研究者詳細 - 中沢　由華

Ubiquitination of DNA Damage-Stalled RNAPII Promotes Transcription-Coupled Repair 査読有り国際共著

Nakazawa, Y; Hara, Y; Oka, Y; Komine, O; van den Heuvel, D; Guo, CW; Daigaku, Y; Isono, M; He, YX; Shimada, M; Kato, K; Jia, N; Hashimoto, S; Kotani, Y; Miyoshi, Y; Tanaka, M; Sobue, A; Mitsutake, N; Suganami, T; Masuda, A; Ohno, K; Nakada, S; Mashimo, T; Yamanaka, K; Luijsterburg, MS; Ogi, T

CELL 180 巻 ( 6 ) 頁： 1228 - + 2020年3月

担当区分：筆頭著者記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Cell

Transcription-coupled nucleotide excision repair (TC-NER) is initiated by the stalling of elongating RNA polymerase II (RNAPIIo) at DNA lesions. The ubiquitination of RNAPIIo in response to DNA damage is an evolutionarily conserved event, but its function in mammals is unknown. Here, we identified a single DNA damage-induced ubiquitination site in RNAPII at RPB1-K1268, which regulates transcription recovery and DNA damage resistance. Mechanistically, RPB1-K1268 ubiquitination stimulates the association of the core-TFIIH complex with stalled RNAPIIo through a transfer mechanism that also involves UVSSA-K414 ubiquitination. We developed a strand-specific ChIP-seq method, which revealed RPB1-K1268 ubiquitination is important for repair and the resolution of transcriptional bottlenecks at DNA lesions. Finally, RPB1-K1268R knockin mice displayed a short life-span, premature aging, and neurodegeneration. Our results reveal RNAPII ubiquitination provides a two-tier protection mechanism by activating TC-NER and, in parallel, the processing of DNA damage-stalled RNAPIIo, which together prevent prolonged transcription arrest and protect against neurodegeneration.

DOI： 10.1016/j.cell.2020.02.010

Comparing the severity of epidermolysis bullosa simplex harboring KRT5 variants with the AlphaMissense score Open Access

Mutations in UVSSA cause UV-sensitive syndrome and impair RNA polymerase IIo processing in transcription-coupled nucleotide-excision repair. 査読有り国際共著

Nakazawa Y, Sasaki K, Mitsutake N, Matsuse M, Shimada M, Nardo T, Takahashi Y, Ohyama K, Ito K, Mishima H, Nomura M, Kinoshita A, Ono S, Takenaka K, Masuyama R, Kudo T, Slor H, Utani A, Tateishi S, Yamashita S, Stefanini M, Lehmann AR, Yoshiura KI, Ogi T§.

Nature Genetics 44 巻頁： 586-592 2012年5月

XRCC4 deficiency in human subjects causes a marked neurological phenotype but no overt immunodeficiency. 査読有り国際共著

Guo C*, Nakazawa Y*, Woodbine L*, Bjorkman A, Shimada M, Fawcett H, Jia N, Ohyama K, Li TS, Nagayama Y, Mitsutake N, Pan-Hammarstrom Q, Gennery AR, Lehmann AR, Jeggo PA, Ogi T§.

Journal of Allergy and Clinical Immunology 136 巻頁： 1007-1017 2015年10月

A rapid comprehensive assay system for DNA repair activity and cytotoxic effects of DNA damaging reagents by measuring unscheduled DNA synthesis and recovery of RNA synthesis after DNA damage. 査読有り国際共著

Jia N*, Nakazawa Y*, Guo C, Shimada M, Sethi M, Takahashi Y, Ueda H, Nagayama Y, Ogi T§.

Nature Protocols 10 巻頁： 12-24 2015年1月

Malfunction of Nuclease ERCC1-XPF Results in Diverse Clinical Manifestations and Causes Cockayne Syndrome, Xeroderma Pigmentosum, and Fanconi Anemia. 査読有り国際共著

Kashiyama K*, Nakazawa Y*, Pilz D*, Guo C*, Shimada M, Sasaki K, Fawcett H, Wing J, Lewin S, Carr L, Li TS, Yoshiura K, Utani A, Hirano A, Yamashita S, Greenblatt D, Nardo T, Stefanini M, McGibbon D, Sarkany R, Fassihi H, Takahashi Y, Nagayama Y, Mitsutake N, Lehmann AR§, Ogi T§.

