INT130385

Context Info Confidence 0.77 First Reported 2005 Last Reported 2008 Negated 1 Speculated 0 Reported most in Body Documents 7 Total Number 27 Disease Relevance 8.36 Pain Relevance 0.63

nucleoplasm (ERCC6) nucleolus (ERCC6) nucleus (ERCC6) DNA binding (ERCC6)

Anatomy Link Frequency skin 1 fibroblasts 1 parasympathetic 1 ERCC6 (Homo sapiens)

Pain Link Frequency Relevance Heat anesthesia 47 98.44 medulla 4 75.00 opiate 1 69.44 Analgesic 1 68.88 Glutamate receptor 42 47.08 Glutamate 42 6.92

Disease Link Frequency Relevance Heat Cockayne Syndrome 1205 100.00 Skin Cancer 21 99.52 Targeted Disruption 47 99.20 Obesity 3 98.20 Repression 21 97.84 Hutchinson-gilford Progeria Syndrome 84 90.76 Osteogenic Sarcomas 42 90.04 Retts Disease 6 88.64 Fibrosarcoma 21 87.16 Aging 42 81.08

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Key:

Protein

Mutation

Event

Anatomy

Negation

Speculation

Pain term

Disease term

Selection for expression of hTERT, CSB, and enhanced green fluorescent protein was maintained with 1 mg/ml G418 and 0.5 µg/ml puromycin, respectively.

Gene_expression (expression) of CSB

1) Confidence 0.77 Published 2008 Journal PLoS Genetics Section Body Doc Link PMC2268245 Disease Relevance 0.36 Pain Relevance 0

Consistent with this hypothesis, 21 of the 24 molecularly characterized CS genotypes appear capable of expressing the CSB-PGBD3 fusion protein (Figure 7 and Table S1).

Gene_expression (expressing) of CSB-PGBD3 associated with cockayne syndrome

2) Confidence 0.67 Published 2008 Journal PLoS Genetics Section Body Doc Link PMC2268245 Disease Relevance 0.86 Pain Relevance 0.06

The conserved CSB-PGBD3 fusion protein is expressed in both primary and established CS cells (Figures 2, 3, 5, and Figure S3), and could explain these mysteries if the fusion protein, which is advantageous in the presence of functional CSB (Tables 1 and 2), were detrimental in its absence.

Gene_expression (expressed) of CSB-PGBD3 associated with cockayne syndrome

3) Confidence 0.67 Published 2008 Journal PLoS Genetics Section Body Doc Link PMC2268245 Disease Relevance 1.00 Pain Relevance 0.10

Immortalized CSB (CS1AN) fibroblasts expressing either wild-type CSB cDNA (CSB-wt line) or enhanced green fluorescent protein (CSB-null line) were generated as described [25].

Gene_expression (expressing) of CSB in fibroblasts

4) Confidence 0.67 Published 2008 Journal PLoS Genetics Section Body Doc Link PMC2268245 Disease Relevance 0.52 Pain Relevance 0

A tabulation of all reported CS cases with known mutations in CSB reveals that 21 of 24 retain at least one allele that should allow continued expression of the CSB-transposase fusion protein (Table S1).

Gene_expression (expression) of CSB-transposase associated with cockayne syndrome

5) Confidence 0.67 Published 2008 Journal PLoS Genetics Section Body Doc Link PMC2268245 Disease Relevance 0.39 Pain Relevance 0

The resulting CSB-transposase fusion protein is as abundant as CSB protein itself in a variety of human cell lines, and continues to be expressed by primary CS cells in which functional CSB is lost due to mutations beyond exon 5.

Gene_expression (expressed) of CSB-transposase associated with cockayne syndrome

6) Confidence 0.67 Published 2008 Journal PLoS Genetics Section Abstract Doc Link PMC2268245 Disease Relevance 0.55 Pain Relevance 0

Anti-CSB antibodies were generated in our laboratory as rabbit polyclonals raised to the C-terminal 158 amino acids or N-terminal 240 amino acids of CSB expressed as bacterial GST fusion proteins.

Gene_expression (expressed) of CSB

7) Confidence 0.67 Published 2008 Journal PLoS Genetics Section Body Doc Link PMC2268245 Disease Relevance 0 Pain Relevance 0

The consistent D352 versus N352 difference in the putative catalytic DDD motif between decaying pseudogenes and PGBD3 itself in all species (Figures S7 and S8) suggests that this change may have been critical for both the stability of PGBD3 within CSB and for the demobilization of PGBD-related pseudogenes and MER elements derived from them.

Gene_expression (within) of CSB

8) Confidence 0.67 Published 2008 Journal PLoS Genetics Section Body Doc Link PMC2268245 Disease Relevance 0 Pain Relevance 0

Western blot analysis confirmed that CSB was depleted by the anti-CSB antibody (Figure 2C, lane 3).

Gene_expression (depleted) of CSB

9) Confidence 0.65 Published 2006 Journal Nucleic Acids Research Section Body Doc Link PMC1331990 Disease Relevance 0 Pain Relevance 0

Western blot analysis confirmed that CSB was depleted by the anti-CSB antibody (Figure 2C, lane 3).

