更新FANTOM网络资源:对研究非编码基因组的增强
Tomoe Nobusada1, Chi Wai Yip1, Saumya Agrawal1
1RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Nucleic acids research
|November 26, 2024
概括
现在,FANTOM资源为长非编码RNAs (lncRNAs) 和转录 cis-regulatory elements (CREs) 提供了扩展的注释,增强了哺乳动物基因组研究. 这些更新为非编码区域及其功能提供了新的见解.
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:
- 哺乳动物基因组的功能注释 (FANTOM) 项目已经为哺乳动物基因组研究建立了一个全面的网络资源.
- 之前的代重点是注释各种基因组特征.
研究的目的:
- 更新和扩展FANTOM网络资源,对长非编码RNAs (lncRNAs) 和转录 cis-regulatory elements (CREs) 进行增强的注释.
- 为研究人员提供更好的工具和数据,用于研究非编码基因组区域的功能作用.
主要方法:
- 在诱导多能干细胞 (iPSC) 和Hi-C数据分析 (FANTOM6) 中使用大规模的lncRNA扰动来扩展lncRNA注释.
- 开发了一个新的平台,fanta.bio,收集从扩展的CAGE资料数据集中识别的转录CREs.
- 对CREs的综合遗传和表观遗传信息.
主要成果:
- 对lncRNAs进行了增强的注释,详细说明它们对细胞/分子表型和潜在的RNA-染色质相互作用的影响,可通过ZENBU-Reports访问.
- 新的平台fanta.bio提供了对转录CREs的访问,并提供了全面的注释.
- 通过专门的界面和UCSC基因组浏览器数据库,可以获得CRE数据.
结论:
- 更新的FANTOM资源为研究哺乳动物非编码基因组功能提供了显著增强的能力.
- 这些进展有助于对 lncRNA 和 CREs 在细胞过程和疾病中的作用进行更深入的研究.
相关概念视频
Genome Annotation and Assembly
18.8K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
18.8K
Genomics
35.9K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
35.9K
Next-generation Sequencing
87.5K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
87.5K
Multi-species Conserved Sequences
3.9K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
3.9K
Evolutionary Relationships through Genome Comparisons
5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K
Protein Families
15.3K
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key...
15.3K


