Research

We are interested in DNA damage, DNA repair, RNA editing, Venom, Toxin and Telomere as following.

DNA damage

Every day naturally occurring DNA damages arise at least ~ 10,000 times per cell in humans. Our cells  produce compounds that damage DNA including reactive oxygen species, lipid peroxidation products and alkylating agents. Our DNA can be damaged via environmental factors, such as UV light, ionizing radiation, and genotoxic chemicals human made. 

Recently we found new type of DNA lesions that acetaldehyde induced. The chemical structure looks like UV light induced DNA lesions,  acetaldehyde-GG intra cross-links are very fragile but replication forks can be stalled due to the chemical structure and double strand breaks will be also a form of DNA damage.

Acetaldehyde forms covalent GG intrastrand crosslinks in DNA.   Sonohara Y, Yamamoto J, Tohashi K, Takatsuka R, Matsuda T, Iwai S, Kuraoka I.

Sci Rep. 2019 Jan 24;9(1):660. doi: 10.1038/s41598-018-37239-6.


Effects of acetaldehyde-induced DNA lesions on DNA metabolism.   Tsuruta H, Sonohara Y, Tohashi K, Aoki Shioi N, Iwai S, Kuraoka I.

Genes Environ. 2020 Jan 6;42:2. doi: 10.1186/s41021-019-0142-7. eCollection 2020.


Acetaldehyde induces NER repairable mutagenic DNA lesions.  Sonohara Y, Takatsuka R, Masutani C, Iwai S, Kuraoka I.

Carcinogenesis. 2021 Sep 21:bgab087. doi: 10.1093/carcin/bgab087. Online ahead of print. PMID: 34546339


DNA repair

Every day innumerable DNA damages arise in our living cells. The cell’s DNA must be repaired precisely for keeping the genetic information maintaining our life, otherwise the damage can cause errors, known as mutations, which cause cancer and death. DNA repair systems are very important cell function.

We developed a in vivo method for the fluorescence detection of the cellular DNA repair ability. One is for Nucleotide Excision Repair (NER), which is a highly conserved mechanism to remove helix-distorting DNA lesions. Another one is  MisMatch Repair (MMR), which is proof-reading mechanism to correct  nucleotide misincorporations by DNA polymerase. Both  maintain genetic integrity.  Now we  focus on  new method for transcription-coupled repair and for the repair of  more complex DNA lesions.

And also we are interested in DNA repair enzymes, the new cellular functions in human, e.g . development , epigenetic and etc...

Nucleotide excision repair genes shaping embryonic development.  Araújo SJ, Kuraoka I.

Open Biol. 2019 Oct 31;9(10):190166. doi: 10.1098/rsob.190166. Epub 2019 Oct 30.

Oligo swapping method for in vitro DNA repair substrate containing a single DNA lesion at a specific site.   Yukutake M, Hayashida M, Shioi Aoki N, Kuraoka I.

Genes Environ. 2018 Nov 12;40:23. doi: 10.1186/s41021-018-0112-5. eCollection 2018.

Fluorescence detection of DNA mismatch repair in human cells. Ito S, Shiraishi M, Tsuchihashi K, Takatsuka R, Yamamoto J, Kuraoka I, Iwai S.

Sci Rep. 2018 Aug 15;8(1):12181. doi: 10.1038/s41598-018-30733-x.

An assay to detect DNA-damaging agents that induce nucleotide excision-repairable DNA lesions in living human cells.   Takatsuka R, Ito S, Iwai S, Kuraoka I.

Mutat Res. 2017 Aug;820:1-7. doi: 10.1016/j.mrgentox.2017.05.009. Epub 2017 May 22.

RNA editing

RNA editing occurs selectively within RNA and can result in codon changes, as inosine is interpreted as guanosine by the translation machinery. This important mechanism is known as genetic regulation  producing genetic plasticity by allowing the production of alternative protein products from a single gene. As other functions, these RNA editing enzyme ADARs (adenosine deaminases acting on RNA) predominantly are thought to hyperedit long viral dsRNA genome. 

