Transcription factor

Summary

In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The function of TFs is to regulate—turn on and off—genes in order to make sure that they are expressed in the desired cells at the right time and in the right amount throughout the life of the cell and the organism. Groups of TFs function in a coordinated fashion to direct cell division, cell growth, and cell death throughout life; cell migration and organization (body plan) during embryonic development; and intermittently in response to signals from outside the cell, such as a hormone. There are 1500-1600 TFs in the human genome. Transcription factors are members of the proteome as well as regulome. TFs work alone or with other proteins in a complex, by promoting (as an activator), or blocking (as a repressor) the recruitment of RNA polymerase (the en

Official source

https://en.wikipedia.org/wiki/Transcription_factor

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Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance

Shiyu Cheng, Ivan Istomin, Maria Lopez Malo, Sebastian Maerkl, Evan James Olson, Amir Shahein

Binding to binding site clusters has yet to be characterized in depth, and the functional relevance of low-affinity clusters remains uncertain. We characterized transcription factor binding to low-affinity clusters in vitro and found that transcription factors can bind concurrently to overlapping sites, challenging the notion of binding exclusivity. Furthermore, small clusters with binding sites an order of magnitude lower in affinity give rise to high mean occupancies at physiologically-relevant transcription factor concentrations. To assess whether the observed in vitro occupancies translate to transcriptional activation in vivo, we tested low-affinity binding site clusters in a synthetic and native gene regulatory network in S. cerevisiae. In both systems, clusters of low-affinity binding sites generated transcriptional output comparable to single or even multiple consensus sites. This systematic characterization demonstrates that clusters of low-affinity binding sites achieve substantial occupancies, and that this occupancy can drive expression in eukaryotic promoters.

NATURE PORTFOLIO2022

Transcription factor binding to a single binding site on DNA and its functional consequence in a promoter context are beginning to be relatively well understood. However, binding to clusters of sites has yet to be characterized in depth, and the functional relevance of binding site clusters remains uncertain. We employed a high-throughput biochemical method to characterize transcription factor binding to clusters varying across a range of affinities and configurations. We found that transcription factors can bind concurrently to overlapping sites, challenging the notion of binding exclusivity. Furthermore, compared to an individual high-affinity binding site, small clusters with binding sites an order of magnitude lower in affinity give rise to higher mean occupancies at physiologically-relevant transcription factor concentrations in vitro. To assess whether the observed in vitro occupancies translate to transcriptional activation in vivo, we tested low-affinity binding site clusters by inserting them into a synthetic minimal CYC1 and the native PHO5 S. cerevisiae promoter. In the minCYC1 promoter, clusters of low-affinity binding sites can generate transcriptional output comparable to a promoter containing three consensus binding sites. In the PHO5 promoter, replacing the native Pho4 binding sites with clusters of low-affinity binding sites recovered activation of these promoters as well. This systematic characterization demonstrates that clusters of low-affinity binding sites achieve substantial occupancies, and that this occupancy can drive expression in eukaryotic promoters. In the antibody discovery phase, before advancing a particular antibody sequence to clinical trials, a large number of candidates are characterized for properties of therapeutic interest. Above all, this includes their ability to bind to the target antigen. Standard processes currently in use to characterize antibody binding are either only semi-quantitative (ELISA), or low-throughput (SPR). We developed an experimental process to first retrieve DNA encoding promising synthetic antibody variants directly from the output pools of phage and ribosome display methods, followed by expressing these variants on a microfluidic chip for characterization in a fluorescence-based binding assay. We applied our method to characterize the binding of retrieved Sybody variants against the Spike trimer and RBD domain of the SARS-CoV-2 variant. After an initial proof-of-concept, we improved our method by removing bottlenecks, reducing costs, and incorporating a large degree of process automation to enable measuring binding affinities at scale.

EPFL2022

CO-REGULATION OF ENDOTHELIAL AND MYOGENIC CELL FATES THROUGH INTERCELLULAR CROSSTALK IN SKELETAL MUSCLE

Umji Lee

Skeletal muscle is one of the most dynamic organs in the human body, which has a vigorous potential to regenerate and adapt to environmental changes. Depending on environments, skeletal muscle enables essential life activities to survive by controlling movement and metabolism. The functional and structural adaptations of skeletal muscle crosstalk with other physiological systems enabling nutrition and oxygen delivery, and the elimination of metabolic waste products. The work in this dissertation focuses on the intercellular signals produced by myogenic cells to dynamically remodel skeletal muscle during exercise or muscle repair, and the reciprocal signals from the local niche and the systemic environment that regulate myogenic cell fate and metabolism according to physiological needs. This complex crosstalk is dissected in three specific chapters where we study the crosstalk of myogenic cells with endothelial cells and the vasculature to coordinate local niche interactions and systemic crosstalks. First, we demonstrate that an exercise-induced myokine called apelin is produced by muscle fiber and mediates intercellular signaling to endothelial cells through the apelin receptor. In addition, through a yeast one-hybrid screen of transcription factor binding to the apelin promoter, we identified the myogenic transcription factor TEA domain family member 1 (Tead1) as a regulator of Apln transcription. We observed via single-cell transcriptomic analysis of regenerating skeletal muscle that Aplnr (Apelin receptor) is enriched in muscle endothelial cells, whereas Tead1 is enriched in myogenic cells. Myofiber-specific over-expression of Tead1 suppresses apelin secretion at the whole-body level, and apelin secretion via Tead1 knock-down in muscle cells stimulates endothelial cell proliferation in co-cultures. By showing that apelin peptide supplementation in vivo enhances endothelial cell expansion following muscle injury, we conclude that paracrine crosstalk in which apelin secretion controlled by Tead1 in myogenic cells influences endothelial remodeling during skeletal muscle repair. Secondly, we show how tissue-resident support cells affect muscle progenitor activation in different metabolic environments. Skeletal muscle progenitors (SKMP) reside in close proximity to supportive cell types in the stem cell niche and dynamically interact with each other to adapt to environmental changes. Here, we studied how different niche cell types affect SKMPs in response to glycemic levels. Using co-cultures of SKMPs and niche cells, we discovered that endothelial cells synergistically enhance SKMP proliferation in a low glycemic environment, while fibroblasts and macrophages had no effect. We observed that the crosstalk between SKMPs and endothelial cells was mediated by direct cell-cell contacts independent of soluble paracrine signals. Transcriptomic analysis revealed that the endothelial alpha/beta hydrolase N-Myc Downstream Regulated1 (NDRG1) is induced by a low glycemic environment and is associated with biological adhesion. SKMPs co-cultured with Ndrg1 knock-down endothelial cells lose their synergistic functional relationship in response to glucose levels. Therefore, our findings suggest that Ndrg1 is a key mediator of endothelial cell-mediated glycemic control of SKMPs and provides a link between systemic energy levels and the skeletal muscle stem cell niche. Lastly, I developed intravital imaging to monitor muscle stem cells and vasculature.

EPFL2021

EPFL2022

CO-REGULATION OF ENDOTHELIAL AND MYOGENIC CELL FATES THROUGH INTERCELLULAR CROSSTALK IN SKELETAL MUSCLE

Umji Lee

EPFL2021