Hilde Nilsen

Active transcriptomic and proteomic reprogramming in the C. elegans nucleotide excision repair mutant xpa-1

Nucleic Acids Research, 2013

Transcription-blocking oxidative DNA damage is believed to contribute to aging and to underlie ac... more Transcription-blocking oxidative DNA damage is believed to contribute to aging and to underlie activation of oxidative stress responses and downregulation of insulin-like signaling (ILS) in Nucleotide Excision Repair (NER) deficient mice. Here, we present the first quantitative proteomic description of the Caenorhabditis elegans NER-defective xpa-1 mutant and compare the proteome and transcriptome signatures. Both methods indicated activation of oxidative stress responses, which was substantiated biochemically by a bioenergetic shift involving increased steady-state reactive oxygen species (ROS) and Adenosine triphosphate (ATP) levels. We identify the lesion-detection enzymes of Base Excision Repair (NTH-1) and global genome NER (XPC-1 and DDB-1) as upstream requirements for transcriptomic reprogramming as RNA-interference mediated depletion of these enzymes prevented up-regulation of genes over-expressed in the xpa-1 mutant. The transcription factors SKN-1 and SLR-2, but not DAF-16, were identified as effectors of reprogramming. As shown in human XPA cells, the levels of transcriptionblocking 8,5'-cyclo-2'-deoxyadenosine lesions were reduced in the xpa-1 mutant compared to the wild type. Hence, accumulation of cyclopurines is unlikely to be sufficient for reprogramming. Instead, our data support a model where the lesion-detection enzymes NTH-1, XPC-1 and DDB-1 play active roles to generate a genomic stress signal sufficiently strong to result in transcriptomic reprogramming in the xpa-1 mutant.

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Uracil-DNA Glycosylase (UNG)-Deficient Mice Reveal a Primary Role of the Enzyme during DNA Replication

Molecular Cell, 2000

promoters and alternative RNA splicing (Nilsen et al., 1997). Endogenous hydrolytic deamination o... more

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Human Uracil-DNA Glycosylase

Advances in DNA Damage and Repair, 1999

18 HUMAN URACIL-DNA GLYCOSYLASE Gene Structure, Regulation, and Structural Basis for Catalysis Ha... more

A two-tiered compensatory response to loss of DNA repair modulates aging and stress response pathways

Aging, Jan 31, 2010

Activation of oxidative stress-responses and downregulation of insulin-like signaling (ILS) is se... more Activation of oxidative stress-responses and downregulation of insulin-like signaling (ILS) is seen in Nucleotide Excision Repair (NER) deficient segmental progeroid mice. Evidence suggests that this is a survival response to persistent transcription-blocking DNA damage, although the relevant lesions have not been identified. Here we show that loss of NTH-1, the only Base Excision Repair (BER) enzyme known to initiate repair of oxidative DNA damage inC. elegans, restores normal lifespan of the short-lived NER deficient xpa-1 mutant. Loss of NTH-1 leads to oxidative stress and global expression profile changes that involve upregulation of genes responding to endogenous stress and downregulation of ILS. A similar, but more extensive, transcriptomic shift is observed in the xpa-1 mutant whereas loss of both NTH-1 and XPA-1 elicits a different profile with downregulation of Aurora-B and Polo-like kinase 1 signaling networks as well as DNA repair and DNA damage response genes. The restor...

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Base excision repair of DNA in mammalian cells

FEBS Letters, 2000

Base excision repair (BER) of DNA corrects a number of spontaneous and environmentally induced ge... more Base excision repair (BER) of DNA corrects a number of spontaneous and environmentally induced genotoxic or miscoding base lesions in a process initiated by DNA glycosylases. An AP endonuclease cleaves at the 5P P side of the abasic site and the repair process is subsequently completed via either short patch repair or long patch repair, which largely require different proteins. As one example, the UNG gene encodes both nuclear (UNG2) and mitochondrial (UNG1) uracil DNA glycosylase and prevents accumulation of uracil in the genome. BER is likely to have a major role in preserving the integrity of DNA during evolution and may prevent cancer.

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Base excision repair of DNA in mammalian cells

FEBS Letters, 2000

Base excision repair (BER) of DNA corrects a number of spontaneous and environmentally induced ge... more Base excision repair (BER) of DNA corrects a number of spontaneous and environmentally induced genotoxic or miscoding base lesions in a process initiated by DNA glycosylases. An AP endonuclease cleaves at the 5P P side of the abasic site and the repair process is subsequently completed via either short patch repair or long patch repair, which largely require different proteins. As one example, the UNG gene encodes both nuclear (UNG2) and mitochondrial (UNG1) uracil DNA glycosylase and prevents accumulation of uracil in the genome. BER is likely to have a major role in preserving the integrity of DNA during evolution and may prevent cancer.

