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Information Integration and Energy Expenditure in Eukaryotic Gene Regulation

真核基因调控中的信息整合和能量消耗

基本信息

批准号：
9899260
负责人：
Angela H DePace
金额：
$ 44.58万
依托单位：
HARVARD MEDICAL SCHOOL
依托单位国家：
美国
项目类别：
财政年份：
2017
资助国家：
美国
起止时间：
2017-04-10 至 2021-09-29
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9899260
关键词：
Affinity Animal Model Area Bacteria Binding Binding Sites Biological Models Biology CREBBP gene Chromatin Complex DNA DNA Methylation DNA Sequence DNA-Directed RNA Polymerase Data Dependence Developmental Gene Disease Drosophila genus Drosophila melanogaster Embryo Energy Metabolism Energy-Generating Resources Enhancers Equilibrium Eukaryota Evolution Foundations Gene Expression Regulation Genes Genetic Transcription Genome Graph Laboratories Lead Light Measures Mediating Mediator of activation protein Medicine Methods Modeling Molecular Mutagenesis Nucleosomes Pattern Phenotype Physics Plant Roots Play Positioning Attribute Post-Translational Protein Processing Process Property Proteins Recording of previous events Regulation Role Study models System Testing Theoretical Studies Thermodynamics Time Transcriptional Regulation Work base chromatin modification chromatin remodeling design experimental study flexibility histone modification information processing interdisciplinary collaboration knock-down mRNA Expression mathematical methods mathematical model mathematical theory neglect protein expression recruit response transcription factor

项目摘要

PROJECT ABSTRACT Gene regulation – how genes are turned on in the right place, at the right time and in the right amount – is a problem central to most areas of biology and medicine. Our understanding of gene regulation began with classical studies in bacteria, which introduced the idea that proteins called “transcription factors” (TFs) determine which gene is turned on by binding to regulatory DNA sequences and recruiting RNA polymerase (RNAP). The situation in eukaryotes, however, is far more complicated. We focus in this proposal on two critical aspects of eukaryotic gene regulation that are not addressed in the bacterial paradigm. First, eukaryotic DNA is packaged into chromatin and accessibility to TF binding sites is dynamically re-organised by continuously expending external sources of energy, such as ATP. Second, in eukaryotes multi-protein co- regulators such as mediator and CREB-binding protein (CBP) intercede between TFs and RNAP, serving as “integrators” of regulatory information. Pioneering studies from several laboratories have identified many of the molecular components involved in this regulatory complexity, however, the quantitative concepts used to reason about how eukaryotic gene regulation are still largely based on the bacterial paradigm. This is an alarming discrepancy in light of the central importance of gene regulation. In recent work, we used mathematical models rooted in physics to show that this bacterial paradigm cannot account for experimentally measured data in eukaryotes. We examined, in particular, the question of how sharply a gene is turned on in response to a TF, an important property in many contexts. We introduced new concepts for analyzing information integration by co-regulators and energy expenditure and showed how these processes could explain the observed sharpness. In this proposal, we seek to build upon this highly-productive, inter-disciplinary collaboration. We will integrate mathematical theory with quantitative experiments in the well-studied model organism Drosophila melanogaster to identify which molecular mechanisms of information integration and energy expenditure are involved in regulating the developmental gene hunchback, whose sharp expression is crucial for patterning the early fruitfly embryo. As in the classical bacterial studies, we anticipate that a deep analysis of this particular gene will provide a new foundation on which to understand in quantitative terms the regulation of other eukaryotic genes and thus, that this study will have broad impact across biology and medicine.

项目摘要