Evaluation of repair activity by quantification of ribonucleotides in the genome.
Evaluation of repair activity by quantification of ribonucleotides in the genome.
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DOI：
10.1111/gtc.12871
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发表时间：
2021-08
期刊：
影响因子：
--
通讯作者：
Kobayashi T
中科院分区：
文献类型：
--
作者：
Iida T;Iida N;Sese J;Kobayashi T
掺入基因组中的核糖核苷酸是内源性DNA损伤的来源，也用作修复的信号。虽然最近的进展核糖核苷酸检测测序，核糖核苷酸的掺入和修复之间的平衡尚未阐明。在这里，我们描述了一种竞争性测序方法，核糖核苷酸扫描定量测序（RiSQ-seq），它可以通过背景归一化和单个样品中的标准调整来绝对定量整个基因组中错误掺入的核糖核苷酸。对携带野生型DNA聚合酶的细胞进行的RiSQ-seq分析显示，核糖核苷酸在基因组中的掺入是不均匀的，具有3′移位分布和对GC序列的偏好。尽管野生型和修复缺陷突变株中的核糖核苷酸谱显示出相似的模式，但通过RiSQ-seq直接比较菌株中不同的核糖核苷酸水平，能够在碱基分辨率下评价核糖核苷酸切除修复活性，并揭示修复的链偏倚。核糖核苷酸掺入和修复的不同偏好产生了与indel热点相关的脆弱区域，这表明核糖核苷酸错误掺入位点的修复有助于保持基因组的完整性，并且RiSQ-seq可以提供indel风险的估计。核糖核苷酸扫描定量测序（RiSQ-seq）通过rNMP和背景之间的竞争性测序，能够对基因组中错误掺入的核糖核苷酸（rNMP）进行绝对定量。rNMP定量显示rNMP的非均匀掺入和修复活性。rNMP修复活性的阴阳模式产生了与插入缺失（indel）突变热点相关的脆弱区域。RiSQ-seq可以提供indel风险的估计。
Ribonucleotides incorporated in the genome are a source of endogenous DNA damage and also serve as signals for repair. Although recent advances of ribonucleotide detection by sequencing, the balance between incorporation and repair of ribonucleotides has not been elucidated. Here, we describe a competitive sequencing method, Ribonucleotide Scanning Quantification sequencing (RiSQ‐seq), which enables absolute quantification of misincorporated ribonucleotides throughout the genome by background normalization and standard adjustment within a single sample. RiSQ‐seq analysis of cells harboring wild‐type DNA polymerases revealed that ribonucleotides were incorporated nonuniformly in the genome with a 3′‐shifted distribution and preference for GC sequences. Although ribonucleotide profiles in wild‐type and repair‐deficient mutant strains showed a similar pattern, direct comparison of distinct ribonucleotide levels in the strains by RiSQ‐seq enabled evaluation of ribonucleotide excision repair activity at base resolution and revealed the strand bias of repair. The distinct preferences of ribonucleotide incorporation and repair create vulnerable regions associated with indel hotspots, suggesting that repair at sites of ribonucleotide misincorporation serves to maintain genome integrity and that RiSQ‐seq can provide an estimate of indel risk. Ribonucleotide Scanning Quantification sequencing (RiSQ‐seq) enables absolute quantification of misincorporated ribonucleotides (rNMPs) in the genome by competitive sequencing between rNMPs and backgrounds. The rNMP quantification revealed non‐uniform incorporation and repair activity of rNMP. The Yin‐yang pattern of rNMP repair activity creates vulnerable regions associated with hotspots of insert‐deletion (indel) mutations. RiSQ‐seq can provide an estimate of indel risk.
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影响因子：
16
作者：
Ghodgaonkar, Medini Manohar;Lazzaro, Federico;Olivera-Pimentel, Maite;Artola-Boran, Mariela;Cejka, Petr;Reijns, Martin A.;Jackson, Andrew P.;Plevani, Paolo;Muzi-Falconi, Marco;Jiricny, Josef
通讯作者：
Jiricny, Josef
从DNA中酶促去除核糖核苷酸对于哺乳动物的基因组完整性和发育至关重要。
影响因子：
64.5
作者：
Reijns MA;Rabe B;Rigby RE;Mill P;Astell KR;Lettice LA;Boyle S;Leitch A;Keighren M;Kilanowski F;Devenney PS;Sexton D;Grimes G;Holt IJ;Hill RE;Taylor MS;Lawson KA;Dorin JR;Jackson AP
通讯作者：
Jackson AP
影响因子：
16
作者：
Sparks, Justin L.;Chon, Hyongi;Cerritelli, Susana M.;Kunkel, Thomas A.;Johansson, Erik;Crouch, Robert J.;Burgers, Peter M.
通讯作者：
Burgers, Peter M.
影响因子：
14.8
作者：
Ding J;Taylor MS;Jackson AP;Reijns MA
通讯作者：
Reijns MA
影响因子：
64.8
作者：
Tumbale, Percy;Williams, Jessica S.;Williams, R. Scott
通讯作者：
Williams, R. Scott