The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface.
The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface.
复制标题
坡道地图集：通过直观的Web界面促进组织和细胞特异性坡道序列分析。
DOI：
10.1093/nargab/lqac039
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发表时间：
2022-06
影响因子：
4.6
通讯作者：
中科院分区：
文献类型：
--
作者：
当高表达基因5′端附近密码子的平均翻译效率显著低于基因序列的其余部分时，就会出现斜坡序列，这与直觉相反，通过减少下游核糖体碰撞来提高翻译效率。在这里，我们表明，不同组织内的相对密码子适应性改变了斜坡序列的存在，而不改变潜在的遗传密码。我们提出了组织和细胞类型特异性的斜坡序列的第一个全面的分析，并报告了3108个基因的斜坡序列，组织和细胞类型之间的变化，这对应于这些组织和细胞内的基因表达增加。Ramp Atlas（https：//ramps.byu.edu/）允许研究人员查询62种组织和66种细胞类型的18388个基因中预先计算的ramp序列，并通过直观的Web界面从用户上传的FASTA文件中计算组织特异性ramp序列。我们使用Ramp Atlas鉴定了7个SARS-CoV-2基因和7个具有组织特异性Ramp序列的人SARS-CoV-2进入因子基因，这可能有助于解释这些组织中的病毒增殖。我们预计，Ramp Atlas将有助于对人类和病毒基因进行个性化和创造性的组织特异性ramp序列分析，这将提高我们利用这一经常被忽视的调控区域的能力。
Ramp sequences occur when the average translational efficiency of codons near the 5′ end of highly expressed genes is significantly lower than the rest of the gene sequence, which counterintuitively increases translational efficiency by decreasing downstream ribosomal collisions. Here, we show that the relative codon adaptiveness within different tissues changes the existence of a ramp sequence without altering the underlying genetic code. We present the first comprehensive analysis of tissue and cell type-specific ramp sequences and report 3108 genes with ramp sequences that change between tissues and cell types, which corresponds with increased gene expression within those tissues and cells. The Ramp Atlas (https://ramps.byu.edu/) allows researchers to query precomputed ramp sequences in 18 388 genes across 62 tissues and 66 cell types and calculate tissue-specific ramp sequences from user-uploaded FASTA files through an intuitive web interface. We used The Ramp Atlas to identify seven SARS-CoV-2 genes and seven human SARS-CoV-2 entry factor genes with tissue-specific ramp sequences that may help explain viral proliferation within those tissues. We anticipate that The Ramp Atlas will facilitate personalized and creative tissue-specific ramp sequence analyses for both human and viral genes that will increase our ability to utilize this often-overlooked regulatory region.
DOI：
10.1002/psp4.12305
发表时间：
2018-07
期刊：
CPT: pharmacometrics & systems pharmacology
影响因子：
--
作者：
Hao Y;Quinnies K;Realubit R;Karan C;Tatonetti NP
通讯作者：
Tatonetti NP
影响因子：
9.3
作者：
Prassas I;Chrystoja CC;Makawita S;Diamandis EP
通讯作者：
Diamandis EP