eRNAbase:一个全面的数据库来解码人类和小鼠中的监管 eRNA
Chao Song1,2, Guorui Zhang1,3,2,4, Xinxin Mu1,2
1The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
Nucleic acids research
|October 27, 2023
概括
增强型RNAs (eRNAs) 是关键的基因调节器,现在已经在eRNAbase.com上进行了分类. 这种全面的数据库为eRNA提供了广泛的注释和新的分析,阐明了它们的监管作用.
科学领域:
- 基因组学就是基因组学.
- 分子生物学分子生物学
- 生物信息学是一种生物信息学.
背景情况:
- 增强器RNAs (eRNAs) 是源自活性增强剂的基因转录的关键调节者.
- 现有的eRNA数据是分散的,需要一个统一的资源进行全面的分析.
- 了解eRNA监管角色需要综合数据和先进的分析工具.
研究的目的:
- 开发 eRNAbase,这是一个针对人类和老鼠 eRNA 资源的集中数据库.
- 为eRNAs提供广泛的 (epi) 基因注释和新的分析功能.
- 为了促进 eRNA 监管格局的探索.
主要方法:
- 从GEO/SRA和ENCODE的14种实验类型中收集并统一处理的eRNA数据.
- 从1012个人类和小鼠样本中整合了10,399,928个eRNA.
- 有注释的eRNA区域具有多种表观遗传标记和基因组特征.
主要成果:
- 目前eRNA数据库拥有超过1000万个eRNA,并提供详细的注释.
- 该数据库包括超级增强剂,TF结合点,染色质可访问性和相互作用数据.
- 新的分析包括eRNA介导的通路,变异和TF目标基因调节.
结论:
- eRNAbase 作为一个强大的,用户友好的平台,用于查询,浏览和可视化 eRNA 监管信息.
- 该数据库显著推进了研究eRNA在基因调节中的功能.
- eRNAbase使研究人员能够探索涉及eRNA的复杂监管网络.
相关概念视频
00:58Eukaryotic RNA Polymerases
RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
All three eukaryotic RNAPs require specific transcription factors, of which the...
02:23RNA Editing
RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
02:39lncRNA - Long Non-coding RNAs
In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA (lncRNA)...
03:21RNA-seq
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
02:15Experimental RNAi
RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
02:39lncRNA - Long Non-coding RNAs
In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA (lncRNA)...