Publications related to Engineered Streptomyces quorum-sensing components enable inducible siRNA-mediated translation control in mammalian cells and adjustable transcription control in mice

Related publications (45)

CircCDYL Association With hnRNPL Modulates CDYL Isoform Switching in Breast Cancer Cells

Circular RNAs (circRNAs) are covalently closed back‐splicing products involved in the regulation of different cellular processes, and their dysregulation has been frequently observed in cancer cells. CircCDYL, a circRNA derived from the back‐splicing of CD ...

Wiley2025

Designing DNA-based nanotubes as near-infrared sensors for detecting cancer biomarkers

Sara Behjati

Optical biosensors offer significant advantages for minimally invasive in vivo and in vitro diagnostics. Optical sensors that are based on the fluorescence of semiconducting single-walled carbon nanotubes (SWCNTs) especially benefit from a near-infrared (n ...

EPFL2025

Oxidative stress at telomeres triggers internal DNA loops, TRF1 dissociation, and TRF2-dependent R-loops

Leona Brandl, Joachim Lingner, Wareed Ahmed, Eftychia Kyriacou, Thomas Frédéric Lunardi, Thu Trang Nguyen

Telomeres are the nucleoprotein structures at chromosome ends. Telomeres are particularly sensitive to oxidative stress, which can induce telomere damage, shortening, and premature cellular senescence. How oxidative damage influences telomere structure has ...

2025

Modelling the metabolism of the polyphosphate-accumulating organism Candidatus Accumulibacter

Pilar Natalia Rodilla Ramírez

Wastewater resulting from human activities must be treated to minimize the impact on the receiving ecosystems. One of such potential impacts in lakes and other water bodies is eutrophication, an excessive increase in their nitrogen and phosphorus content. ...

EPFL2025

The Regulation of Transcription Factors Binding Site Occupancies by Their Concentrations

Romane Joséphine Madeleine Mizeret

The precise control of transcription factor (TF) concentrations is crucial for While TF concentration gradients are well-characterized in model organisms like Drosophila and Caenorhabditis elegans, their quantitative relationship with genomic occupancy in ...

EPFL2025

Heartbeat on repeat: noncanonical KZFP and its transposable element targets shape cardiac cell specification

Danica Milovanovic

KRAB Zinc Finger Proteins (KZFPs) are a large mammalian transcription factor family, which has mainly been studied for its ability to silence and tame transposable elements (TEs) - a controlling effect brought by the ubiquitous KZFP protein partner, TRIM28 ...

EPFL2025

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Christina Ernst

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

Nature Portfolio2024

Custom CRISPR—Cas9 PAM variants via scalable engineering and machine learning

Bruno Emanuel Ferreira De Sousa Correia, Martin Pacesa

Engineering and characterizing proteins can be time-consuming and cumbersome, motivating the development of generalist CRISPR-Cas enzymes1–4 to enable diverse genome editing applications. However, such enzymes have caveats such as an increased risk of off- ...

Springer Science and Business Media LLC2025

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

Maria Brbic

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...

Nature Publishing Group2024

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Wayo Matsushima, Didier Trono, Evaristo Jose Planet Letschert

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

2024

Formaldehyde regulates one-carbon metabolism and epigenetics

Yimon Aye

Recently, Pham et al. used an array of model systems to uncover a role for the enzyme methionine adenosyltransferase (MAT) -1A, which is mainly expressed in liver, in both sensing formaldehyde and regulating transcriptional responses that protect against i ...

Cell Press2024

Bioengineering functional organoid models across scales

Tania Hübscher

The last two decades have seen the development of organoid models for many different tissues and organs. Organoids are three-dimensional organ-mimetics derived from stem or progenitor cells comprising various specialized cell types, resembling the architec ...

EPFL2024

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

Beat Fierz, Pauline Franz

Since Strahl and Allis proposed the "language of covalent histone modifications", a host of experimental studies have shed light on the different facets of chromatin regulation by epigenetic mechanisms. Initially proposed as a concept for controlling gene ...

Academic Press Ltd- Elsevier Science Ltd2024

The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation

Pauline Ambre Melenec, Andrea Ablasser, Jonathan Jean-Pierre Ricci, Baptiste Claude André Guey, Chong Liu, Pengbiao Xu, Ying Liu, Lingyun Li

Cyclic GMP-AMP synthase (cGAS) senses aberrant DNA during infection, cancer and inflammatory disease, and initiates potent innate immune responses through the synthesis of 2 ' 3 '-cyclic GMP-AMP (cGAMP)1-7. The indiscriminate activity of cGAS towards DNA d ...

Nature Portfolio2024

Androgen Receptor Signaling in in vivo models of Estrogen Receptor-positive Breast Cancer and Normal Breast Epithelium

Andrea Agnoletto

Steroid hormone receptors (HRs) are ligand-activated transcription factors that play a pivotal role in breast development and carcinogenesis. It is well established that estrogen receptor (ER) signaling is a major proliferative driver in estrogen receptor ...

EPFL2024

Inheritance of H3K9 methylation regulates genome architecture in Drosophila early embryos

Fides Zenk

Constitutive heterochromatin is essential for transcriptional silencing and genome integrity. The establishment of constitutive heterochromatin in early embryos and its role in early fruitfly development are unknown. Lysine 9 trimethylation of histone H3 ( ...

Springernature2024

Next-Generation Modeling of Cancer Using Organoids

Wouter Richard Karthaus, Jillian Rose Love

In the last decade, organoid technology has become a cornerstone in cancer research. Organoids are long-term primary cell cultures, usually of epithelial origin, grown in a three-dimensional (3D) protein matrix and a fully defined medium. Organoids can be ...

Cold Spring Harbor Lab Press, Publications Dept2024

Deconvolution of ex-vivo drug screening data and bulk tissue expression predicts the abundance and viability of cancer cell subpopulations

Alexandre Coudray

Ex-vivo drug sensitivity screening (DSS) allows the prediction of cancer treatment effectiveness in a personalized fashion. However, it only provides a readout on mixtures of cells, potentially occulting important information on clinically relevant cell su ...

EPFL2023

Meeting our Makers: Uncovering the cis-regulatory activity of transposable elements using statistical learning

Cyril David Son-Tuyên Pulver

The adaptation of organisms to their environment depends on the innovative potential inherent to genetic variation. In complex organisms such as mammals, processes like development and immunity require tight gene regulation. Complex forms emerge more often ...

EPFL2024

A modular toolbox for the optogenetic deactivation of transcription

Matteo Fiumara, Johannes Gräff, Davide Martino Coda

Light-controlled transcriptional activation is a commonly used optogenetic strategy that allows researchers to regulate gene expression with high spatiotemporal precision. The vast majority of existing tools are, however, limited to light-triggered inducti ...

OXFORD UNIV PRESS2025