树多项式识别了共转录R循环和新生的RNA折叠之间的联系
Pengyu Liu1, Jacob Lusk1, Nataša Jonoska2
1Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, United States of America.
PLoS computational biology
|December 13, 2024
概括
研究人员开发了一个使用树多项式的计算管道来预测R循环的形成. 这种方法将RNA二次结构与R循环发生联系起来,识别与这些核酸结构相关的特定结构特征.
科学领域:
- 分子生物学分子生物学
- 生物信息学是一种生物信息学.
- 遗传学 遗传学 是一个
背景情况:
- R环是非正规的核酸结构,在生物过程中至关重要.
- R环的形成受到DNA序列和拓学的影响,但确切的机制尚未完全理解.
- 研究新生RNA折叠在R循环形成中的作用对于理解它们的功能和调节至关重要.
研究的目的:
- 为了研究新生RNA折叠和R循环形成之间的联系.
- 开发一种基于基因组序列的R循环形成预测的计算方法.
- 为了确定与R环形成相关的特定RNA二次结构特征.
主要方法:
- 引入树多项式,这是RNA二次结构没有伪结的新表示.
- 开发一个集成共转录RNA折叠软件和树多项式分析的计算管道.
- 该管道应用于含有R循环形成基因的等离子体序列.
主要成果:
- 树多项式的系数和R循环形成的实验概率之间建立了强烈的相关性.
- 计算管道在预测R循环形成方面表现出高准确度.
- 特定的RNA二次结构特征,包括有短茎的分支和中间的突起/循环,被确定与R-循环有关.
结论:
- 开发的树多项式方法为预测R循环形成提供了一个准确和可解释的方法.
- 新生的RNA二次结构在R环的形成中起着重要作用.
- 这些发现提供了对R环形成的结构决定因素的见解,有助于进一步研究核酸结构和功能.
相关概念视频
RNA Structure
4.7K
The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
4.7K
Bacterial RNA Polymerase
28.8K
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
28.8K
Transcription Initiation
16.2K
Initiation is the first step of transcription in eukaryotes. Prokaryotic RNA Polymerase (RNAP) can bind to the template DNA and start transcribing. On the other hand, transcription in eukaryotes requires additional proteins, called transcription factors, to first bind to the promoter region in the DNA template. This binding helps recruit the specific RNAP that can assemble on the DNA and start transcription.
The promoters and enhancers and their accessory proteins allow tight regulation of...
The promoters and enhancers and their accessory proteins allow tight regulation of...
16.2K
Bacterial Transcription
28.0K
RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
28.0K
Eukaryotic RNA Polymerases
23.5K
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...
23.5K
Nucleic Acids
43.7K
Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
43.7K


