LncPepAtlas:一个全面的资源,用于探索长非编码RNA的翻译格局
Xinyuan Zhou1,2, Yanxia Qin1, Jiangxue Li1
1Binzhou People's Hospital Affiliated to Shandong First Medical University/College of Medical Information and Artificial Intelligence, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China.
Nucleic acids research
|October 22, 2024
概括
长非编码RNAs (lncRNAs) 可以转化为蛋白质,影响细胞过程和疾病. LncPepAtlas数据库收集了关于lncRNA翻译和潜在的癌症免疫治疗应用的证据.
科学领域:
- 分子生物学分子生物学
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 长非编码RNAs (lncRNAs) 在历史上被认为是非编码的,但现在被认为具有蛋白质编码潜力.
- 这种翻译能力表明lncRNAs在细胞功能和疾病发病过程中起着重要作用.
- 生物技术和计算方法的进步使 lncRNA 翻译的新研究成为可能.
研究的目的:
- 开发LncPepAtlas,这是一个全面的数据库,收集了lncRNA转换的证据.
- 为 lncRNA 上游调节和跨物种和条件的表达特征提供注释.
- 为了使 lncRNA编码的新型抗原预测成为潜在的免疫疗法应用.
主要方法:
- 来自九个不同的来源的IncRNA转化综合证据.
- 分析了来自9个物种的2631个公开可用的Ribo-seq样本的数据集.
- 标注 lncRNA上游调节和表达在转录和翻译水平.
- 通过评估与MHC类I和II分子的结合,对 lncRNA编码的进行了新型抗原预测.
- 推断的功能是通过将它们与实验检测到的蛋白质对齐.
主要成果:
- 开发了LncPepAtlas,这是一个数据库,汇编了为lncRNA翻译提供多条证据.
- 整合了广泛的Ribo-seq数据和注释,用于lncRNA调节和表达.
- 从lncRNA中确定了许多候选者,这些具有结合MHC分子的潜力.
- 与已知的蛋白质相比,这些的预测功能.
结论:
- LncPepAtlas 作为探索可翻译 lncRNA 的宝贵资源.
- 已识别的lncRNA编码为癌症免疫治疗提供了潜在的标.
- 这项工作强调了 lncRNA 翻译在生物过程和疾病中的功能意义.
相关概念视频
lncRNA - Long Non-coding RNAs
2.8K
2.8K
Non-LTR Retrotransposons
11.4K
As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
11.4K
Ribosome Profiling
3.5K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.5K
Translational Regulation
1
Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
1
Leaky Scanning
5.1K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.1K
LTR Retrotransposons
17.4K
LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
17.4K


