在DNA元素百科全书中的法规可转移元素
Alan Y Du1,2, Jason D Chobirko3, Xiaoyu Zhuo1,2
1Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
Nature communications
|August 31, 2024
概括
可转移元素 (TE) 显著塑造了人类基因组,有助于调节元素和转录因子结合. 这些DNA序列在基因组进化和功能中起着至关重要的作用.
科学领域:
- 基因组学就是基因组学.
- 分子生物学分子生物学
- 进化生物学 进化生物学
背景情况:
- 可转移元素 (TE) 约占人类基因组的50%.
- 试验体对基因组进化,特别是调控基因组的确切影响尚未完全理解.
研究的目的:
- 使用ENCODE4数据对TE对人类调控基因组的贡献进行全面分析.
- 研究TE衍生 cis调节元件 (cCREs) 的进化起源和功能影响.
主要方法:
- 利用ENCODE4数据来识别和描述TE衍生的候选cis-regulatory元素 (cCREs).
- 分析了转录因子 (TF) 基因组合和TE衍生cCREs内的进化保存.
- 使用MPRA和GWAS数据评估了TE衍生的cCREs的监管活动和功能意义.
主要成果:
- 确定了236,181个TE衍生的cCREs,约占人类cCREs的25%.
- 发现,自从人与老鼠分歧以来,超过90%的这些TE衍生的cCREs是特定于血统的.
- 证明TE对转录因子结合位点的周转有显著的贡献,并且与非TEcCREs具有功能上的相似性.
结论:
- 可转化元素在塑造人类监管格局方面发挥了重要作用.
- 来自TE的监管元素是进化动态和功能相关的.
- 这项研究提供了对TEs对基因组进化和基因调节的影响的全面观点.
相关概念视频
Overview of Transposition and Recombination
Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
DNA-only Transposons
DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
The donor site from where the transposon is excised is either degraded or...
LTR Retrotransposons
LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Transposons
Transposons, or "jumping genes," are small mobile genetic elements (MGEs) that range from 700 to 40,000 base pairs in length. They are found in all organisms and can move within the same chromosome or transfer to different chromosomes. In some cases, transposons can also jump between different host DNA molecules, such as plasmids or viruses, contributing to genetic variability.Barbara McClintock first discovered these mobile genetic elements in the 1940s while studying maize genetics, and she...