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Loss of Caenorhabditis elegans UNG-1 uracil-DNA glycosylase affects apoptosis in response to DNA damaging agents

DNA Repair, 2010

Activation of oxidative stressͲresponses and downregulation of insulinͲlike signaling (ILS) is se... more Activation of oxidative stressͲresponses and downregulation of insulinͲlike signaling (ILS) is seen in Nucleotide Excision Repair (NER) deficient segmental progeroid mice. Evidence suggests that this is a survival response to persistent transcriptionͲblocking DNA damage, although the relevant lesions have not been identified. Here we show that loss of NTHͲ1, the only Base Excision Repair (BER) enzyme known to initiate repair of oxidative DNA damage in C. elegans, restores normal lifespan of the shortͲlived NER deficient xpaͲ1 mutant. Loss of NTHͲ1 leads to oxidative stress and global expression profile changes that involve upregulation of genes responding to endogenous stress and downregulation of ILS. A similar, but more extensive, transcriptomic shift is observed in the xpaͲ1 mutant whereas loss of both NTHͲ1 and XPAͲ1 elicits a different profile with downregulation of AuroraͲB and PoloͲlike kinase 1 signaling networks as well as DNA repair and DNA damage response genes. The restoration of normal lifespan and absence oxidative stress responses in nthͲ1;xpaͲ1 indicate that BER contributes to generate transcription blocking lesions from oxidative DNA damage. Hence, our data strongly suggests that the DNA lesions relevant for aging are repair intermediates resulting from aberrant or attempted processing by BER of lesions normally repaired by NER.

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Active transcriptomic and proteomic reprogramming in the C. elegans nucleotide excision repair mutant xpa-1

by Jessica Lindvall and Hilde Nilsen

Nucleic Acids Research, 2013

Transcription-blocking oxidative DNA damage is believed to contribute to aging and to underlie ac... more Transcription-blocking oxidative DNA damage is believed to contribute to aging and to underlie activation of oxidative stress responses and downregulation of insulin-like signaling (ILS) in Nucleotide Excision Repair (NER) deficient mice. Here, we present the first quantitative proteomic description of the Caenorhabditis elegans NER-defective xpa-1 mutant and compare the proteome and transcriptome signatures. Both methods indicated activation of oxidative stress responses, which was substantiated biochemically by a bioenergetic shift involving increased steady-state reactive oxygen species (ROS) and Adenosine triphosphate (ATP) levels. We identify the lesion-detection enzymes of Base Excision Repair (NTH-1) and global genome NER (XPC-1 and DDB-1) as upstream requirements for transcriptomic reprogramming as RNA-interference mediated depletion of these enzymes prevented up-regulation of genes over-expressed in the xpa-1 mutant. The transcription factors SKN-1 and SLR-2, but not DAF-16, were identified as effectors of reprogramming. As shown in human XPA cells, the levels of transcriptionblocking 8,5'-cyclo-2'-deoxyadenosine lesions were reduced in the xpa-1 mutant compared to the wild type. Hence, accumulation of cyclopurines is unlikely to be sufficient for reprogramming. Instead, our data support a model where the lesion-detection enzymes NTH-1, XPC-1 and DDB-1 play active roles to generate a genomic stress signal sufficiently strong to result in transcriptomic reprogramming in the xpa-1 mutant.

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Loss of Caenorhabditis elegans UNG-1 uracil-DNA glycosylase affects apoptosis in response to DNA damaging agents

by Eshrat Babaie and Hilde Nilsen

DNA Repair, 2010

The nematode Caenorhabditis elegans has been used extensively to study responses to DNA damage. I... more The nematode Caenorhabditis elegans has been used extensively to study responses to DNA damage. In contrast, little is known about DNA repair in this organism. C. elegans is unusual in that it encodes few DNA glycosylases and the uracil-DNA glycosylase (UDG) encoded by the ung-1 gene is the only known UDG. C. elegans could therefore become a valuable model organism for studies of the genetic interaction networks involving base excision repair (BER). As a first step towards characterization of BER in C. elegans, we show that the UNG-1 protein is an active uracil-DNA glycosylase. We demonstrate that an ung-1 mutant has reduced ability to repair uracil-containing DNA but that an alternative Ugi-inhibited activity is present in ung-1 nuclear extracts. Finally, we demonstrate that ung-1 mutants show altered levels of apoptotic cell corpses formed in response to DNA damaging agents. Increased apoptosis in the ung-1 mutant in response to ionizing radiation (IR) suggests that UNG-1 contributes to repair of IR-induced DNA base damage in vivo. Following treatment with paraquat however, the apoptotic corpse-formation was reduced. Gene expression profiling suggests that this phenotype is a consequence of compensatory transcriptomic shifts that modulate oxidative stress responses in the mutant and not an effect of reduced DNA damage signaling.

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Human Uracil-DNA Glycosylase

by Camilla Skjelbred, Hilde Nilsen, and Marit Otterlei

Advances in DNA Damage and Repair, 1999

18 HUMAN URACIL-DNA GLYCOSYLASE Gene Structure, Regulation, and Structural Basis for Catalysis Ha... more

The Human Base Excision Repair Enzyme SMUG1 Directly Interacts with DKC1 and Contributes to RNA Quality Control

by Bjørn Dalhus and Hilde Nilsen

Molecular Cell, 2013

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