Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin.
Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin.
复制标题
DOI：
10.1038/s41592-021-01135-1
复制
发表时间：
2021-05
期刊：
影响因子：
48
通讯作者：
Nicodemi M
中科院分区：
文献类型：
--
作者：
Fiorillo L;Musella F;Conte M;Kempfer R;Chiariello AM;Bianco S;Kukalev A;Irastorza-Azcarate I;Esposito A;Abraham A;Prisco A;Pombo A;Nicodemi M
Hi-C，通过标签扩展进行的相互作用的分裂池识别（SPRITE）和基因组结构映射（GAM）是用于探测基因组范围内染色质相互作用的强大技术，但它们如何忠实地捕获三维（3D）接触以及它们彼此之间的相对表现尚不清楚，因为没有基准存在。在这里，我们将这些方法与已知的小鼠和人类基因座聚合物模型的3D结构进行了比较，这些模型可以概括Hi-C， GAM和SPRITE实验以及多路荧光原位杂交（FISH）单分子构象。我们发现在硅中，Hi-C， GAM和SPRITE体数据忠实于参考三维结构，而单细胞数据反映了单分子之间的强变异性。在重复实验中返回统计上相似的接触所需的最小细胞数在不同的技术中是不同的，在相同的条件下，SPRITE最低，GAM最高。三种方法的噪声-信号水平与检测效率呈反幂律关系，且随基因组距离的增加而增长，在GAM中最低，当基因组分离为1 Mb时。本分析报告了一种计算方法来实现Hi-C， SPRITE和GAM，这使得研究人员能够评估这三种技术在染色质三维模型中捕获DNA接触的性能。
Hi-C, split-pool recognition of interactions by tag extension (SPRITE) and genome architecture mapping (GAM) are powerful technologies utilized to probe chromatin interactions genome wide, but how faithfully they capture three-dimensional (3D) contacts and how they perform relative to each other is unclear, as no benchmark exists. Here, we compare these methods in silico in a simplified, yet controlled, framework against known 3D structures of polymer models of murine and human loci, which can recapitulate Hi-C, GAM and SPRITE experiments and multiplexed fluorescence in situ hybridization (FISH) single-molecule conformations. We find that in silico Hi-C, GAM and SPRITE bulk data are faithful to the reference 3D structures whereas single-cell data reflect strong variability among single molecules. The minimal number of cells required in replicate experiments to return statistically similar contacts is different across the technologies, being lowest in SPRITE and highest in GAM under the same conditions. Noise-to-signal levels follow an inverse power law with detection efficiency and grow with genomic distance differently among the three methods, being lowest in GAM for genomic separations >1 Mb. This Analysis reports a computational approach to implement Hi-C, SPRITE and GAM, which allows researchers to assess the performances of the three technologies to capture DNA contacts in chromatin three-dimensional models.
登录
查看更多内容
影响因子：
64.5
作者：
Dekker J;Mirny L
通讯作者：
Mirny L
影响因子：
16.6
作者：
Cattoni DI;Cardozo Gizzi AM;Georgieva M;Di Stefano M;Valeri A;Chamousset D;Houbron C;Déjardin S;Fiche JB;González I;Chang JM;Sexton T;Marti-Renom MA;Bantignies F;Cavalli G;Nollmann M
通讯作者：
Nollmann M
影响因子：
16.6
作者：
Conte, Mattia;Fiorillo, Luca;Nicodemi, Mario
通讯作者：
Nicodemi, Mario
影响因子：
64.8
作者：
Beagrie RA;Scialdone A;Schueler M;Kraemer DC;Chotalia M;Xie SQ;Barbieri M;de Santiago I;Lavitas LM;Branco MR;Fraser J;Dostie J;Game L;Dillon N;Edwards PA;Nicodemi M;Pombo A
通讯作者：
Pombo A
DOI：
10.1073/pnas.1613607113
发表时间：
2016-10-25
影响因子：
11.1
作者：
Di Pierro, Michele;Zhang, Bin;Onuchic, Jose N.
通讯作者：
Onuchic, Jose N.