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next turned to UV-based cellular assays including unscheduled DNA synthesis after UV irradiation (UV-UDS), recovery of RNA synthesis after UV irradiation (UV-RRS), and UV survival, which report on the NER subpathways (global genome NER and transcription-coupled NER) and total NER, respectively. In none of these assays was the response to UV improved in compound heterozygotes relative to TTD homozygotes (Figure 4A–4C). However, unlike the in vivo TTD phenotypes described above, in which XpdTTD/TTD and XpdTTD/KO animals were indistinguishable, XpdTTD dosage effects were observed in UV survival, UV-UDS, and UV-RRS, indicating that cellular parameters as measured in fibroblasts here do not always correlate with the phenotype at the level of the intact organism. XpdTTD/KO hemizygous cells were thus used as the baseline on which to compare the activity of compound heterozygous cells. Relative to XpdTTD/KO hemizygote cells, UV survival was improved by the homozygous lethal Xpd†XPCS allele in XpdTTD/†XPCS compound heterozygous cells and to a lesser degree by the Xpd†XP allele (Figure 4A). Because of embryonic and cellular lethality, we were unable to test UV survival associated exclusively with the Xpd†XPCS or Xpd†XP alleles. However, homozygous XPDXP (XPDR683W) and hemizygous XPDXPCS (XPDG602D) human cells are known to be highly sensitive to UV [19,25], as are cells from a homozygous viable XpdXPCS/XPCS (XPDG602D/G602D) mouse model (Figure 4A, dotted line) [23]. Thus, the survival of XpdTTD/†XPCS (and XpdTTD/†XP) cells likely represents a level of UV resistance that neither mutant allele can impart on its own (Table 2). Significant effects of compound heterozygosity on NER subpathways relative to XpdTTD/KO cells were observed in XpdTTD/†XP cells but only for UV-UDS activity. Finally, none of the mutant TFIIH combinations (carrying alterations associated with TTD [XPDR722W], XPCS [XPDG602D], or XP [XPDR683W]) exhibited synergism in an in vitro NER reaction reconstituted with different mutant TFIIH complexes (Figure 4D). Taken together, these data are consistent with interallelic complementation of UV sensitivity in cells but underscore the lack of any correlation between UV-related repair characteristics and TTD progeroid phenotypes in animal models."}

{"project":"craft-ca-core-dev","denotations":[{"id":"T3068","span":{"begin":65,"end":78},"obj":"GO:0071897"},{"id":"T3069","span":{"begin":122,"end":135},"obj":"GO:0032774"},{"id":"T3070","span":{"begin":204,"end":207},"obj":"GO:0006289"},{"id":"T3071","span":{"begin":228,"end":234},"obj":"SO:0001026"},{"id":"T3072","span":{"begin":235,"end":238},"obj":"GO:0006289"},{"id":"T3073","span":{"begin":243,"end":268},"obj":"GO:0006283"},{"id":"T3074","span":{"begin":280,"end":283},"obj":"GO:0006289"},{"id":"T3075","span":{"begin":494,"end":497},"obj":"PR:000007164"},{"id":"T3076","span":{"begin":509,"end":512},"obj":"PR:000007164"},{"id":"T3077","span":{"begin":519,"end":526},"obj":"NCBITaxon:33208"},{"id":"T3078","span":{"begin":551,"end":554},"obj":"PR:000007164"},{"id":"T3079","span":{"begin":674,"end":685},"obj":"CL:0000057"},{"id":"T3080","span":{"begin":761,"end":769},"obj":"NCBITaxon:1"},{"id":"T3081","span":{"begin":771,"end":774},"obj":"PR:000007164"},{"id":"T3082","span":{"begin":906,"end":909},"obj":"PR:000007164"},{"id":"T3083","span":{"begin":984,"end":987},"obj":"PR:000007164"},{"id":"T3084","span":{"begin":993,"end":999},"obj":"SO:0001023"},{"id":"T3085","span":{"begin":1003,"end":1006},"obj":"PR:000007164"},{"id":"T3086","span":{