脚印
计算生物学
基因组
结合位点
DNA
碱基对
生物
复制的起源
序列(生物学)
类核
DNA测序
超分辨率
基因
遗传学
计算机科学
基序列
大肠杆菌
人工智能
图像(数学)
作者
Onuma Chumsakul,Kensuke Nakamura,Kazuki Fukamachi,Shu Ishikawa,Taku Oshima
出处
期刊:Methods in molecular biology
日期:2024-01-01
卷期号:: 39-53
标识
DOI:10.1007/978-1-0716-3930-6_3
摘要
Nucleotide sequences recognized and bound by DNA-binding proteins (DBPs) are critical to controlling and maintaining gene expression, replication, chromosome segregation, cell division, and nucleoid structure in bacterial cells. Therefore, determination of the binding sequences of DBPs is important not only to study DBP recognition mechanisms but also to understand the fundamentals of cell homeostasis. While ChIP-seq analysis appears to be an effective way to determine DBP binding sites on the genome, the resolution is sometimes not sufficient to identify the sites precisely. Here we introduce a simple and effective method named Genome Footprinting with high-throughput sequencing (GeF-seq) to determine binding sites of DBPs with single base-pair resolution. GeF-seq detects binding sites of DBPs as sharp peaks and thus makes it possible to identify the recognition sequence in each "binding peak" more easily and accurately compared to the common ChIP-seq.
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