Hardy Alexis, Matelot Mélody, Touzeau Amandine, Klopp Christophe, Lopez-Roques Céline, Duharcourt Sandra, Defrance Matthieu
Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France.
Plateforme bioinformatique Genotoul, UR875 Mathématique et Informatique Appliquée de Toulouse, INRA, 31326 Castanet-Tolosan, France.
Bioinformatics. 2021 Sep 9;37(17):2738-2740. doi: 10.1093/bioinformatics/btab032.
Long-read sequencing technologies can be employed to detect and map DNA modifications at the nucleotide resolution on a genome-wide scale. However, published software packages neglect the integration of genomic annotation and comprehensive filtering when analyzing patterns of modified bases detected using Pacific Biosciences (PacBio) or Oxford Nanopore Technologies (ONT) data. Here, we present DNA Modification Annotation (DNAModAnnot), a R package designed for the global analysis of DNA modification patterns using adapted filtering and visualization tools.
We tested our package using PacBio sequencing data to analyze patterns of the 6-methyladenine (6mA) in the ciliate Paramecium tetraurelia, in which high 6mA amounts were previously reported. We found P. tetraurelia 6mA genome-wide distribution to be similar to other ciliates. We also performed 5-methylcytosine (5mC) analysis in human lymphoblastoid cells using ONT data and confirmed previously known patterns of 5mC. DNAModAnnot provides a toolbox for the genome-wide analysis of different DNA modifications using PacBio and ONT long-read sequencing data.
DNAModAnnot is distributed as a R package available via GitHub (https://github.com/AlexisHardy/DNAModAnnot).
Supplementary data are available at Bioinformatics online.
长读长测序技术可用于在全基因组范围内以核苷酸分辨率检测和定位DNA修饰。然而，已发表的软件包在分析使用太平洋生物科学公司（PacBio）或牛津纳米孔技术（ONT）数据检测到的修饰碱基模式时，忽略了基因组注释的整合和全面筛选。在此，我们展示了DNA修饰注释（DNAModAnnot），这是一个R软件包，旨在使用经过调整的筛选和可视化工具对DNA修饰模式进行全局分析。
我们使用PacBio测序数据测试了我们的软件包，以分析纤毛虫四膜虫中6-甲基腺嘌呤（6mA）的模式，此前报道该纤毛虫中6mA含量很高。我们发现四膜虫全基因组范围内的6mA分布与其他纤毛虫相似。我们还使用ONT数据对人类淋巴母细胞进行了5-甲基胞嘧啶（5mC）分析，并证实了先前已知的5mC模式。DNAModAnnot提供了一个工具箱，用于使用PacBio和ONT长读长测序数据对不同的DNA修饰进行全基因组分析。
DNAModAnnot作为一个R软件包分发，可通过GitHub（https://github.com/AlexisHardy/DNAModAnnot）获得。
补充数据可在《生物信息学》在线获取。
