阿拉比多普西斯和大米中的冷反应转录因子:利用数组数据和基因共表达网络进行调控网络分析
Khazar Edrisi Maryan1,2, Naser Farrokhi1, Habibollah Samizadeh Lahiji2
1Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran.
PloS one
|June 8, 2023
概括
寒冷压力影响植物生长,由转录因子 (TFs) 和微RNA (miRNAs) 调节. 这项研究在阿拉比多普西斯和大米中发现了新型对寒冷反应的TF和miRNA,为开发耐寒作物提供了标记物.
科学领域:
- 植物生物学 植物生物学
- 分子生物学分子生物学
- 遗传学 遗传学 是一个
背景情况:
- 寒冷压力显著影响植物的生长和发育.
- 了解分子机制,包括转录因子 (TF) 和微RNA (miRNA),对于植物冷反应至关重要.
- 识别差异表达的TFs和miRNAs提供了对寒冷应激适应的见解.
研究的目的:
- 在Arabidopsis和大米中计算识别冷反应TF和miRNA.
- 为这些监管要素建立共同表达网络.
- 发现用于作物改善的新型冷反应标记物.
主要方法:
- 在冷处理下对阿拉比多普西斯和大米进行转录组分析.
- 对差异表达的TFs和miRNAs进行计算识别.
- 同表达网络的构建和分析.
- 在TF推广者中确定cis-regulatory元素.
主要成果:
- 181个阿拉比多普西斯和168个大米TF基因显示出差异性表达,发现了几种新型候选者.
- 在两种物种中都发现了常见的TF家族 (ERF,MYB,bHLH,NFY,bZIP,GATA,HSF,WRKY) 和枢纽TF (NFY A4/C2/A10).
- 植物激素反应的cis元素 (ABRE,TGA,TCA,LTR) 在TF促进剂中很常见.
- 阿拉比多普西斯具有更响应的TFs,而大米具有更相关的miRNAs,可能是由于基因组大小和适应性.
- 对寒冷反应的TF与能量代谢 (光合作用) 和信号传导有关.
- 发现特定的miRNAs (米中的miR5075) 和不同的miRNA组 (Arabidopsis) 针对TFs.
结论:
- 新型TFs,miRNAs和共同表达的基因被确定为潜在的冷反应标记物.
- 这些发现可以帮助开发具有增强耐寒性的作物品种.
- 对比分析揭示了TF和miRNA对寒冷应激反应的物种特异性差异.
相关概念视频
Co-activators and Co-repressors
7.4K
Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
7.4K
Transcriptional Regulation: Riboswitches
63
Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...
63
Cooperative Binding of Transcription Regulators
6.5K
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
6.5K
RNA Polymerase II Accessory Proteins
9.3K
Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
9.3K
Transcription Factors
76.2K
Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
76.2K
Cis-regulatory Sequences
10.0K
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...
10.0K


