Genome Structure and Variation Workshop to be held in the summer 2011 at Rutgers Center for Discrete Mathematics and Theoretical Computer Science (DIMACS).

基因组结构和变异研讨会将于 2011 年夏季在罗格斯大学离散数学和理论计算机科学中心 (DIMACS) 举行。

• 批准号: 1062170
• 负责人: Fred Roberts
• 金额: $ 3.62万
• 依托单位: Rutgers University New Brunswick
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-10-01 至 2011-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1062170&HistoricalAwards=false
• 关键词: Genome; Structure; Variation; Workshop; held

DNA commonly is viewed as an evenly spaced double helix and often depicted simply as a string of letters or even as two parallel lines. Genomes typically are analyzed by treating DNA sequences as if they actually were composed of strings of letters. In addition, both evolutionary biologists and computational biologists often make the assumption that all genetic variation is generated in a random manner. In reality, however, the structure of DNA is not monotonous, but rather varies along its sequence, sometimes dramatically so. Such variation in structure leads to sequence-dependent variations in the fidelity of DNA copying and repair. That the probability of distinct classes of mutations varies along a DNA sequence has implications for evolutionary theory because selection acts on heritable variation when this variation affects fitness. Highly mutable sequences have, in fact, evolved in genome regions such as those encoding pathogen coats, where increased diversity in a population favors survival. In addition, the fidelity of DNA replication and repair is affected by the activities of multiple enzymes (which can be induced by environmental or cell-type specific factors), and furthermore, it is becoming increasingly obvious that some of the information in DNA is carried in forms that can be obscured by treating DNA as if it actually were comprised only of a sequence of letters. Often it is the conformation of DNA (or RNA) or the relationship among sequences that carries the information. It is factors such as these that will be the focus of the Genome Structure and Variation Conference. A broad interdisciplinary group of researchers will gather to explore the impact of our increasing understanding of DNA structure, repair, replication, and organization on subjects ranging from evolution and the dependence of the effect of mutagens on environmental and sequence context to non-canonical forms of information representation in genomes. Incorporating our knowledge of the sequence-dependent effects of DNA structure and context on the analysis of genome sequence and variation is a computational challenge. However, in order for new methods to be developed, the appropriate communities must be made aware of the existence of novel biochemical and genetic observations on the one hand, and the potential for creation of novel computational tools on the other. By bringing together experts in these different areas to share ideas and begin a dialog, this workshop should serve as a catalyst for new collaborations and insights, along with the development of algorithms that will enable us to discover novel ways in which information affecting genetic variation and regulation is represented within genomes. In addition, this meeting is designed to facilitate productive interactions between early-career scientists, including graduate students, and the leading researchers at the conference.

DNA通常被认为是一个均匀分布的双螺旋，通常被简单地描绘为一串字母，甚至两条平行线。基因组通常是通过处理DNA序列来分析的，就像它们实际上是由字母串组成一样。此外，进化生物学家和计算生物学家经常假设所有的遗传变异都是以随机的方式产生的。然而，在现实中，DNA的结构并不是单调的，而是随着其序列的变化而变化，有时甚至是戏剧性的变化。这种结构上的变化导致DNA复制和修复的保真度与序列相关的变化。随着DNA序列的不同，不同类别突变的概率会有所不同，这对进化理论具有重要意义，因为当可遗传变异影响适应度时，选择就会作用于可遗传变异。事实上，高度可变的序列已经在基因组区域进化，比如那些编码病原体外壳的区域，在这些区域，种群的多样性增加有利于生存。此外，DNA复制和修复的保真度受到多种酶活性的影响(环境或细胞类型特定因素可以诱导)，此外，越来越明显的是，DNA中的一些信息是以某种形式携带的，这种形式可以通过将DNA视为实际上只由一个字母序列组成的方式来掩盖。通常情况下，携带信息的是DNA(或RNA)的构象或序列之间的关系。正是这些因素将成为基因组结构和变异会议的焦点。一个广泛的跨学科研究小组将聚集在一起，探索我们对DNA结构、修复、复制和组织的日益了解对从进化和诱变剂对环境和序列背景的影响的依赖到基因组中非规范信息表示形式等主题的影响。将我们对DNA结构和背景对基因组序列和变异分析的序列依赖效应的知识融入到基因组序列和变异的分析中是一个计算挑战。然而，为了开发新的方法，必须让适当的社区一方面认识到新的生化和遗传观测的存在，另一方面也认识到创造新的计算工具的潜力。通过将这些不同领域的专家聚集在一起分享想法并开始对话，这次研讨会应该成为新的合作和见解的催化剂，以及算法的开发，使我们能够发现影响遗传变异和调控的信息在基因组中表现的新方式。此外，这次会议的目的是促进包括研究生在内的早期职业科学家与会议上的主要研究人员之间的富有成效的互动。