correlation analyses between our dataset and that published by Hill et al for each developmental stage(3) indicated that the wild type and ercc-1 mixed populations that we analyzed had similar distributions of developmental stages (data not shown). In addition, the visible developmental and growth defects in the ercc-1 mutant were very diverse, affecting individual animals in different ways. Thus it seems unlikely that there was a specific enrichment of early developmental stages or enrichment of a specific defective developmental process in the ercc-1 mixed stage populations, which had a great influence on the transcriptomic data. Rather, in UV irradiated cultured mammalian cells similar changes in gene expression occur as in naturally aged tissues, which is reverted when UV-photolesions are removed(4). This suggests that accumulating DNA damage can directly influence transcriptional regulation. Supplementary Materials and Methods Extended microarray data analysis After pre-processing and normalization, “Two Group Comparison” t-tests were executed on all four replicates per sample group (ercc-1 and N2, respectively) in Qlucore (http://qlucore.se/) in order to identify genes differentially regulated at the 95% confidence level (p<0.05) in ercc-1 relative to the wild type, N2. Principal Component Analysis (PCA) was performed on the differentially expressed (p<0.05) genes after normalization to mean 0 and variance 1 and correction for a False Discovery Rate (FDR), q<0.07(5). Gene Set Enrichment Analysis (GSEA) to reveal over- or underrepresented Gene Ontology Biological Processes (BP) was performed using Cytoscape (http://www.cytoscape.org/) and the plugin BiNGO(6). The analysis was executed using the Hyper-geometric Test with Benjamini-Hochberg False Discovery Rate (FDR) correction. Comparisons with other high throughput studies(3, 7-9) were performed; For the studies where a fold-change (linear signal) or a Difference of Means (log2 signal) was presented, the Pearson correlation was calculated using the function PEARSON in Excel 2010. Where no fold-change (Difference of Means) was reported for specific lists we added up the number of genes/transcripts overlapping between the respective studies and the transcripts found in the ercc-1 regulated gene list (p<0.05). The counted numbers of genes overlapping two studies were then subjected to a 2x2 contingency table for the Fisher Exact test or Chi-square with Yates correction test in order to calculate for the statistical significance regarding the association between the two different studies. Here, we used the web-based http://www.graphpad.com/quickcalcs/index.cfm. statistical tool found at References 1. 2. 3. 4. 5. 6. 7. 8. 9. Zucchero T, Ahmed S. Genetics of proliferative aging. Exp Gerontol. 2006 Oct;41(10):992-1000. Meier B, Clejan I, Liu Y, Lowden M, Gartner A, Hodgkin J, Ahmed S. trt-1 is the Caenorhabditis elegans catalytic subunit of telomerase. PLoS Genet. 2006 Feb;2(2):e18. Hill AA, Hunter CP, Tsung BT, Tucker-Kellogg G, Brown EL. Genomic analysis of gene expression in C. elegans. Science (New York, NY. 2000 Oct 27;290(5492):809-812. Garinis GA, Uittenboogaard LM, Stachelscheid H, Fousteri M, van Ijcken W, Breit TM, van Steeg H, Mullenders LH, van der Horst GT, Bruning JC, Niessen CM, Hoeijmakers JH, Schumacher B. Persistent transcription-blocking DNA lesions trigger somatic growth attenuation associated with longevity. Nat Cell Biol. 2009 May;11(5):604-615. Benjamini Y, Hochberg Y. Controlling the False Discovery Rate: A Powerful and Practical Approach to Multiple Testing. J Roy Stat Soc B. 1995;57:289-300. Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics. 2005 Aug 15;21(16):3448-3449. Budovskaya YV, Wu K, Southworth LK, Jiang M, Tedesco P, Johnson TE, Kim SK. An elt-3/elt-5/elt-6 GATA transcription circuit guides aging in C. elegans. Cell. 2008 Jul 25;134(2):291-303. Lee SS, Kennedy S, Tolonen AC, Ruvkun G. DAF-16 target genes that control C. elegans life-span and metabolism. Science (New York, NY. 2003 Apr 25;300(5619):644-647. Roh JY, Sim SJ, Yi J, Park K, Chung KH, Ryu DY, Choi J. Ecotoxicity of silver nanoparticles on the soil nematode Caenorhabditis elegans using functional ecotoxicogenomics. Environ Sci Technol. 2009 May 15;43(10):3933-3940.