Genome Assemblies, Analyses, and Comparisons

基因组组装、分析和比较

• 批准号: 8943234
• 负责人: Leonardo Marino-Ramirez
• 金额: $ 16.64万
• 依托单位: NATIONAL LIBRARY OF MEDICINE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8943234
• 关键词: Algorithms; Animal Model; Area; Binding Sites; Biological; Biology; Biomedical Research; Computing Methodologies; DNA Sequence; DNA Transposable Elements; Disease; Elements; Enhancers; Exercise; Family; Gene Expression Profile; Genes; Genome; Genomics; Genotype; Hela Cells; Human; Human Genome; Investigation; K-562; Knowledge; Methods; Pathway interactions; Phenotype; Research; Role; Source; Technology; Testing; Variant; cell type; genome sequencing; improved; insight; interest; transcription factor

Technological advances in DNA sequencing are enabling new areas of genomic research allowing fine connections between genomic variants and phenotype. We are studying transcriptomes and genomes from a variety of eukaryotic and prokaryotic non model organisms and have contributed to gain biological insights. We have used the generalized Ruzzo-Tompa algorithm to find repeats in genomic sequences and made an implementation of the algorithm called RepWords. In another study related to the investigation of repeated sequences in genomes we tested the possibility that mammalian-wide interspersed repeats (MIRs) contribute functional enhancers to the human genome. We found that MIRs are highly concentrated in enhancers of the K562 and HeLa human cell-types and MIR-derived enhancers were found to be a rich source of transcription factor binding sites. Therefore, MIRs can exercise a regulatory function in the human genome and this study contributes to explain why their role as the most ancient family of transposable elements.

DNA测序的技术进步正在开辟基因组研究的新领域，从而实现基因组变异和表型之间的精细联系。我们正在研究各种真核和原核非模式生物的转录组和基因组，并有助于获得生物学的见解。我们使用广义Ruzzo-Tompa算法来查找基因组序列中的重复序列，并实现了名为RepWords的算法。在另一项与基因组中重复序列研究相关的研究中，我们测试了全麦散布重复序列（MIRs）为人类基因组提供功能增强子的可能性。我们发现MIRs高度集中在K562和HeLa人类细胞类型的增强子中，并且发现MIRs衍生的增强子是转录因子结合位点的丰富来源。因此，MIRs可以在人类基因组中发挥调节功能，这项研究有助于解释为什么它们作为最古老的转座因子家族的作用。