Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants.
Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants.
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DOI：
10.1038/s41467-023-41023-0
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发表时间：
2023-08-28
影响因子：
16.6
通讯作者：
Mirouze, Marie
中科院分区：
文献类型：
--
作者：
Zhang, Panpan;Mbodj, Assane;Soundiramourtty, Abirami;Llauro, Christel;Ghesquiere, Alain;Ingouff, Mathieu;Slotkin, R. Keith;Pontvianne, Frederic;Catoni, Marco;Mirouze, Marie
丰富的染色体外环状 DNA (eccDNA) 与转座元件 (TE) 活性相关。然而，eccDNA 区室如何受表观遗传调控以及它对基因组的影响尚待研究。在这里，我们使用长读长，对受 DNA 甲基化和转录后基因沉默影响的拟南芥突变体植物的 eccDNA 区室和基因组进行测序。我们检测到高负载的 TE 衍生的 eccDNA，具有截短和嵌合形式。在基因组方面，除了截短的全长 TE 新插入之外，我们还检测到复杂的结构变异 (SV)，特别是在作为 SV 天然热点的抗病簇处。最后，我们偶然发现低甲基化植物中存在大量串联重复，这表明表观遗传突变体中的 SV 可能被忽视。我们认为高 eccDNA 负载可能会改变 DNA 修复途径，导致基因组不稳定和 SV 积累，至少在植物中是这样。染色体外环状 DNA (eccDNA) 区室的表观遗传控制以及 eccDNA 与植物基因组稳定性之间的关系仍不清楚。在这里，作者研究了拟南芥表观遗传突变体的 eccDNA 和结构变异，以揭示 eccDNA 库及其对基因组稳定性的影响。
Abundant extrachromosomal circular DNA (eccDNA) is associated with transposable element (TE) activity. However, how the eccDNA compartment is controlled by epigenetic regulations and what is its impact on the genome is understudied. Here, using long reads, we sequence both the eccDNA compartment and the genome of Arabidopsis thaliana mutant plants affected in DNA methylation and post-transcriptional gene silencing. We detect a high load of TE-derived eccDNA with truncated and chimeric forms. On the genomic side, on top of truncated and full length TE neo-insertions, we detect complex structural variations (SVs) notably at a disease resistance cluster being a natural hotspot of SV. Finally, we serendipitously identify large tandem duplications in hypomethylated plants, suggesting that SVs could have been overlooked in epigenetic mutants. We propose that a high eccDNA load may alter DNA repair pathways leading to genome instability and the accumulation of SVs, at least in plants. Epigenetic control of extrachromosomal circular DNA (eccDNA) compartment and the relationships between eccDNA and plant genome stability remain unclear. Here, the authors investigate eccDNA and structural variations in Arabidopsis epigenetic mutants to reveal the eccDNA repertoire and its impact on genome stability.
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影响因子：
12.3
作者：
Kim S;Park J;Yeom SI;Kim YM;Seo E;Kim KT;Kim MS;Lee JM;Cheong K;Shin HS;Kim SB;Han K;Lee J;Park M;Lee HA;Lee HY;Lee Y;Oh S;Lee JH;Choi E;Choi E;Lee SE;Jeon J;Kim H;Choi G;Song H;Lee J;Lee SC;Kwon JK;Lee HY;Koo N;Hong Y;Kim RW;Kang WH;Huh JH;Kang BC;Yang TJ;Lee YH;Bennetzen JL;Choi D
通讯作者：
Choi D
影响因子：
4.5
作者：
Lanciano S;Carpentier MC;Llauro C;Jobet E;Robakowska-Hyzorek D;Lasserre E;Ghesquière A;Panaud O;Mirouze M
通讯作者：
Mirouze M
影响因子：
4
作者：
Burrage, Joe;Termanis, Ausma;Stancheva, Irina
通讯作者：
Stancheva, Irina
影响因子：
14.9
作者：
Xuan YH;Piao HL;Je BI;Park SJ;Park SH;Huang J;Zhang JB;Peterson T;Han CD
通讯作者：
Han CD
DOI：
10.1126/science.abg5289
发表时间：
2021-08-06
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Hufford MB;Seetharam AS;Woodhouse MR;Chougule KM;Ou S;Liu J;Ricci WA;Guo T;Olson A;Qiu Y;Della Coletta R;Tittes S;Hudson AI;Marand AP;Wei S;Lu Z;Wang B;Tello-Ruiz MK;Piri RD;Wang N;Kim DW;Zeng Y;O'Connor CH;Li X;Gilbert AM;Baggs E;Krasileva KV;Portwood JL 2nd;Cannon EKS;Andorf CM;Manchanda N;Snodgrass SJ;Hufnagel DE;Jiang Q;Pedersen S;Syring ML;Kudrna DA;Llaca V;Fengler K;Schmitz RJ;Ross-Ibarra J;Yu J;Gent JI;Hirsch CN;Ware D;Dawe RK
通讯作者：
Dawe RK