One of the foundations of molecular biology is how the interactions of proteins with DNA control many aspects of gene expression. Since the mid-20th century, from discoveries of the lac repressor and operator and the competition between the cI and cro proteins for the same segment of DNA, we have learned an enormous amount about the interactions of proteins with DNA and their control of fundamental processes in the cell. Introduction to Protein–DNA Interactions: Structure, Thermodynamics, and Bioinformatics describes what we know about protein–DNA interactions from the complementary perspectives of molecular and structural biology and bioinformatics and how each perspective informs the others. A particular emphasis is on how insights from experimental work can be translated into specific computational approaches to create a unified view of the field and a fuller understanding of protein–DNA interactions.
- by James L ShepherdsonThe transcription factor (TF) cone-rod homeobox (CRX) is essential for the differentiation and maintenance of photoreceptor cell identity. Several human CRX variants cause degenerative retinopathies, but most are variants of […]
- by James L ShepherdsonCone-Rod Homeobox, encoded by CRX, is a transcription factor (TF) essential for the terminal differentiation and maintenance of mammalian photoreceptors. Structurally, CRX comprises an ordered DNA-binding homeodomain and an intrinsically […]
- by Yiqiao ZhengPaired-class homeodomain transcription factors (HD TFs) play essential roles in vertebrate development, and their mutations are linked to human diseases. One unique feature of paired-class HD is cooperative dimerization on […]
- by James L ShepherdsonDozens of variants in the gene for the homeodomain transcription factor (TF) cone-rod homeobox (CRX) are linked with human blinding diseases that vary in their severity and age of onset. […]
- by Ryan Z FriedmanCis-regulatory elements (CREs) direct gene expression in health and disease, and models that can accurately predict their activities from DNA sequences are crucial for biomedicine. Deep learning represents one emerging […]
- by James L ShepherdsonDozens of variants in the photoreceptor-specific transcription factor (TF) CRX are linked with human blinding diseases that vary in their severity and age of onset. It is unclear how different […]
- by Shane K ChuMOTIVATION: Motifs play a crucial role in computational biology, as they provide valuable information about the binding specificity of proteins. However, conventional motif discovery methods typically rely on simple combinatoric […]
- by Zheng ZuoThe human genome contains about 800 C2H2 zinc finger proteins (ZFPs), and most of them are composed of long arrays of zinc fingers. Standard ZFP recognition model asserts longer finger […]
- by Siqi ZhaoMassively parallel reporter gene assays are key tools in regulatory genomics but cannot be used to identify cell-type-specific regulatory elements without performing assays serially across different cell types. To address […]
- by Zheng ZuoNo abstract
- by Ryan Z FriedmanEnhancers and silencers often depend on the same transcription factors (TFs) and are conflated in genomic assays of TF binding or chromatin state. To identify sequence features that distinguish enhancers […]
- by Daisylyn Senna TanTranscription factor-driven cell fate engineering in pluripotency induction, transdifferentiation, and forward reprogramming requires efficiency, speed, and maturity for widespread adoption and clinical translation. Here, we used Oct4, Sox2, Klf4, and […]
- by Basab RoyPost-transcriptional autoregulation of gene expression is common in bacteria but many fewer examples are known in eukaryotes. We used the yeast collection of genes fused to GFP as a rapid […]
- by Manishi PandeyGenome-wide analysis of transcriptome data in Chlamydomonas reinhardtii shows periodic patterns in gene expression levels when cultures are grown under alternating light and dark cycles so that G1 of the […]
- by Citlalli Mejía-AlmonteDespite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived […]
- by Dana M KingIn embryonic stem cells (ESCs), a core transcription factor (TF) network establishes the gene expression program necessary for pluripotency. To address how interactions between four key TFs contribute to cis-regulation […]
- by Yiming K ChangCONCLUSIONS: The specificities of BATF, BATF2 and BATF3 are all very similar as are their interactions with IRF4 and IRF8. IRF proteins binding adjacent to BATF sites increases affinity substantially […]
- by Shuxiang RuanCONCLUSION: To appropriately compare different models for TF bind sites, optimized models must be used. PWMs and their extensions are good representations of binding specificity for most TFs, and more […]
- by Zheng ZuoMethylation of CpG (cytosine-phosphate-guanine) dinucleotides is a common epigenetic mark that influences gene expression. The effects of methylation on transcription factor (TF) binding are unknown for most TFs and, even […]
- by Caizhen HuSox2 and Pax6 co-regulate genes in neural lineages and the lens by forming a ternary complex likely facilitated allosterically through DNA. We used the quantitative and scalable cooperativity-by-sequencing (Coop-seq) approach […]