We have shown that hEndoV could cleave dsRNA treated by ADARs, hEndoV can also cleave locally distorted ssRNA structures containing inosine. The functions of hyperedited long dsRNA are not fully understood. We believed that hEndoV may have a role in the antiviral response by removing the hyperedited long viral dsRNA genome.

Human endonuclease V is a ribonuclease specific for inosine-containing RNA.

Morita Y, Shibutani T, Nakanishi N, Nishikura K, Iwai S, Kuraoka I.

Nat Commun. 2013;4:2273. doi: 10.1038/ncomms3273.

Diversity of Endonuclease V: From DNA Repair to RNA Editing.  Kuraoka I.

Biomolecules. 2015 Sep 24;5(4):2194-206. doi: 10.3390/biom5042194. Review.

Inosine-specific ribonuclease activity of natural variants of human endonuclease V.

Kim JI, Tohashi K, Iwai S, Kuraoka I.

FEBS Lett. 2016 Dec;590(23):4354-4360. doi: 10.1002/1873-3468.12470. Epub 2016 Nov 14.

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.

Wu J, Samara NL, Kuraoka I, Yang W.

Mol Cell. 2019 Oct 3;76(1):44-56.e3. doi: 10.1016/j.molcel.2019.06.046. Epub 2019 Aug 20.

Telomere

Among more than 30 helicases reported, RTEL1 (Regulator of telomere elongation helicase 1) is of particular interest to us. RTEL1 is DNA helicase that has a function in the maintenance of telomere homeostasis, homologous recombination and DNA replication, yet its precise role still reminds to be elucidated. The importance of RTEL1 in DNA metabolism is underscored by the fact that mutations in the RTEL1 gene are causative of Hoyeraal-Hreidarsson syndrome (HHS), an inherited disease that is characterized by intrauterine growth retardation, microcephaly, cerebellar hypoplasia, progressive combined immune deficiency and aplastic anemia.  

   Our recent studies from Cancer research center of Marseille (France) shed light on the new roles of RTEL1 in the maintenance of genome stability. We found a new interaction between RTEL1 and SLX4(FANCP), the regulator of structure-specific endonucleases (XPF-ERCC1, MUS81-EME1 and SLX1). RTEL1 interacts with SLX4 via its Harmonin domain (HD) that has been newly identified as a functional domain in RTEL1. How is the RTEL1-SLX4 interaction important in the maintenance of genome stability? An answer key was found in a regulation of DNA replication instead of in the maintenance telomere homeostasis that it is so far supposed to be involved. The interaction plays a role in efficient progression of genome-wide replication by removing conflicts between transcription-replication. These findings open up the new avenues for understanding how RTEL1 functions in the maintenance of genome stability.


SLX4 interacts with RTEL1 to prevent transcription-mediated DNA replication perturbations.

Takedachi A, Despras E, Scaglione S, Guérois R, Guervilly JH, Blin M, Audebert S, Camoin L, Hasanova Z, Schertzer M, Guille A, Churikov D, Callebaut I, Naim V, Chaffanet M, Borg JP, Bertucci F, Revy P, Birnbaum D, Londoño-Vallejo A, Kannouche PL, Gaillard PHL.

Nat Struct Mol Biol. 2020 May;27(5):438-449. doi: 10.1038/s41594-020-0419-3. Epub 2020 May 11.

PMID: 32398829

Compartmentalization of the SUMO/RNF4 pathway by SLX4 drives DNA repair.

Alghoul E, Paloni M, Takedachi A, Urbach S, Barducci A, Gaillard PH, Basbous J, Constantinou A.

Mol Cell. 2023 Apr 5:S1097-2765(23)00211-3. doi: 10.1016/j.molcel.2023.03.021.


Venom

Toxin