Comprehensive linking of DNA Elements in high-priority ENCODE Biosamples to their promoter targets

高优先级 ENCODE 生物样本中的 DNA 元件与其启动子靶标的全面连接

• 批准号: 10241100
• 负责人: Erez Lieberman-Aiden
• 金额: $ 94.76万
• 依托单位: BAYLOR COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-02-01 至 2023-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10241100
• 关键词: 3-Dimensional; Binding; Cell Line; Cell Nucleus; Cell physiology; Cells; ChIP-seq; Chromatin; Chromosomes; DNA; Data; Disease; Elements; Environment; Frequencies; Genes; Genome; Genomics; Hi-C; Human Genome; In Situ; Link; Maps; Methods; Play; Regulation; Role; Structure; Tissues; Visualization; analytical method; cell type; cohesin; genome sequencing; genome-wide; meter; new technology; open source; promoter

ABSTRACT. The roughly two meters of DNA in the human genome is intricately packaged to form the chromatin and chromosomes in each cell nucleus. In addition to its structural role, this organization has critical regulatory functions. In particular, the formation of loops in the human genome plays an essential role in regulating genes. We recently demonstrated the ability to create reliable maps of these loops, using an in situ Hi-C method for three-dimensional genome sequencing. Hi-C characterizes the three- dimensional configuration of the genome by determining the frequency of physical contact between all pairs of loci, genome-wide. The proposed center will apply Hi-C and other new technologies to characterize genomic loops, their regulation, and their functions. We will specifically examine these structures in a wide variety of ENCODE cell types. The principles deduced from our study will be applicable to any mammalian tissue type.

摘要。 人类基因组中大约两米长的DNA被复杂地包装成染色质， 每个细胞核中的染色体。除了其结构性作用外，该组织还具有重要的监管职能， 功能协调发展的特别是，人类基因组中环的形成在调节基因中起着至关重要的作用。 我们最近展示了使用原位Hi-C方法创建这些循环的可靠地图的能力， 三维基因组测序。Hi-C表征了基因组的三维结构 通过确定全基因组所有基因座对之间的物理接触频率。拟议的中心 将应用Hi-C和其他新技术来表征基因组环，它们的调节和功能。 我们将专门研究各种ENCODE细胞类型中的这些结构。推导出的原理 将适用于任何哺乳动物组织类型。

项目成果

Chromosome size affects sequence divergence between species through the interplay of recombination and selection.

• DOI: 10.1111/evo.14467
• 发表时间: 2022-04
• 期刊: Evolution; international journal of organic evolution

The genome sequence of the Eurasian red squirrel, Sciurus vulgaris Linnaeus 1758.

• DOI: 10.12688/wellcomeopenres.15679.1
• 发表时间: 2020-01-01
• 期刊: Wellcome open research
• 作者: Mead, Daniel;Fingland, Kathryn;Blaxter, Mark
• 通讯作者: Blaxter, Mark

De novo chromosome-length assembly of the mule deer (Odocoileus hemionus) genome.

• DOI: 10.46471/gigabyte.34
• 发表时间: 2021
• 期刊: GigaByte (Hong Kong, China)
• 作者: Lamb S;Taylor AM;Hughes TA;McMillan BR;Larsen RT;Khan R;Weisz D;Dudchenko O;Aiden EL;Edelman NB;Frandsen PB
• 通讯作者: Frandsen PB

Exploring chromosomal structural heterogeneity across multiple cell lines.

• DOI: 10.7554/elife.60312
• 发表时间: 2020-10-13
• 期刊: eLife
• 影响因子: 7.7
• 作者: Cheng RR;Contessoto VG;Lieberman Aiden E;Wolynes PG;Di Pierro M;Onuchic JN
• 通讯作者: Onuchic JN

A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers.

• DOI: 10.1016/j.cell.2019.07.011
• 发表时间: 2019-08-22
• 期刊: Cell
• 影响因子: 64.5
• 作者: El Khattabi L;Zhao H;Kalchschmidt J;Young N;Jung S;Van Blerkom P;Kieffer-Kwon P;Kieffer-Kwon KR;Park S;Wang X;Krebs J;Tripathi S;Sakabe N;Sobreira DR;Huang SC;Rao SSP;Pruett N;Chauss D;Sadler E;Lopez A;Nóbrega MA;Aiden EL;Asturias FJ;Casellas R
• 通讯作者: Casellas R