2019年7月24日 · In this study, we employ a synthetic biology reporter assay and in vivo SHAPE-seq (Lucks et al., 2011, Spitale et al., 2013, Flynn et al., 2016) approach to study the regulatory effect controlled by an RBP bound to a hairpin within the 5′ UTR of bacterial mRNA, following a design introduced by Saito et al. (2010).

2025年1月1日 · The 5′ UTR of whiB7/wblC includes a 110-codon uORF that overlaps with a potential antiterminator stem-loop structure and a Rho-independent terminator. In the absence of ribosome-targeting antibiotics or amino acid starvation, uORF is fully translated to promote the formation of the terminator and premature transcriptional termination.

2021年1月18日 · Genome-wide analysis of RNA-binding protein (RBP) target sites identifies a major role for RBP dysregulation in complex psychiatric disorders and implicates DDHD2 as a candidate risk gene for...

2025年1月15日 · Reimão-Pinto et al. introduce thousands of different mRNA reporters into zebrafish embryos to investigate the contribution of 5′ UTR features to translation initiation during embryogenesis. The work defines the regulatory potential of 5′ UTRs and develops a deep learning model that predicts translational dynamics based on the 5′ UTR ...

We study translational regulation by a 5’ UTR sequence encoding the binding site of an RNA-binding protein (RBP) in bacteria, using a reporter assay and Selective 2′-hydroxyl acylation analysed by primer extension sequencing (SHAPE-Seq).

使用合成生物学方法与SHAPE-seq结合，我们探索了细菌5'UTR中RNA结合蛋白（RBP）-RNA相互作用的调节作用。 通过将一个RNA发夹文库定位在报告基因的上游，并与匹配的RBP共表达它们，我们观察到了一组调控反应，包括翻译刺激，翻译抑制和合作行为。 我们的组合方法揭示 了体内的 三种不同状态：在不存在RBP的情况下，可以发现RNA分子处于易于翻译的熔融状态或抑制翻译的结构化阶段。 在存在RBP的情况下，RNA分子处于具有部分翻译能力的半结构相。 我们 …

2019年7月24日 · Using a synthetic biology approach combined with SHAPE-seq, we explored the regulatory effect of RNA-binding protein (RBP)-RNA interactions in bacterial 5' UTRs. By positioning a library of RNA hairpins upstream of a reporter gene and co-expressing them with the matching RBP, we observed a set of regulatory responses, including translational ...

2019年3月28日 · By positioning a library of RNA hairpins upstream of a reporter gene and co-expressing them with the matching RBP, we observed a set of regulatory responses, including translational stimulation, translational repression, and cooperative behavior.

2018年4月13日 · We study translational regulation by a 5’ UTR sequence encoding the binding site of an RNA-binding protein (RBP) in bacteria, using a reporter assay and Selective 2’-hydroxyl acylation analysed by primer extension sequencing (SHAPE-Seq).

2024年5月23日 · Both 5′UTR and 3′UTR of mRNAs modulate mRNA functions through interactions with RNA-binding proteins (RBPs) and microRNAs via specific cis-regulatory elements [1, 6, 7]. Within the 5′UTR, upstream open reading frames (uORFs) interact with the translational machinery to modulate the translation rates of downstream coding sequence [ 8 ].