Gene_expression (depleted) of CSB

10) Confidence 0.65 Published 2006 Journal Nucleic Acids Research Section Body Doc Link PMC1331990 Disease Relevance 0 Pain Relevance 0

Repression of PiggyBac and/or MER85 mobility may explain the initial domestication of PGBD3 more than 43 Mya, but the CSB-PGBD3 fusion protein continues to be conserved and abundantly expressed in primates despite the passage of sufficient time to inactivate existing PGBD-related transposases.

Gene_expression (expressed) of CSB-PGBD3 associated with repression

11) Confidence 0.59 Published 2008 Journal PLoS Genetics Section Body Doc Link PMC2268245 Disease Relevance 0.16 Pain Relevance 0

Finally, we show that the CSB-transposase fusion protein continues to be expressed in CS primary cells lacking functional CSB protein, implying that the fusion protein could contribute to the CS phenotype, or even transform the mild UV sensitivity caused by complete loss of CSB-related proteins [33] into a true progeria.

Gene_expression (expressed) of CSB-transposase associated with hutchinson-gilford progeria syndrome and cockayne syndrome

12) Confidence 0.59 Published 2008 Journal PLoS Genetics Section Body Doc Link PMC2268245 Disease Relevance 0.34 Pain Relevance 0

Of course, leaky terminators and weak frameshifts might have been expected to rescue expression of both the CSB-PGBD3 fusion and full length CSB protein, but it should be kept in mind that the CSB-PGBD3 and CSB mRNAs are alternatively spliced and polyadenylated transcripts with different intron/exon structures and different 3?

Gene_expression (expression) of CSB-PGBD3

13) Confidence 0.59 Published 2008 Journal PLoS Genetics Section Body Doc Link PMC2268245 Disease Relevance 0.18 Pain Relevance 0

Baseline levels of CVT and CSB also differed within the phenotypes indicating differences in parasympathetic activities.

Gene_expression (levels) of CSB in parasympathetic

14) Confidence 0.58 Published 2005 Journal Brain Dev. Section Abstract Doc Link 16182494 Disease Relevance 0.68 Pain Relevance 0.24

The fusion products exhibited the expected size ( 2B) and sequence (data not shown), and were approximately 2-fold more abundant than the equivalent CSB products (Figure S1).

Gene_expression (products) of CSB

15) Confidence 0.58 Published 2008 Journal PLoS Genetics Section Body Doc Link PMC2268245 Disease Relevance 0.07 Pain Relevance 0

And third, mouse models with either a truncating mutation similar to a severe human CSB allele (CS1AN; K337STOP) [55] or a CSA knockout [56] manifest the characteristic UV sensitivity of CS, as well as an unexpected susceptibility to skin cancer not observed for human CSB and CSA mutations, but only a subtle developmental phenotype.

Neg (not) Gene_expression (mutations) of CSB in skin associated with targeted disruption, skin cancer and cockayne syndrome

16) Confidence 0.58 Published 2008 Journal PLoS Genetics Section Body Doc Link PMC2268245 Disease Relevance 1.02 Pain Relevance 0.08

Moreover, we readily detected fusion products using forward primers for CSB exons 2, 3 and 4, indicating that a significant fraction of the CSB-PGBD3 fusion transcripts initiate far upstream of the putative cryptic promoter, presumably at a natural CSB initiation site.

Gene_expression (exons) of CSB

17) Confidence 0.58 Published 2008 Journal PLoS Genetics Section Body Doc Link PMC2268245 Disease Relevance 0.07 Pain Relevance 0

According to this hypothesis, mutations downstream of CSB exon 5 would cause CS by impairing expression of functional CSB without affecting expression of the fusion protein; nonsense and frameshift mutations upstream of exon 6 would not cause CS [33] because they would also abolish expression of the fusion protein; mutations that do cause CS would be recessive because functional CSB masks the effects of the CSB-PGBD3 fusion protein; and mouse models of severe CSB mutations or a CSA knockout would not exhibit the full range of CS symptoms because rodents lack the PGBD3 insertion that generates the CSB-PGBD3 fusion protein.

Gene_expression (expression) of CSB associated with targeted disruption and cockayne syndrome

18) Confidence 0.58 Published 2008 Journal PLoS Genetics Section Body Doc Link PMC2268245 Disease Relevance 0.94 Pain Relevance 0.08

The CSB-PGBD3 fusion transcript, apparently initiating at or near the normal CSB start site, appears to be the only major alternatively spliced transcript expressed from the CSB/PGBD3 gene.

Gene_expression (expressed) of CSB

19) Confidence 0.58 Published 2008 Journal PLoS Genetics Section Body Doc Link PMC2268245 Disease Relevance 0 Pain Relevance 0

region (data not shown), arguing that the putative cryptic promoter within CSB exon 5 does not generate significant quantities of an N-terminally truncated CSB mRNA (?

Gene_expression (exon) of CSB

20) Confidence 0.58 Published 2008 Journal PLoS Genetics Section Body Doc Link PMC2268245 Disease Relevance 0 Pain Relevance 0

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