Quantitative profiling of protein-DNA binding on microarrays
Jiannis Ragoussis1, Simon Field, Irina A Udalova
1Wellcome Trust Center for Human Genetics, University of Oxford, Oxford, UK.
Methods in Molecular Biology (Clifton, N.J.)
|August 5, 2006
Summary
Transcription factor (TF) binding to DNA is not well-represented by current databases. A new high-throughput microarray platform offers systematic profiling of protein-DNA interactions for accurate analysis.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- Current transcription factor (TF) binding site databases lack systematic data and may contain biases.
- A significant portion of experimentally identified TF binding sequences do not match predicted motifs.
Purpose of the Study:
- To address the limitations of existing TF binding databases.
- To develop a systematic method for profiling vertebrate transcription factor binding to DNA.
Main Methods:
- Development of a high-throughput platform.
- Utilizing microarray technology for quantitative analysis of protein-DNA interactions.
Main Results:
- The study presents a novel platform for analyzing protein-DNA interactions.
- This platform enables quantitative and systematic profiling of TF binding.
Conclusions:
- The developed microarray-based platform provides a systematic approach to studying transcription factor binding.
- This method overcomes limitations of current databases and offers more accurate insights into gene regulation.
Related Concept Videos
02:34DNA Microarrays
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
01:33Proteomics
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...