Absence of a simple code: how transcription factors read the genome
Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …
Transcriptional Regulation in Saccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and …
S Hahn, ET Young - Genetics, 2011 - academic.oup.com
Here we review recent advances in understanding the regulation of mRNA synthesis in
Saccharomyces cerevisiae. Many fundamental gene regulatory mechanisms have been …
Saccharomyces cerevisiae. Many fundamental gene regulatory mechanisms have been …
The MEME suite
The MEME Suite is a powerful, integrated set of web-based tools for studying sequence
motifs in proteins, DNA and RNA. Such motifs encode many biological functions, and their …
motifs in proteins, DNA and RNA. Such motifs encode many biological functions, and their …
Nucleosome dynamics define transcriptional enhancers
Chromatin plays a central role in eukaryotic gene regulation. We performed genome-wide
mapping of epigenetically marked nucleosomes to determine their position both near …
mapping of epigenetically marked nucleosomes to determine their position both near …
In pursuit of design principles of regulatory sequences
Instructions for when, where and to what level each gene should be expressed are encoded
within regulatory sequences. The importance of motifs recognized by DNA-binding …
within regulatory sequences. The importance of motifs recognized by DNA-binding …
Two strategies for gene regulation by promoter nucleosomes
Chromatin structure is central for the regulation of gene expression, but its genome-wide
organization is only beginning to be understood. Here, we examine the connection between …
organization is only beginning to be understood. Here, we examine the connection between …
Modeling the specificity of protein-DNA interactions
GD Stormo - Quantitative biology, 2013 - Springer
The specificity of protein-DNA interactions is most commonly modeled using position weight
matrices (PWMs). First introduced in 1982, they have been adapted to many new types of …
matrices (PWMs). First introduced in 1982, they have been adapted to many new types of …
Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading
HK MacAlpine, R Gordân, SK Powell… - Genome …, 2010 - genome.cshlp.org
The origin recognition complex (ORC) is an essential DNA replication initiation factor
conserved in all eukaryotes. In Saccharomyces cerevisiae, ORC binds to specific DNA …
conserved in all eukaryotes. In Saccharomyces cerevisiae, ORC binds to specific DNA …
Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
Clustering of multiple transcription factor binding sites (TFBSs) for the same transcription
factor (TF) is a common feature of cis-regulatory modules in invertebrate animals, but the …
factor (TF) is a common feature of cis-regulatory modules in invertebrate animals, but the …
Motif discovery and transcription factor binding sites before and after the next-generation sequencing era
Motif discovery has been one of the most widely studied problems in bioinformatics ever
since genomic and protein sequences have been available. In particular, its application to …
since genomic and protein sequences have been available. In particular, its application to …