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Transcriptomic analysis of HEK293A cells with a CRISPR/Cas9-mediated TDP1 knockout.
Dyrkheeva, Nadezhda S; Zakharenko, Alexandra L; Malakhova, Anastasia A; Okorokova, Larisa S; Shtokalo, Dmitry N; Medvedev, Sergey P; Tupikin, Alexey A; Kabilov, Marsel R; Lavrik, Olga I.
Affiliation
  • Dyrkheeva NS; Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia. Electronic address: dyrkheeva.n.s@gmail.com.
  • Zakharenko AL; Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia. Electronic address: a.zakharenko73@gmail.com.
  • Malakhova AA; Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; Federal research center Institute of Cytology and Genetics, SB RAS, 10 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia. El
  • Okorokova LS; AcademGene LLC, 6 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia. Electronic address: larisaok123@gmail.com.
  • Shtokalo DN; AcademGene LLC, 6 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; A.P. Ershov Institute of Informatics Systems, SB RAS, 6 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia. Electronic address: shtokalod2@gmail.com.
  • Medvedev SP; Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; Federal research center Institute of Cytology and Genetics, SB RAS, 10 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia. El
  • Tupikin AA; Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia. Electronic address: alenare@niboch.nsc.ru.
  • Kabilov MR; Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia. Electronic address: kabilov@niboch.nsc.ru.
  • Lavrik OI; Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia. Electronic address: lavrik@niboch.nsc.ru.
Biochim Biophys Acta Gen Subj ; 1868(7): 130616, 2024 Jul.
Article in En | MEDLINE | ID: mdl-38621596
ABSTRACT
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a human DNA repair protein. It is a member of the phospholipase D family based on structural similarity. TDP1 is a key enzyme of the repair of stalled topoisomerase 1 (TOP1)-DNA complexes. Previously, with the CRISPR/Cas9 method, we obtained HEK293A cells with a homozygous knockout of the TDP1 gene and used the TDP1 knockout cells as a cellular model for studying mechanisms of action of an anticancer therapy. In the present work, we hypothesized that the TDP1 knockout would alter the expression of DNA repair-related genes. By transcriptomic analysis, we investigated for the first time the effect of the TDP1 gene knockout on genes' expression changes in the human HEK293A cell line. We obtained original data implying a role of TDP1 in other processes besides the repair of the DNA-TOP1 complex. Differentially expressed gene analysis revealed that TDP1 may participate in cell adhesion and communication, spermatogenesis, mitochondrial function, neurodegeneration, a cytokine response, and the MAPK signaling pathway.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Phosphoric Diester Hydrolases / CRISPR-Cas Systems Limits: Humans Language: En Journal: Biochim Biophys Acta Gen Subj Year: 2024 Document type: Article Country of publication: Países Bajos

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Phosphoric Diester Hydrolases / CRISPR-Cas Systems Limits: Humans Language: En Journal: Biochim Biophys Acta Gen Subj Year: 2024 Document type: Article Country of publication: Países Bajos