Computational Biology of Transcription Factor Binding: (674 Methods in Molecular Biology)

Transcriptional regulation controls the basic processes of life. Its complex, dynamic, and hierarchical networks control the momentary availability of messenger RNAs for protein synthesis. Transcriptional regulation is key to cell division, development, tissue differen- ation, and cancer as discussed in Chapters 1 and 2. We have witnessed rapid, major developments at the intersection of computational biology, experimental technology, and statistics. A decade ago, researches were struggling with notoriously challenging predictions of isolated binding sites from low-throughput experiments. Now we can accurately predict cis-regulatory modules, conserved cl- ters of binding sites (Chapters 13 and 15), partly based on high-throughput ch- matin immunoprecipitation experiments in which tens of millions of DNA segments are sequenced by massively parallel, next-generation sequencers (ChIP-seq, Chapters 9, 10, and 11). These spectacular developments have allowed for the genome-wide mappings of tens of thousands of transcription factor binding sites in yeast, bacteria, mammals, insects, worms, and plants. Please also note the no less spectacular failures in many laboratories around the world.

Table of Contents:
An Overview of the Computational Analyses and Discovery of Transcription Factor Binding Sites.- Components and Mechanisms of Regulation of Gene Expression.- Regulatory Regions in DNA: Promoters, Enhancers, Silencers, and Insulators.- Three-Dimensional Structures of DNA-Bound Transcriptional Regulators.- Identification of Promoter Regions and Regulatory Sites.- Motif Discovery Using Expectation Maximization and Gibbs’ Sampling.- Probabilistic Approaches to Transcription Factor Binding Site Prediction.- The Motif Tool Assessment Platform (MTAP) for Sequence-Based Transcription Factor Binding Site Prediction Tools.- Computational Analysis of ChIP-seq Data.- Probabilistic Peak Calling and Controlling False Discovery Rate Estimations in Transcription Factor Binding Site Mapping from ChIP-seq.- Sequence Analysis of Chromatin Immunoprecipitation Data for Transcription Factors.- Inferring Protein–DNA Interaction Parameters from SELEX Experiments.- Kernel-Based Identification of Regulatory Modules.- Identification of Transcription Factor Binding Sites Derived from Transposable Element Sequences Using ChIP-seq.- Target Gene Identification via Nuclear Receptor Binding Site Prediction.- Computing Chromosome Conformation.- Large-Scale Identification and Analysis of C-Proteins.- Evolution of cis-Regulatory Sequences in Drosophila.- Regulating the Regulators: Modulators of Transcription Factor Activity.- Annotating the Regulatory Genome.- Computational Identification of Plant Transcription Factors and the Construction of the PlantTFDB Database.- Practical Computational Methods for Regulatory Genomics: A cisGRN-Lexicon and cisGRN-Browser for Gene Regulatory Networks.- Reconstructing Transcriptional Regulatory Networks Using Three-Way Mutual Information and Bayesian Networks.-Computational Methods for Analyzing Dynamic Regulatory Networks.

Review :
From the reviews: “Gives us an overview of transcription and its regulation. … The methods are very up-to-date and clearly presented by authors … . The use of tools for predicting transcription factors binding sites is also very carefully presented in a text that is accessible for beginners … . In summary, this book presents an important tool for entering the growing field of bioinformatics and its use for the study of transcription. … If we cannot read all books ever written, this one is a good choice.” (Carla Columbano Oliveira, Brazilian Journal of Pharmaceutical Sciences, Vol. 47 (2), Summer, 2011)