小柯机器人

荷兰拉德堡德大学Michiel Vermeulen等研究人员合作使用BANC-seq对原生染色质背景下的绝对转录因子结合亲和力进行量化。该研究于2023年3月27日在线发表于国际一流学术期刊《自然—生物技术》。

研究人员报告了一种称为通过测序与原生染色质结合亲和力的方法（BANC-seq），以确定转录因子与整个基因组中原生DNA的绝对表观结合亲和力。在BANC-seq中，一个浓度范围的标记转录因子被添加到分离的细胞中。然后测量每个样本的浓度依赖性结合，以量化整个基因组的表观结合亲和力。BANC-seq为转录因子生物学增加了一个定量的维度，它能根据转录因子的浓度对基因组靶标进行分层，并预测非生理条件下的转录因子结合位点，如疾病相关的过度表达的（原癌）基因。

值得注意的是，虽然转录因子的一致DNA结合模体对于建立高亲和力的结合位点很重要，但这些模体并不总是严格要求在基因组中产生纳摩尔亲和力的相互作用。

据介绍，转录因子在整个基因组的结合受DNA序列和染色质特征的调节。然而，目前还不可能量化染色质背景对转录因子结合亲和力的影响。

附：英文原文

Title: Quantification of absolute transcription factor binding affinities in the native chromatin context using BANC-seq

Author: Neikes, Hannah K., Kliza, Katarzyna W., Grwe, Cathrin, Wester, Roelof A., Jansen, Pascal W. T. C., Lamers, Lieke A., Baltissen, Marijke P., van Heeringen, Simon J., Logie, Colin, Teichmann, Sarah A., Lindeboom, Rik G. H., Vermeulen, Michiel

Issue&Volume: 2023-03-27

Abstract: Transcription factor binding across the genome is regulated by DNA sequence and chromatin features. However, it is not yet possible to quantify the impact of chromatin context on transcription factor binding affinities. Here, we report a method called binding affinities to native chromatin by sequencing (BANC-seq) to determine absolute apparent binding affinities of transcription factors to native DNA across the genome. In BANC-seq, a concentration range of a tagged transcription factor is added to isolated nuclei. Concentration-dependent binding is then measured per sample to quantify apparent binding affinities across the genome. BANC-seq adds a quantitative dimension to transcription factor biology, which enables stratification of genomic targets based on transcription factor concentration and prediction of transcription factor binding sites under non-physiological conditions, such as disease-associated overexpression of (onco)genes. Notably, whereas consensus DNA binding motifs for transcription factors are important to establish high-affinity binding sites, these motifs are not always strictly required to generate nanomolar-affinity interactions in the genome.

DOI: 10.1038/s41587-023-01715-w

Source: https://www.nature.com/articles/s41587-023-01715-w

Nature Biotechnology：《自然—生物技术》，创刊于1996年。隶属于施普林格·自然出版集团，最新IF：68.164
官方网址：https://www.nature.com/nbt/
投稿链接：https://mts-nbt.nature.com/cgi-bin/main.plex