"begin":1074,"end":1077},"obj":"PR:000007164"},{"id":"T3087","span":{"begin":1081,"end":1087},"obj":"SO:0001023"},{"id":"T3088","span":{"begin":1112,"end":1121},"obj":"UBERON:0000922"},{"id":"T3089","span":{"begin":1213,"end":1216},"obj":"PR:000007164"},{"id":"T3090","span":{"begin":1225,"end":1228},"obj":"PR:000007164"},{"id":"T3091","span":{"begin":1232,"end":1239},"obj":"SO:0001023"},{"id":"T3092","span":{"begin":1261,"end":1264},"obj":"PR:000007164"},{"id":"T3093","span":{"begin":1268,"end":1271},"obj":"PR:000007164"},{"id":"T3094","span":{"begin":1293,"end":1296},"obj":"PR:000007164"},{"id":"T3095","span":{"begin":1302,"end":1305},"obj":"PR:000007164"},{"id":"T3096","span":{"begin":1312,"end":1317},"obj":"NCBITaxon:9606"},{"id":"T3097","span":{"begin":1410,"end":1413},"obj":"PR:000007164"},{"id":"T3098","span":{"begin":1424,"end":1427},"obj":"PR:000007164"},{"id":"T3099","span":{"begin":1440,"end":1445},"obj":"NCBITaxon:10088"},{"id":"T3100","span":{"begin":1505,"end":1508},"obj":"PR:000007164"},{"id":"T3101","span":{"begin":1523,"end":1526},"obj":"PR:000007164"},{"id":"T3102","span":{"begin":1604,"end":1610},"obj":"SO:0001023"},{"id":"T3103","span":{"begin":1694,"end":1697},"obj":"GO:0006289"},{"id":"T3104","span":{"begin":1722,"end":1725},"obj":"PR:000007164"},{"id":"T3105","span":{"begin":1755,"end":1758},"obj":"PR:000007164"},{"id":"T3106","span":{"begin":1830,"end":1835},"obj":"GO:0005675"},{"id":"T3107","span":{"begin":1892,"end":1895},"obj":"PR:000007164"},{"id":"T3108","span":{"begin":1909,"end":1912},"obj":"PR:000007164"},{"id":"T3109","span":{"begin":1927,"end":1930},"obj":"PR:000007164"},{"id":"T3110","span":{"begin":1973,"end":1976},"obj":"GO:0006289"},{"id":"T3111","span":{"begin":2022,"end":2037},"obj":"GO:0005675"},{"id":"T3112","span":{"begin":2103,"end":2110},"obj":"SO:0001023"},{"id":"T3113","span":{"begin":2216,"end":2222},"obj":"GO:0006281"},{"id":"T3114","span":{"begin":2271,"end":2277},"obj":"NCBITaxon:33208"}],"text":"We next turned to UV-based cellular assays including unscheduled DNA synthesis after UV irradiation (UV-UDS), recovery of RNA synthesis after UV irradiation (UV-RRS), and UV survival, which report on the NER subpathways (global genome NER and transcription-coupled NER) and total NER, respectively. In none of these assays was the response to UV improved in compound heterozygotes relative to TTD homozygotes (Figure 4A–4C). However, unlike the in vivo TTD phenotypes described above, in which XpdTTD/TTD and XpdTTD/KO animals were indistinguishable, XpdTTD dosage effects were observed in UV survival, UV-UDS, and UV-RRS, indicating that cellular parameters as measured in fibroblasts here do not always correlate with the phenotype at the level of the intact organism. XpdTTD/KO hemizygous cells were thus used as the baseline on which to compare the activity of compound heterozygous cells. Relative to XpdTTD/KO hemizygote cells, UV survival was improved by the homozygous lethal Xpd†XPCS allele in XpdTTD/†XPCS compound heterozygous cells and to a lesser degree by the Xpd†XP allele (Figure 4A). Because of embryonic and cellular lethality, we were unable to test UV survival associated exclusively with the Xpd†XPCS or Xpd†XP alleles. However, homozygous XPDXP (XPDR683W) and hemizygous XPDXPCS (XPDG602D) human cells are known to be highly sensitive to UV [19,25], as are cells from a homozygous viable XpdXPCS/XPCS (XPDG602D/G602D) mouse model (Figure 4A, dotted line) [23]. Thus, the survival of XpdTTD/†XPCS (and XpdTTD/†XP) cells likely represents a level of UV resistance that neither mutant allele can