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OncoSplicing 3.0:一个更新的数据库,用于识别在癌症中调节替代拼接事件的RBP

Yangjun Zhang^1,2,3,4, Kai Liu³, Zhenzhen Xu³

¹Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital, Wuhan University, Wuhan 430000, China.

Nucleic acids research

|November 18, 2024

概括

更新的OncoSplicing数据库有助于识别调节癌症替代拼接 (AS) 的RNA结合蛋白 (RBPs). 该资源有助于研究人员了解癌症特异性AS事件,并验证潜在的RBP目标.

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:

替代拼接 (AS) 是基因表达和蛋白质多样性的关键调节者.
RNA结合蛋白 (RBPs) 与癌症异常AS有关,但识别特定RBPs的资源有限.
子拼接数据库最初是为了分析TCGA癌症拼接事件而开发的.

研究的目的:

增强OncoSplicing数据库,作为一种全面的资源,用于识别调节癌症中特定AS事件的RBP.
为AS事件及其监管RBP提供实验验证工具.

主要方法:

集成的TCGA和GTEx拼接和mRNA表达数据.
将RNA结合动机和eCLIP-seq峰值映射到AS事件中.
从RBP扰动实验 (ENCODE) 中分析了RNA-seq数据.
每个AS事件的内置的外子和内子序列.

主要成果:

更新的OncoSplicing数据库将AS事件与潜在的监管RBPs联系起来.
用户可以识别特定的AS事件的候选RBP.
可用于设计验证构造的序列 (原始,小基因) 已提供.

结论:

经过大量更新的OncoSplicing数据库 (www.oncosplicing.com) 是癌症研究的宝贵资源.
有助于识别驱动癌症特异性替代拼接的RBPs.
支持对癌症中AS调节机制的实验验证.

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Alternative RNA Splicing

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...

RNA Splicing

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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...