Biology subjects

Loubiere, V.

Publications and source records attributed to Loubiere, V..

4 recordsLinked to original sources

bioRxiv2025

Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo

Enhancers control tissue-specific gene expression across metazoans. Although deep learning has enabled enhancer prediction and design in mammalian cell lines and invertebrate systems, it remains unclear whether such approaches can operate within the regulatory complexity of mammalian tissues in vivo. Here, we present a general strategy for designing tissue-specific enhancers that function reliably in mice. We use deep learning to train compact convolutional neural networks (CNNs) on genome-wide chromatin accessibility and fine-tune them via transfer learning on validated human and mouse enhancers. Guided by these models, we design fifteen synthetic enhancers for the heart, limb, and central nervous system (CNS) in mouse embryos, all of which are active in their intended target tissue. Our work establishes a generalizable framework for programmable control of mammalian gene expression in vivo, opening new avenues in functional genomics, synthetic biology, and gene therapy.

synthetic biology↗

bioRxiv2025

Systematic Discovery of Pathogen Effector Functions across Human Pathogens and Pathways

Pathogens deploy effector proteins to exploit host cell biology, and most pathogen open reading frames (ORFs) are rapidly evolving and lack functional annotation. We developed the eORFeome, a scalable functional genomics platform encompassing 3,835 effector ORFs from diverse viruses, bacteria, and parasites. High-throughput barcoded screens across NF{kappa}B, apoptosis, p53, cGAS-STING and MHC-I pathways revealed functions for hundreds of uncharacterized eORFs, unexpected new activities for known effectors, and distinct pathway-specific functions encoded by single ORFs. Illustrating the power of the approach, we identify HHV6A U14 as a p53 antagonist, HHV7 U21 as a dual-function STING antagonist and MHC-I antigen display inhibitor, and adenoviral 13.6K/i-leader protein as a de novo evolved TAP inhibitor that suppresses MHC-I display. These results establish a general framework for systematic effector annotation, uncover new mechanisms of host-pathogen interaction across kingdoms, and highlight pathogen effectors as a versatile toolkit for rewiring and probing human cellular pathways.

systems biology↗

bioRxiv2024

Proteome-scale tagging and functional screening in mammalian cells by ORFtag

Determining protein function in a systematic manner is a key goal of modern biology, but remains challenging with current approaches. Here, we present ORFtag, a versatile, cost-effective and highly efficient method for the massively-parallel tagging and functional interrogation of proteins at proteome scale. Using mouse embryonic stem cells, we showcase ORFtags utility through screens for transcriptional activators, repressors and post-transcriptional regulators. Each screen finds known and novel regulators, including long ORFs not accessible to other methods, revealing that Zfp574 is a highly selective transcriptional activator and that oncogenic fusions frequently function as transactivators.

systems biology↗

bioRxiv2022

Functionally distinct promoter classes initiate transcription via different mechanisms reflected in focused versus dispersed initiation patterns

Recruitment of RNA polymerase II (Pol II) to promoter regions is essential for transcription. Despite conflicting evidence, the Pol II Pre-Initiation Complex (PIC) is often thought to be of uniform composition and assemble at all promoters via an identical mechanism. Here, we show using Drosophila melanogaster S2 cells as a model that promoter classes with distinct functions and initiation patterns function via PICs that display different compositions and dependencies: developmental promoter DNA readily associates with the canonical Pol II PIC, whereas housekeeping promoter DNA does not and instead recruit different factors such as DREF. Consistently, TBP and DREF are required by distinct sets of promoters, and TBP and its paralog TRF2 function at different promoter types, partly exclusively and partly redundantly. In contrast, TFIIA is required for transcription from all promoters, and we identify factors that can recruit and/or stabilize TFIIA at housekeeping promoters and activate transcription. We show that promoter activation by these factors is sufficient to induce the dispersed transcription initiation patterns characteristic of housekeeping promoters. Thus, different promoter classes direct distinct mechanisms of transcription initiation, which relate to different focused versus dispersed initiation patterns.

molecular biology↗