impart on its own (Table 2). Significant effects of compound heterozygosity on NER subpathways relative to XpdTTD/KO cells were observed in XpdTTD/†XP cells but only for UV-UDS activity. Finally, none of the mutant TFIIH combinations (carrying alterations associated with TTD [XPDR722W], XPCS [XPDG602D], or XP [XPDR683W]) exhibited synergism in an in vitro NER reaction reconstituted with different mutant TFIIH complexes (Figure 4D). Taken together, these data are consistent with interallelic complementation of UV sensitivity in cells but underscore the lack of any correlation between UV-related repair characteristics and TTD progeroid phenotypes in animal models."}

{"project":"craft-ca-core-ex-dev","denotations":[{"id":"T3203","span":{"begin":1225,"end":1228},"obj":"PR_EXT:000007164"},{"id":"T3169","span":{"begin":27,"end":35},"obj":"CL_GO_EXT:cell"},{"id":"T3170","span":{"begin":65,"end":68},"obj":"CHEBI_SO_EXT:DNA"},{"id":"T3171","span":{"begin":65,"end":78},"obj":"GO:0071897"},{"id":"T3172","span":{"begin":122,"end":125},"obj":"CHEBI_SO_EXT:RNA"},{"id":"T3173","span":{"begin":122,"end":135},"obj":"GO:0032774"},{"id":"T3174","span":{"begin":204,"end":207},"obj":"GO:0006289"},{"id":"T3175","span":{"begin":228,"end":234},"obj":"SO_EXT:0001026"},{"id":"T3176","span":{"begin":235,"end":238},"obj":"GO:0006289"},{"id":"T3177","span":{"begin":243,"end":268},"obj":"GO:0006283"},{"id":"T3178","span":{"begin":280,"end":283},"obj":"GO:0006289"},{"id":"T3179","span":{"begin":331,"end":339},"obj":"GO_EXT:reaction_or_response"},{"id":"T3180","span":{"begin":494,"end":497},"obj":"PR_EXT:000007164"},{"id":"T3181","span":{"begin":509,"end":512},"obj":"PR_EXT:000007164"},{"id":"T3182","span":{"begin":519,"end":526},"obj":"NCBITaxon:33208"},{"id":"T3183","span":{"begin":551,"end":554},"obj":"PR_EXT:000007164"},{"id":"T3184","span":{"begin":639,"end":647},"obj":"CL_GO_EXT:cell"},{"id":"T3185","span":{"begin":674,"end":685},"obj":"CL:0000057"},{"id":"T3186","span":{"begin":761,"end":769},"obj":"NCBITaxon:1"},{"id":"T3187","span":{"begin":771,"end":774},"obj":"PR_EXT:000007164"},{"id":"T3188","span":{"begin":792,"end":797},"obj":"CL_GO_EXT:cell"},{"id":"T3189","span":{"begin":887,"end":892},"obj":"CL_GO_EXT:cell"},{"id":"T3190","span":{"begin":906,"end":909},"obj":"PR_EXT:000007164"},{"id":"T3191","span":{"begin":927,"end":932},"obj":"CL_GO_EXT:cell"},{"id":"T3192","span":{"begin":977,"end":983},"obj":"GO_EXT:fatality_or_lethality"},{"id":"T3193","span":{"begin":984,"end":987},"obj":"PR_EXT:000007164"},{"id":"T3194","span":{"begin":993,"end":999},"obj":"SO_EXT:0001023"},{"id":"T3195","span":{"begin":1003,"end":1006},"obj":"PR_EXT:000007164"},{"id":"T3196","span":{"begin":1038,"end":1043},"obj":"CL_GO_EXT:cell"},{"id":"T3197","span":{"begin":1074,"end":1077},"obj":"PR_EXT:000007164"},{"id":"T3198","span":{"begin":1081,"end":1087},"obj":"SO_EXT:0001023"},{"id":"T3199","span":{"begin":1112,"end":1121},"obj":"UBERON:0000922"},{"id":"T3200","span":{"begin":1126,"end":1134},"obj":"CL_GO_EXT:cell"},{"id":"T3201","span":{"begin":1135,"end":1144},"obj":"GO_EXT:fatality_or_lethality"},{"id":"T3202","span":{"begin":1213,"end":1216},"obj":"PR_EXT:000007164"},{"id":"T3204","span":{"begin":1232,"end":1239},"obj":"SO_EXT:0001023"},{"id":"T3205","span":{"begin":1261,"end":1264},"obj":"PR_EXT:000007164"},{"id":"T3206","span":{"begin":1268,"end":1271},"obj":"PR_EXT:000007164"},{"id":"T3207","span":{"begin":1293,"end":1296},"obj":"PR_EXT:000007164"},{"id":"T3208","span":{"begin":1302,"end":1305},"obj":"PR_EXT:000007164"},{"id":"T3209","span":{"begin":1312,"end":1317},"obj":