Publications related to Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons

Related publications (38)

The Regulation of Transcription Factors Binding Site Occupancies by Their Concentrations

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

Accessible and highly observable gastrointestinal organoid model systems for studying host-pathogen interactions

Moritz Hofer

Traditional cell cultures have long been fundamental to biological research, offering an alternative to animal models burdened by ethical constraints and procedural intricacies, often lacking relevance to human physiology and disease. Moreover, their inabi ...

EPFL2024

Deciphering the nature of cell state transitions in single cells using quantitative modeling of temporal dynamics

Alex Russell Lederer

Cells are the smallest operational units of living systems. Through synthesis of various biomolecules and exchange of signals with the environment, cells tightly regulate their composition to realize a specific functional state. The transformation of a cel ...

EPFL2024

Clinically compliant cryopreservation of differentiated retinal pigment epithelial cells

Cheng Zhao, Gioele La Manno, Alex Russell Lederer

Background aims: Age-related macular degeneration (AMD) is the most common cause of blindness in elderly patients within developed countries, affecting more than 190 million worldwide. In AMD, the retinal pigment epithelial (RPE) cell layer progressively d ...

Elsevier Sci Ltd2024

Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems

Fides Zenk

Cell fate progression of pluripotent progenitors is strictly regulated, resulting in high human cell diversity. Epigenetic modifications also orchestrate cell fate restriction. Unveiling the epigenetic mechanisms underlying human cell diversity has been di ...

Nature Portfolio2024

ERK signalling eliminates Nanog and maintains Oct4 to drive the formative pluripotency transition

David Michael Suter

Naïve epiblast cells in the embryo and pluripotent stem cells in vitro undergo developmental progression to a formative state competent for lineage specification. During this transition, transcription factors and chromatin are rewired to encode new functio ...

2024

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

Characterization of the gut-bone marrow axis through bile acid signaling

Alejandro Alonso Calleja

Communication between the intestine and other organs such as the lungs, brain or bones is mediated by several metabolites, like short-chain fatty acids or bile acids, that relay information about nutritional and microbiota status. Bile acids are endogenous ...

EPFL2024

Fluorescent fatty acid conjugates for live cell imaging of peroxisomes

Luc Reymond, Fabien Kuttler, Milena Maria Schuhmacher, Daria Korotkova, Triana Amen, Manon Sandra Bardyn

Peroxisomes are eukaryotic organelles that are essential for multiple metabolic pathways, including fatty acid oxidation, degradation of amino acids, and biosynthesis of ether lipids. Consequently, peroxisome dysfunction leads to pediatric-onset neurodegen ...

Nature Research2024

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

Reciprocal inhibition of NOTCH and SOX2 shapes tumor cell plasticity and therapeutic escape in triple-negative breast cancer

Joaquim Roland Guy Bernard Javary, Freddy Radtke, Nadine Fournier, Morgane Fournier

Cancer cell plasticity contributes significantly to the failure of chemo- and targeted therapies in triple-negative breast cancer (TNBC). Molecular mechanisms of therapy-induced tumor cell plasticity and associated resistance are largely unknown. Using a g ...

2024

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

Engineering hydrogel microenvironments for epithelial organoid culture

Antonius Chrisnandy

Organoids, miniature tissues generated from self-organizing stem cells within three-dimensional (3D) extracellular matrices (ECM), have opened up exciting possibilities for in vitro studies of complex physiological processes. A key factor in the success of ...

EPFL2024

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

An autologous antigen-agnostic dendritic cell therapy that forgoes antigen loading

Michele De Palma

We developed a method for generating dendritic cell progenitors (DCPs) from hematopoietic stem and progenitor cells isolated from bone marrow or blood. When engineered to express IL-12 and FLT3L, these DCPs reprogram the tumor microenvironment and elicit a ...

Nature Portfolio2024

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

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

Individual transcription factors modulate both the micromovement of chromatin and its long-range structure

David Michael Suter, Natalya Katanayeva, Haitham Ahmed Shaban Ahmed, Armelle Inge Marie Eleonore Tollenaere

The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local chromatin opening and closing. However, it is unclear ...

National Academy of Sciences2024

Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network

Shiyu Cheng

Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...

EPFL2024

Multimodal transcriptomic atlases of mouse spinal cord injury

Matthieu Pierre Gautier

A spinal cord injury (SCI) triggers a cascade of molecular and cellular responses involving inflammatory cell infiltration and cytokine release, apoptosis, demyelination, excitotoxicity, ischemia, and the formation of a fibrotic scar surrounded by an astro ...

EPFL2024