American Journal of Human Genetics 92 巻頁： 807-819 2013年5月

Transcription-coupled repair - mechanisms of action, regulation, and associated human disorders 招待有り査読有り Open Access

Nakazawa, Y; Oka, Y; Matsunaga, T; Ogi, T

FEBS LETTERS 599 巻 ( 2 ) 頁： 166 - 167 2025年1月

Estimating the proportions of allele frequencies for SERPINA12 pathogenic variants in Japanese patients with Nagashima-type palmoplantar keratosis/keratoderma.

Ebata A, Takeichi T, Nishida K, Chretien B, Miyazaki A, Yoshikawa T, Suzuki Y, Tanahashi K, Fukaura R, Seishima M, Suga Y, Muro Y, Nakazawa Y, Ogi T, Akiyama M

The British journal of dermatology 2025年3月

Omi, M; Takeichi, T; Yoshikawa, T; Inoue, Y; Fukaura, R; Hattori, I; Nakazawa, Y; Noda, T; Muro, Y; Akiyama, M

JOURNAL OF DERMATOLOGY 52 巻 ( 3 ) 頁： e235 - e237 2025年3月

Clearance of DNA damage-arrested RNAPII is selectively impaired in Cockayne syndrome cells

Paula J. van der Meer, George Yakoub, Yuka Nakazawa, Tomoo Ogi, Martijn Luijsterburg

2024年5月

Inducing multiple nicks promotes interhomolog homologous recombination to correct heterozygous mutations in somatic cells 査読有り国際誌

Tomita, A; Sasanuma, H; Owa, T; Nakazawa, Y; Shimada, M; Fukuoka, T; Ogi, T; Nakada, S

NATURE COMMUNICATIONS 14 巻 ( 1 ) 頁： 5607 - 5607 2023年9月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Nature Communications

CRISPR/Cas9-mediated gene editing has great potential utility for treating genetic diseases. However, its therapeutic applications are limited by unintended genomic alterations arising from DNA double-strand breaks and random integration of exogenous DNA. In this study, we propose NICER, a method for correcting heterozygous mutations that employs multiple nicks (MNs) induced by Cas9 nickase and a homologous chromosome as an endogenous repair template. Although a single nick near the mutation site rarely leads to successful gene correction, additional nicks on homologous chromosomes strongly enhance gene correction efficiency via interhomolog homologous recombination (IH-HR). This process partially depends on BRCA1 and BRCA2, suggesting the existence of several distinct pathways for MN-induced IH-HR. According to a genomic analysis, NICER rarely induces unintended genomic alterations. Furthermore, NICER restores the expression of disease-causing genes in cells derived from genetic diseases with compound heterozygous mutations. Overall, NICER provides a precise strategy for gene correction.

DOI： 10.1038/s41467-023-41048-5

A case of Cockayne syndrome with unusually mild clinical manifestations 査読有り

Tsujimoto, M; Nakano, E; Nakazawa, Y; Kanda, F; Ueda, T; Ogi, T; Nishigori, C

JOURNAL OF DERMATOLOGY 50 巻 ( 4 ) 頁： 541 - 545 2023年4月

記述言語：英語出版者・発行元：Journal of Dermatology

We present a mild case of Cockayne syndrome that was referred to us with an extreme sunburn at the age of 3. In early teens, although her cutaneous symptoms alleviated without any medications, she developed tremor and dysarthria. Neurological examination and brain imaging suggested demyelination disorders. The patient's cells indicated a reduced recovery of RNA synthesis, which was partially restored by the introduction of CSB (Cockayne Syndrome B)-cDNA. In addition, her cells indicated a substantially reduced level of CSB protein. Despite the insidious progression of neurological symptoms, she gave birth to a child. Such mild cases of Cockayne syndrome may be misdiagnosed.

DOI： 10.1111/1346-8138.16679

Aicardi-Goutieres syndrome with SAMHD1 deficiency can be diagnosed by unscheduled DNA synthesis test 査読有り国際誌

Senju, C; Nakazawa, Y; Shimada, M; Iwata, D; Matsuse, M; Tanaka, K; Miyazaki, Y; Moriwaki, S; Mitsutake, N; Ogi, T

FRONTIERS IN PEDIATRICS 10 巻頁： 1048002 - 1048002 2022年11月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Frontiers in Pediatrics