"NCBITaxon:9606"},{"id":"T3210","span":{"begin":1318,"end":1323},"obj":"CL_GO_EXT:cell"},{"id":"T3211","span":{"begin":1379,"end":1384},"obj":"CL_GO_EXT:cell"},{"id":"T3212","span":{"begin":1410,"end":1413},"obj":"PR_EXT:000007164"},{"id":"T3213","span":{"begin":1424,"end":1427},"obj":"PR_EXT:000007164"},{"id":"T3214","span":{"begin":1440,"end":1445},"obj":"NCBITaxon:10088"},{"id":"T3215","span":{"begin":1505,"end":1508},"obj":"PR_EXT:000007164"},{"id":"T3216","span":{"begin":1523,"end":1526},"obj":"PR_EXT:000007164"},{"id":"T3217","span":{"begin":1535,"end":1540},"obj":"CL_GO_EXT:cell"},{"id":"T3218","span":{"begin":1597,"end":1603},"obj":"SO_EXT:sequence_altered_entity_or_alteration_process"},{"id":"T3219","span":{"begin":1604,"end":1610},"obj":"SO_EXT:0001023"},{"id":"T3220","span":{"begin":1694,"end":1697},"obj":"GO:0006289"},{"id":"T3221","span":{"begin":1722,"end":1725},"obj":"PR_EXT:000007164"},{"id":"T3222","span":{"begin":1732,"end":1737},"obj":"CL_GO_EXT:cell"},{"id":"T3223","span":{"begin":1755,"end":1758},"obj":"PR_EXT:000007164"},{"id":"T3224","span":{"begin":1766,"end":1771},"obj":"CL_GO_EXT:cell"},{"id":"T3225","span":{"begin":1823,"end":1829},"obj":"SO_EXT:sequence_altered_entity_or_alteration_process"},{"id":"T3226","span":{"begin":1830,"end":1835},"obj":"GO:0005675"},{"id":"T3227","span":{"begin":1859,"end":1870},"obj":"SO_EXT:sequence_alteration_entity_or_process"},{"id":"T3228","span":{"begin":1892,"end":1895},"obj":"PR_EXT:000007164"},{"id":"T3229","span":{"begin":1909,"end":1912},"obj":"PR_EXT:000007164"},{"id":"T3230","span":{"begin":1927,"end":1930},"obj":"PR_EXT:000007164"},{"id":"T3231","span":{"begin":1973,"end":1976},"obj":"GO:0006289"},{"id":"T3232","span":{"begin":2015,"end":2021},"obj":"SO_EXT:sequence_altered_entity_or_alteration_process"},{"id":"T3233","span":{"begin":2022,"end":2037},"obj":"GO:0005675"},{"id":"T3234","span":{"begin":2103,"end":2110},"obj":"SO_EXT:0001023"},{"id":"T3235","span":{"begin":2148,"end":2153},"obj":"CL_GO_EXT:cell"},{"id":"T3236","span":{"begin":2216,"end":2222},"obj":"GO:00062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next turned to UV-based cellular assays including unscheduled DNA synthesis after UV irradiation (UV-UDS), recovery of RNA synthesis after UV irradiation (UV-RRS), and UV survival, which report on the NER subpathways (global genome NER and transcription-coupled NER) and total NER, respectively. In none of these assays was the response to UV improved in compound heterozygotes relative to TTD homozygotes (Figure 4A–4C). However, unlike the in vivo TTD phenotypes described above, in which XpdTTD/TTD and XpdTTD/KO animals were indistinguishable, XpdTTD dosage effects were observed in UV survival, UV-UDS, and UV-RRS, indicating that cellular parameters as measured in fibroblasts here do not always correlate with the phenotype at the level of the intact organism. XpdTTD/KO hemizygous cells were thus used as the baseline on which to compare the activity of compound heterozygous cells. Relative to XpdTTD/KO hemizygote cells, UV survival was improved by the homozygous lethal Xpd†XPCS allele in XpdTTD/†XPCS compound heterozygous cells and to a lesser degree by the Xpd†XP allele (Figure 4A). Because of embryonic and cellular lethality, we were unable to test UV survival associated exclusively with the Xpd†XPCS or Xpd†XP alleles. However, homozygous XPDXP (XPDR683W) and hemizygous XPDXPCS (XPDG602D) human cells are known to be highly sensitive to UV [19,25], as are cells from a homozygous viable XpdXPCS/XPCS (XPDG602D/G602D) mouse model (Figure 4A, dotted