Patterned Gene Expression in Drosophila Development

果蝇发育中的模式基因表达

基本信息

批准号：
10018883
负责人：
SUSAN E CELNIKER
金额：
$ 48.59万
依托单位：
UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB
依托单位国家：
美国
项目类别：
财政年份：
2006
资助国家：
美国
起止时间：
2006-09-01 至 2023-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10018883
关键词：
Address Alzheimer&apos s Disease Anatomy Animals Antisense RNA Atlases Binding Binding Sites Biochemical Biological Assay Catalogs Cell division Code Collection Communities Complement Complex Complex Mixtures Computing Methodologies DNA Sequence Data Data Set Databases Development Developmental Biology Differentiated Gene Differentiation and Growth Disease Drosophila genome Drosophila genus Elements Embryo Embryonic Development Enhancers Eukaryota Event Evolution Expression Profiling Foundations Gene Activation Gene Expression Gene Expression Profile Gene Expression Regulation Gene Family Genes Genetic Genetic Transcription Genome Genomics Goals Health Human Image Image Analysis In Situ Hybridization Individual Knowledge Life Link Location Malignant Neoplasms Maps Metabolism Modeling Movement Network-based Nucleic Acid Regulatory Sequences Oncogenes Ontology Organ Organism Parents Pattern Phosphotransferases Play Process Proteins RNA Regulator Genes Regulatory Element Reporter Research Research Personnel Resources Role Standardization System Systems Biology Time Tissues Transcript Transcriptional Regulation Tumor Suppressor Genes Untranslated RNA analog automated image analysis base bioimaging body system chromatin modification experimental study fly functional group gene function gene interaction genome wide association study genomic data human disease insight knock-down network models small hairpin RNA spatiotemporal tool transcription factor transcriptome sequencing virtual web site

项目摘要

PROJECT SUMMARY Animal development and differentiation proceeds by the sequential activation of gene expression accompanied by cell division, differential development and movement to form organ primordia. Our primary goal is to elucidate the complex network of spatial and genetic interactions that underlies the processes of normal development, disease and evolution. A comprehensive analysis of these interactions requires knowledge of the gene expression profiles for the complement of protein-coding and non-coding genes in an organism. The Berkeley Drosophila Genome Project (BDGP) has established a gene expression resource for Drosophila embryonic development that contains spatial and temporal expression patterns determined from whole mount RNA in-situ hybridization. These patterns are annotated using a standardized controlled anatomical ontology and the images are presented in a standardized virtual representation of the patterns to facilitate ontology and image based search and analysis. Specifically we propose to produce organ system and gene family RNA expression networks based on spatial patterns of expression and expand the collection to include non-coding genes; assay patterns of expression driven by putative CRMs for transcription factors (TFs) and selected TF target genes and analyze the expression using our computational image analysis tools. The organ system expression profiles produced by our study will provide fundamental information for elucidating embryonic development in Drosophila and, by homology, in other eukaryotes, including humans. The roles of most non- coding RNAs in particular remain unknown. The spatial expression driven by cis-regulatory regions will provide insights into the developmental roles of the transcription factors. The integration of spatiotemporal expression data from coding transcripts, non-coding transcripts and CRM reporters will promote discovery of networks of regulatory interactions. These studies are directed toward the understanding of life processes and lay the foundation for promoting better human health.

项目概要动物的发育和分化是通过基因表达的连续激活来进行的通过细胞分裂、分化发育和运动形成器官原基。我们的首要目标是阐明正常过程背后的空间和遗传相互作用的复杂网络发育、疾病和进化。对这些相互作用的全面分析需要了解生物体中蛋白质编码和非编码基因互补的基因表达谱。这伯克利果蝇基因组计划（BDGP）建立了果蝇基因表达资源胚胎发育包含由整体确定的空间和时间表达模式 RNA原位杂交。这些模式使用标准化受控解剖本体进行注释并且图像以模式的标准化虚拟表示形式呈现，以促进本体论和基于图像的搜索和分析。具体来说，我们建议生产器官系统和基因家族 RNA 基于表达空间模式的表达网络，并将集合扩展为包括非编码基因；由假定的 CRM 驱动的转录因子 (TF) 和选定 TF 的表达测定模式目标基因并使用我们的计算图像分析工具分析表达。器官系统我们的研究产生的表达谱将为阐明胚胎果蝇的发育，以及通过同源性，在包括人类在内的其他真核生物中的发育。大多数非尤其是编码 RNA 仍然未知。由顺式调控区域驱动的空间表达将提供深入了解转录因子的发育作用。时空表达的整合来自编码转录本、非编码转录本和 CRM 报告者的数据将促进网络的发现监管互动。这些研究旨在理解生命过程并奠定基础为促进人类健康奠定基础。

项目成果

期刊论文数量（14）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Diverse Hormone Response Networks in 41 Independent Drosophila Cell Lines.

41 个独立果蝇细胞系中的多种激素反应网络。

DOI：
10.1534/g3.115.023366
发表时间：
2016
期刊：
G3 (Bethesda, Md.)
影响因子：
0
作者：
Stoiber,Marcus;Celniker,Susan;Cherbas,Lucy;Brown,Ben;Cherbas,Peter
通讯作者：
Cherbas,Peter

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development.

DOI：
10.1186/gb-2011-12-5-r43
发表时间：
2011
期刊：
Genome biology
影响因子：
12.3
作者：
Thomas S;Li XY;Sabo PJ;Sandstrom R;Thurman RE;Canfield TK;Giste E;Fisher W;Hammonds A;Celniker SE;Biggin MD;Stamatoyannopoulos JA
通讯作者：
Stamatoyannopoulos JA

Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape.

DOI：
10.1038/msb.2009.102
发表时间：
2010
期刊：
MOLECULAR SYSTEMS BIOLOGY
影响因子：
9.9
作者：
Frise, Erwin;Hammonds, Ann S.;Celniker, Susan E.
通讯作者：
Celniker, Susan E.

Spatial expression of transcription factors in Drosophila embryonic organ development.

DOI：
10.1186/gb-2013-14-12-r140
发表时间：
2013-12-20
期刊：
Genome biology
影响因子：
12.3
作者：
Hammonds AS;Bristow CA;Fisher WW;Weiszmann R;Wu S;Hartenstein V;Kellis M;Yu B;Frise E;Celniker SE
通讯作者：
Celniker SE

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.

DOI：
10.1371/journal.pbio.0060027
发表时间：
2008-02
期刊：
PLoS biology
影响因子：
9.8
作者：
Li XY;MacArthur S;Bourgon R;Nix D;Pollard DA;Iyer VN;Hechmer A;Simirenko L;Stapleton M;Luengo Hendriks CL;Chu HC;Ogawa N;Inwood W;Sementchenko V;Beaton A;Weiszmann R;Celniker SE;Knowles DW;Gingeras T;Speed TP;Eisen MB;Biggin MD
通讯作者：
Biggin MD