一个drosophila基因组的cis调节地图
Nicolas Nègre1, Christopher D Brown, Lijia Ma
1Institute for Genomics and Systems Biology, Department of Human Genetics, The University of Chicago, 900 East 57th Street, Chicago, Illinois 60637, USA.
Nature
|March 25, 2011
概括
在ModENCODE项目中,使用广泛的染色体数据绘制了Drosophila melanogaster调节基因组的图. 这确定了超过20,000个候选调节元素,并揭示了新的转录因子相互作用.
科学领域:
- 基因组学就是基因组学.
- 分子生物学分子生物学
- 发育生物学 发展生物学
背景情况:
- 对基因调节元件的系统注释在基因组科学中至关重要但具有挑战性.
- 之前在Drosophila的研究中确定了特定的调节元素,如多体反应元素和转录因子结合位.
- 对整个监管基因组进行全面的注释仍然是一个未解决的挑战.
研究的目的:
- 为了创建Drosophila melanogaster调节基因组的全面地图.
- 识别和验证候选监管元素,包括促进剂,增强剂和绝缘剂.
- 揭示转录因子结合关系并构建一个监管网络.
主要方法:
- 利用300多个ChIP-seq数据集对八种染色体特征,五种基因素脱乙酶和38种跨发育阶段的转录因子进行了分析.
- 应用计算分析,从集成的数据集中推断出候选的cis-regulatory元素.
- 对预测的促进剂,增强剂和隔离剂的子集进行了体内验证.
主要成果:
- 生成了Drosophila调节基因组的地图,识别了超过20,000个候选调节元素.
- 在体内对促进剂,增强剂和绝缘剂的验证预测.
- 确定了近2000个密集的转录因子结合区域,与染色体活性和可访问性有关.
- 发现了数百种新的转录因子联合结合关系,并定义了一个拥有800多个潜在调节相互作用的网络.
结论:
- modENCODE项目为了解Drosophila的基因组调节提供了一个宝贵的资源.
- 这项研究显著推进了对cis-regulatory元素和转录因子网络的全面注释.
- 研究结果提供了关于开发过程中监管元素和转录因子的复杂相互作用的见解.
相关概念视频
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02:02Cis-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...
02:13Cooperative Binding of Transcription Regulators
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02:23Master Transcription Regulators
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02:38Heterochromatin
The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th...
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th...
02:02Cis-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...