To be specific or not: the critical relationship between Hox and TALE proteins
Hox proteins are key regulatory transcription factors that act in different tissues of the embryo
to provide specific spatial and temporal coordinates to each cell. These patterning functions …
to provide specific spatial and temporal coordinates to each cell. These patterning functions …
[HTML][HTML] Prediction of protein–ligand binding affinity from sequencing data with interpretable machine learning
Protein–ligand interactions are increasingly profiled at high throughput using affinity
selection and massively parallel sequencing. However, these assays do not provide the …
selection and massively parallel sequencing. However, these assays do not provide the …
Transcriptional Enhancers in Drosophila
S Small, DN Arnosti - Genetics, 2020 - academic.oup.com
Key discoveries in Drosophila have shaped our understanding of cellular “enhancers.” With
a special focus on the fly, this chapter surveys properties of these adaptable cis-regulatory …
a special focus on the fly, this chapter surveys properties of these adaptable cis-regulatory …
The interaction landscape between transcription factors and the nucleosome
Nucleosomes cover most of the genome and are thought to be displaced by transcription
factors in regions that direct gene expression. However, the modes of interaction between …
factors in regions that direct gene expression. However, the modes of interaction between …
[HTML][HTML] A high-throughput mutational scan of an intrinsically disordered acidic transcriptional activation domain
Transcriptional activation domains are essential for gene regulation, but their intrinsic
disorder and low primary sequence conservation have made it difficult to identify the amino …
disorder and low primary sequence conservation have made it difficult to identify the amino …
[HTML][HTML] Deconvolving the recognition of DNA shape from sequence
Protein-DNA binding is mediated by the recognition of the chemical signatures of the DNA
bases and the 3D shape of the DNA molecule. Because DNA shape is a consequence of …
bases and the 3D shape of the DNA molecule. Because DNA shape is a consequence of …
Accurate and sensitive quantification of protein-DNA binding affinity
Transcription factors (TFs) control gene expression by binding to genomic DNA in a
sequence-specific manner. Mutations in TF binding sites are increasingly found to be …
sequence-specific manner. Mutations in TF binding sites are increasingly found to be …
Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655
Y Gao, JT Yurkovich, SW Seo… - Nucleic Acids …, 2018 - academic.oup.com
Transcriptional regulation enables cells to respond to environmental changes. Of the
estimated 304 candidate transcription factors (TFs) in Escherichia coli K-12 MG1655, 185 …
estimated 304 candidate transcription factors (TFs) in Escherichia coli K-12 MG1655, 185 …
Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery
Abstract High-Throughput (HT) SELEX combines SELEX (Systematic Evolution of Ligands
by EXponential Enrichment), a method for aptamer discovery, with massively parallel …
by EXponential Enrichment), a method for aptamer discovery, with massively parallel …
[HTML][HTML] Quantitative analysis of the DNA methylation sensitivity of transcription factor complexes
Although DNA modifications play an important role in gene regulation, the underlying
mechanisms remain elusive. We developed EpiSELEX-seq to probe the sensitivity of …
mechanisms remain elusive. We developed EpiSELEX-seq to probe the sensitivity of …