Pan-cancer survey of candidate non-coding RNA transcripts on the cloud using a targeted de novo assembly approach

使用靶向从头组装方法在云上对候选非编码 RNA 转录本进行泛癌调查

• 批准号: 9167382
• 负责人: Inanc Birol
• 金额: $ 4.32万
• 依托单位: BRITISH COLUMBIA CANCER AGENCY
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-17 至 2016-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9167382
• 关键词: 3' Untranslated Regions; Adopted; Amino Acid Sequence; Binding Sites; Bioinformatics; Biological; Cleavage And Polyadenylation Specificity Factor; Communities; Computer software; DNA; Data; Data Set; Development; Disease; Elements; Enzymes; Event; Funding; Genes; Genetic Transcription; Genomics; Goals; Guidelines; Health; High-Throughput Nucleotide Sequencing; Human; Investigation; Investments; Laboratories; Large-Scale Sequencing; Lead; Literature; Location; Malignant Neoplasms; Messenger RNA; Methods; MicroRNAs; Molecular Profiling; Mutation; Peptide Sequence Determination; Physiological; Play; Poly A; Poly(A) Tail; Polyadenylation; Positron-Emission Tomography; Process; Property; Proteins; Protocols documentation; RNA; RNA Processing; Reading; Recruitment Activity; Reporting; Research Personnel; Resource Sharing; Role; Running; Sampling; Site; Surveys; Tail; Technology; The Cancer Genome Atlas; Time; Transcript; Transcriptional Regulation; Translating; United States National Institutes of Health; Untranslated RNA; Untranslated Regions; Validation; Work; cancer risk; cancer subtypes; cohort; cost; experience; high standard; improved; method development; reference genome; research study; tool; transcriptome; transcriptome sequencing

DESCRIPTION (provided by applicant): When a gene is activated, it is copied ("transcribed") from DNA into a string of molecules called a messenger RNA (mRNA). The middle section of each mRNA encodes the information that is translated into the corresponding protein sequence; the two ends, called untranslated regions (UTRs), play a number of other important roles. This proposal concerns the tail end of the mRNA, known as the 3' UTR, which helps to regulate the stability and location of the mRNA and the amount of the corresponding protein that is produced. The point at which the transcription of a given mRNA ends is determined by the presence of a sequence called a polyadenylation site. Some genes have more than one such site, meaning that there can be two or more different forms of the corresponding mRNA, with different 3' UTRs and therefore different levels of activity. Changes in the ratio of the different forms are thought to contribute to the development of a range of disorders, including some cancers. The methods currently used to study polyadenylation require an extra set of experiments to be run, which is expensive and slow. However, Drs. Birol and Karsan and their teams have obtained evidence that polyadenylation can be studied alongside other important types of transcriptional regulation, using data from experiments that are already performed as part of standard analysis. This will make studies of polyadenylation sites affordable by more laboratories, and will add value to existing data.

描述（由申请人提供）：当一个基因被激活时，它被从DNA复制（“转录”）成一串称为信使RNA （mRNA）的分子。每个mRNA的中间部分编码的信息被翻译成相应的蛋白质序列；这两个末端，被称为非翻译区（utr），扮演着许多其他重要的角色。这一建议涉及到mRNA的尾部，被称为3' UTR，它有助于调节mRNA的稳定性和位置以及产生的相应蛋白质的数量。给定mRNA转录结束的点是由一个称为聚腺苷化位点的序列的存在决定的。一些基因有不止一个这样的位点，这意味着相应的mRNA可能有两种或两种以上不同的形式，具有不同的3' utr，因此活性水平也不同。变化的比例不同

项目成果

Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes.

• DOI: 10.1186/s12864-018-4903-7
• 发表时间: 2018-07-13
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Xue Z;Warren RL;Gibb EA;MacMillan D;Wong J;Chiu R;Hammond SA;Yang C;Nip KM;Ennis CA;Hahn A;Reynolds S;Birol I
• 通讯作者: Birol I