line) [23]. Thus, the survival of XpdTTD/†XPCS (and XpdTTD/†XP) cells likely represents a level of UV resistance that neither mutant allele can impart on its own (Table 2). Significant effects of compound heterozygosity on NER subpathways relative to XpdTTD/KO cells were observed in XpdTTD/†XP cells but only for UV-UDS activity. Finally, none of the mutant TFIIH combinations (carrying alterations associated with TTD [XPDR722W], XPCS [XPDG602D], or XP [XPDR683W]) exhibited synergism in an in vitro NER reaction reconstituted with different mutant TFIIH complexes (Figure 4D). Taken together, these data are consistent with interallelic complementation of UV sensitivity in cells but underscore the lack of any correlation between UV-related repair characteristics and TTD progeroid phenotypes in animal models."}

{"project":"2_test","denotations":[{"id":"17020410-9238033-84795150","span":{"begin":1364,"end":1366},"obj":"9238033"},{"id":"17020410-7825573-84795151","span":{"begin":1367,"end":1369},"obj":"7825573"},{"id":"17020410-16904611-84795152","span":{"begin":1478,"end":1480},"obj":"16904611"},{"id":"T77924","span":{"begin":1364,"end":1366},"obj":"9238033"},{"id":"T64659","span":{"begin":1367,"end":1369},"obj":"7825573"},{"id":"T30893","span":{"begin":1478,"end":1480},"obj":"16904611"}],"text":"We next turned to UV-based cellular assays including unscheduled DNA synthesis after UV irradiation (UV-UDS), recovery of RNA synthesis after UV irradiation (UV-RRS), and UV survival, which report on the NER subpathways (global genome NER and transcription-coupled NER) and total NER, respectively. In none of these assays was the response to UV improved in compound heterozygotes relative to TTD homozygotes (Figure 4A–4C). However, unlike the in vivo TTD phenotypes described above, in which XpdTTD/TTD and XpdTTD/KO animals were indistinguishable, XpdTTD dosage effects were observed in UV survival, UV-UDS, and UV-RRS, indicating that cellular parameters as measured in fibroblasts here do not always correlate with the phenotype at the level of the intact organism. XpdTTD/KO hemizygous cells were thus used as the baseline on which to compare the activity of compound heterozygous cells. Relative to XpdTTD/KO hemizygote cells, UV survival was improved by the homozygous lethal Xpd†XPCS allele in XpdTTD/†XPCS compound heterozygous cells and to a lesser degree by the Xpd†XP allele (Figure 4A). Because of embryonic and cellular lethality, we were unable to test UV survival associated exclusively with the Xpd†XPCS or Xpd†XP alleles. However, homozygous XPDXP (XPDR683W) and hemizygous XPDXPCS (XPDG602D) human cells are known to be highly sensitive to UV [19,25], as are cells from a homozygous viable XpdXPCS/XPCS (XPDG602D/G602D) mouse model (Figure 4A, dotted line) [23]. Thus, the survival of XpdTTD/†XPCS (and XpdTTD/†XP) cells likely represents a level of UV resistance that neither mutant allele can impart on its own (Table 2). Significant effects of compound heterozygosity on NER subpathways relative to XpdTTD/KO cells were observed in XpdTTD/†XP cells but only for UV-UDS activity. Finally, none of the mutant TFIIH combinations (carrying alterations associated with TTD [XPDR722W], XPCS [XPDG602D], or XP [XPDR683W]) exhibited synergism in an in vitro NER reaction reconstituted with different mutant TFIIH complexes (Figure 4D). Taken together, these data are consistent with interallelic complementation of UV sensitivity in cells but underscore the lack of any correlation between UV-related repair characteristics and TTD progeroid phenotypes in animal models."}