Aicardi–Goutières syndrome (AGS) is a rare genetic disorder characterised by progressive encephalopathy, involving microcephaly, intracranial calcification, and cerebrospinal fluid lymphocytosis with increased interferon-α concentrations. The clinical features of AGS overlap with fetal cerebral anomalies caused by congenital infections, such as TORCH (toxoplasmosis, other, rubella, cytomegalovirus, and herpes), or with those of other genetic disorders showing neonatal microcephaly, including Cockayne syndrome (CS) with transcription-coupled DNA repair deficiency, and Seckel syndrome (SS) showing aberrant cell-cycle checkpoint signaling. Therefore, a differential diagnosis to confirm the genetic cause or a proof of infection should be considered. In this report, we describe an individual who showed primordial dwarfism and encephalopathy, and whose initial diagnosis was CS. First, we conducted conventional DNA repair proficiency tests for the patient derived fibroblast cells. Transcription-coupled nucleotide excision repair (TC-NER) activity, which is mostly compromised in CS cases, was slightly reduced in the patient's cells. However, unscheduled DNA synthesis (UDS) was significantly diminished. These cellular traits were inconsistent with the diagnosis of CS. We further performed whole exome sequencing for the case and identified a compound heterozygous loss-of-function variants in the SAMHD1 gene, mutations in which are known to cause AGS. As SAMHD1 encodes deoxyribonucleoside triphosphate triphosphohydrolase, we reasoned that the deoxyribonucleoside triphosphate (dNTP) pool size in the patient's cells was elevated, and the labeling efficiency of UDS-test was hindered due to the reduced concentration of phosphorylated ethynyl deoxyuridine (EdU), a nucleoside analogue used for the assay. In conclusion, UDS assay may be a useful diagnostic tool to distinguish between AGS with SAMHD1 mutations and other related diseases.

DOI： 10.3389/fped.2022.1048002

Dealing with transcription-blocking DNA damage: Repair mechanisms, RNA polymerase II processing and human disorders 査読有り国際共著

Jia, N; Guo, CW*; Nakazawa, Y*; van den Heuvel, D*; Luijsterburg, MS; Ogi, T

DNA REPAIR 106 巻頁： 103192 2021年10月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：DNA Repair

Transcription-blocking DNA lesions (TBLs) in genomic DNA are triggered by a wide variety of DNA-damaging agents. Such lesions cause stalling of elongating RNA polymerase II (RNA Pol II) enzymes and fully block transcription when unresolved. The toxic impact of DNA damage on transcription progression is commonly referred to as transcription stress. In response to RNA Pol II stalling, cells activate and employ transcription-coupled repair (TCR) machineries to repair cytotoxic TBLs and resume transcription. Increasing evidence indicates that the modification and processing of stalled RNA Pol II is an integral component of the cellular response to and the repair of TBLs. If TCR pathways fail, the prolonged stalling of RNA Pol II will impede global replication and transcription as well as block the access of other DNA repair pathways that may act upon the TBL. Consequently, such prolonged stalling will trigger profound genome instability and devastating clinical features. In this review, we will discuss the mechanisms by which various types of TBLs are repaired by distinct TCR pathways and how RNA Pol II processing is regulated during these processes. We will also discuss the clinical consequences of transcription stress and genotype-phenotype correlations of related TCR-deficiency disorders.

DOI： 10.1016/j.dnarep.2021.103192

ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation 査読有り国際共著国際誌

van der Weegen, Y; de Lint, K; van den Heuvel, D; Nakazawa, Y; Mevissen, TET; van Schie, JJM; Alonso, MS; Boer, DEC; González-Prieto, R; Narayanan, IV; Klaassen, NHM; Wondergem, AP; Roohollahi, K; Dorsman, JC; Hara, Y; Vertegaal, ACO; de Lange, J; Walter, JC; Noordermeer, SM; Ljungman, M; Ogi, T; Wolthuis, RMF; Luijsterburg, MS

NATURE CELL BIOLOGY 23 巻 ( 6 ) 頁： 595 - 607 2021年6月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Nature Cell Biology

Cells employ transcription-coupled repair (TCR) to eliminate transcription-blocking DNA lesions. DNA damage-induced binding of the TCR-specific repair factor CSB to RNA polymerase II (RNAPII) triggers RNAPII ubiquitylation of a single lysine (K1268) by the CRL4CSA ubiquitin ligase. How CRL4CSA is specifically directed towards K1268 is unknown. Here, we identify ELOF1 as the missing link that facilitates RNAPII ubiquitylation, a key signal for the assembly of downstream repair factors. This function requires its constitutive interaction with RNAPII close to K1268, revealing ELOF1 as a specificity factor that binds and positions CRL4CSA for optimal RNAPII ubiquitylation. Drug–genetic interaction screening also revealed a CSB-independent pathway in which ELOF1 prevents R-loops in active genes and protects cells against DNA replication stress. Our study offers key insights into the molecular mechanisms of TCR and provides a genetic framework of the interplay between transcriptional stress responses and DNA replication.

DOI： 10.1038/s41556-021-00688-9