24 papers · ranked by Valyu relevance
Elia Mascolo, Réka Borbély, Santiago Herrera-Álvarez, Călin C. Guet + 2 more
Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an individual TF binds arbitrary DNA sequences and how individual binding events…
Jianping Wang, Szymon Kubala
Gene regulation in plants is orchestrated through a multilayered network of molecular mechanisms encompassing chromatin organization, transcriptional control, RNA processing, RNA modification, and other processes. Epigenetics and transcriptomics have long provided foundational frameworks for understanding how gene…
Yu-Li He, Loh, Youshin
The emerging field of epigenetics has recently unveiled a dynamic landscape in which gene expression is not determined solely by genetic sequences but also by intricate regulatory mechanisms. This review examines the interactions between these regulatory mechanisms, including DNA methylation and non-coding RNAs…
Miriam Ruhinda, Roenick P. Olmo, Bianca C. Burini
Stability with Small Molecules: A Review of the ecDHFR Destabilizing Domain System Authors: Miriam Ruhinda, Roenick P. Olmo, Bianca C. Burini The E. coli dihydrofolate reductase (ecDHFR) destabilizing domain (DD) is a versatile post-translational tool for the conditional control of protein stability via ligand-induced…
Weijie Yan, Ruiying Fu, Xuena Huang, Aibin Zhan
Biological invasions significantly threaten global biodiversity and disrupt the stability of ecosystems worldwide. Effective responses to environmental stressors are crucial for invasion success; however, the underlying epigenetic regulatory mechanisms remain poorly understood, especially regarding the interplay among…
David Granas, Anirudh Kesanapally, Michael A. White, Gary D. Stormo
Yeast ribosomal protein genes RPL18B, RPL28 and RPS22B are autoregulated by inhibition of splicing. This is demonstrated by inserting their introns into a chromosomal copy of GFP and observing repression upon induction of the cognate protein. In RPL18B and RPS22B, a predicted conserved secondary structure within the…
Seth Weaver, Craig B. Lowe
Gene regulatory innovation underlies many phenotypic transitions. Transposable elements are an established mechanism for creating families of cis-acting elements with shared sequence features and the potential to establish co-regulatory networks. To understand additional mechanisms by which co-regulatory networks form…
Ananda L. Roy, Ranjan Sen, Dinah S. Singer
Before the advent of modern life saving medicines, the immune system protected human beings from deadly pathogens and foreign objects for thousands of years. Given that the diversity of pathogens and microbes far outnumber human beings, it is no wonder that the immune system had to evolve extremely intricate and…
Elia Mascolo, Réka Borbély, Noa Ottilie Borst, Nick Barton + 2 more
Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an individual TF binds arbitrary DNA sequences and how individual binding events…
Iryna Zabaikina, Ramon Grima
Imperfect molecular detection in single-cell experiments introduces technical noise that obscures the true stochastic dynamics of gene regulatory networks. While binomial models of molecular capture provide a principled description of imperfect detection, they have so far been analyzed only for simple gene-expression…
Danithza S. Rojas, Gregory I. Lang
Regulatory evolution can alter phenotypes, but cis- and trans-regulatory mechanisms may also diverge extensively while total transcript abundance remains stable. Comparisons of parental expression with allele-specific expression in F1 hybrids provide a framework for separating cis- and trans-regulatory effects because…
Sheryl Li Yan Lim, Sofia Gialamoidou, Rajinder Kaur, Ioscani Jimenez del Val
This paper reviews the design and application of mammalian synthetic gene circuits for biopharmaceutical manufacturing. It discusses key design principles and outlines transcription factors, DNA-binding proteins, and RNA as input and regulatory modules, while also presenting computational modelling as a driver for…
Ryan Weber, Maria Carilli, Elisabeth Rebboah, Ghassan Filimban + 16 more
Understanding the genetic architecture of gene expression is fundamental to evolutionary biology and medicine. As part of the IGVF Consortium, we present a single-nucleus RNA-seq resource of 5.3 million nuclei across eight tissue groups, featuring seven F1 hybrids from C57BL/6J dams crossed with the other Collaborative…
Domitilla Del Vecchio
Summary. This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other applications is the ability to control the concentration of specific…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…
Zhihua Jiang, Michee van Rooyen, Jennifer J. Michal, Isyana Khaerunnisa + 4 more
Despite decades of genome sequencing and annotation, a fundamental paradox remains unresolved: how organisms with finite and relatively stable gene numbers generate extraordinary phenotypic diversity. In this review, we propose that regulated RNA variant diversity provides a critical level of resolution for…
Julie Gilbert, Francesco Calzaferri
DNA methylation can function as a toxic alkylation reaction exploited by chemotherapeutic agents to induce cancer cell death. However, finely tuned DNA methylation plays a fundamental role in cellular physiology, particularly in the epigenetic regulation of gene expression. Once thought to act solely as a repressor of…
Authors not listed
We present a chemical framework in which adaptive organization is achieved by tuning a gated quantum resonator (adaptive genomic resonator) {driven quantum oscillator} across a driven, dissipative reaction manifold (fitness landscape) {Hamiltonian potential surface}. In this view, catalytic elements set gain and phase…
Authors not listed
Bromodomain PHD finger Transcription Factor (BPTF) is an epigenetic regulator implicated in cancer progression. However, despite its oncogenic significance, highly selective and potent inhibitors of the BPTF bromodomain (BRD) with suitable physicochemical properties are lacking. Previously, we reported BZ1, a…
Authors not listed
Histone deacetylases (HDACs) 1-3 are key regulators of gene expression and represent important therapeutic targets in cancer, neurodegenerative, and immune disorders. Many potent class I HDAC inhibitors display slow- and tight-binding kinetics, which profoundly influence their efficacy and pharmacodynamics. In…
Fujia Han, Vishnu Raj, Robert D. Lemon, Qianru A. Wu + 3 more
Endogenous gene tagging allows researchers to study genes in their native genomic context, underscoring the need for efficient and scalable tagging approaches. Here, we report TAG-IN, a streamlined and swappable strategy for tagging virtually any gene in the C. elegans genome. A seed allele for the gene of interest is…
Authors not listed
The intricate bidirectional communication between mitochondria and the gut microbiota – termed mitochondria-microbiome crosstalk – plays a pivotal role in regulating host metabolism, immune responses, and overall physiological homeostasis. Emerging evidence highlights how microbial-derived metabolites, such as…
Authors not listed
Methicillin-resistant Staphylococcus aureus (MRSA) is one of a leading cause of antibiotic-resistant bacterial infections. Based on our previous findings, we utilized thiazole-fused nootkatone hit compounds to develop a simple phenol-substituted thiazole scaffold as potent antibacterial agents, particularly active…
Authors not listed
The new European (EU) regulation on water reuse explicitly incorporates antimicrobial resistance (AMR) into routine monitoring and risk management, creating an urgent need to define target antibiotic resistance genes (ARGs) for reclaimed irrigation water and agricultural sludge. However, existing global data largely…