Cédric Feschotte

Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system

The paper identifies two rodent-specific transposable element subfamilies that function as cell-type-specific enhancers in the mouse immune system, contributing to cell identity and gene regulation.

piRNA loss unleashes episodic transposition bursts

This study shows that loss of the piRNA pathway in Drosophila leads to episodic and stochastic transposition bursts, not just increased transposition rates.

Transposable Elements Profiling Reveals DUXA-associated MLT1D Endogenous Retroviral Elements Activation During Bovine Maternal to Zygotic Transition

The paper profiles transposable elements in bovine embryos to show that DUXA-associated MLT1D retroviral elements are activated during zygotic genome activation, and their dysregulation in SCNT embryos contributes to developmental defects.

POGZ safeguards neuronal gene chromatin architecture and transcription

This paper investigates the role of POGZ in maintaining chromatin architecture and transcription in the developing mouse cortex, finding that its loss disrupts H3K9me3 distribution and impairs neuronal gene expression.

Endogenous retroviral elements LTR8B and MER65 rewire PSG9regulation to control trophoblast syncytialization and pre-eclampsia risk

The paper identifies retroviral elements LTR8B and MER65 that regulate PSG9 expression, influencing trophoblast syncytialization and pre-eclampsia risk.

Temperature and genetic background drive mobilization of diverse transposable elements in a global human fungal pathogen

This study shows that temperature and genetic background influence transposable element (TE) mobilization in Cryptococcus neoformans, increasing antifungal resistance and genomic changes.

Selective persistence of HIV-1-infected T cell clones can occur through immune reprogramming driven by defective, transcriptionally active proviruses

This study shows that defective HIV-1 proviruses can reprogram CD4+ T cells by altering BACH2 and STAT5B gene expression, leading to immune evasion and persistence in ART-treated individuals.

Gag proteins encoded by endogenous retroviruses are required for zebrafish development

This study shows that active endogenous retroviruses in zebrafish encode Gag proteins essential for embryonic development, with specific roles in mesoderm and neural crest formation.

Complete sequencing of ape genomes

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

Regulatory Transposable Elements in the Encyclopedia of DNA Elements

The paper analyzes the contribution of transposable elements to regulatory elements in the human genome using ENCODE data, finding that ~25% of cCREs are TE-derived and show regulatory features similar to non-TE cCREs.

Transposable elements drive the evolution of metazoan zinc finger genes

This study shows that transposable elements drive the evolution of metazoan zinc finger genes through genomic conflict, with ZNFs binding TEs and repressing them during early development.

PNMA2 forms non-enveloped virus-like capsids that trigger paraneoplastic neurological syndrome

This study shows PNMA2 forms virus-like capsids that trigger an autoimmune response, leading to paraneoplastic neurological syndrome.

Evolution and antiviral activity of a human protein of retroviral origin

The paper identifies a human protein of retroviral origin that restricts retroviral infection, showing its expression in embryos and placenta and its antiviral activity against type D retroviruses.

Transposable element competition shapes the deer mouse genome

The paper examines the unique TE landscape in deer mice, showing LTR retrotransposons dominate over LINEs due to ERV invasion and KZNF gene expansion.

A genomic portrait of zebrafish transposable elements and their spatiotemporal embryonic expression

This study characterizes zebrafish transposable elements (TEs) using bulk and single-cell RNA sequencing, revealing their dynamic genomic distribution and spatiotemporal expression patterns during embryogenesis.

Evolution of mouse circadian enhancers from transposable elements

The paper investigates how transposable elements, specifically RSINE1, contribute to the evolution of circadian enhancers in mouse liver by analyzing their binding sites and sequence maturation.

Recurrent evolution of vertebrate transcription factors by transposase capture.

The paper shows DNA transposons have repeatedly contributed exons and splice sites to form new vertebrate genes, particularly transcription factors, through exon shuffling and alternative splicing over 350 million years.

Human Endogenous Retrovirus K Rec forms a regulatory loop with MITF that opposes the progression of melanoma to an invasive stage

The paper identifies a regulatory loop between MITF and HERV-K Rec that influences melanoma progression from proliferative to invasive stages.

A single-cell RNA expression map of human coronavirus entry factors

The paper maps human coronavirus entry factors using single-cell RNA-seq to identify permissive cell types and tissues for SARS-CoV-2 infection.

RepeatModeler2: automated genomic discovery of transposable element families

With a new structural LTR module, RepeatModeler2 recovers 2.9 to 4.7 times more curated TE families near-perfectly than RepeatModeler 1.0.11 in fruit fly, zebrafish, and rice.

TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data

TypeTE improves Alu insertion genotype accuracy from 83% to 92% in the 1000 Genomes dataset by reassembling and re-mapping sequencing data.

Contribution of unfixed transposable element insertions to human regulatory variation

The paper identifies TE-eQTL in lymphoblastoid and stem cell lines, showing unfixed TEs influence gene expression and regulatory elements across cell types.

Structures of virus-like capsids formed by the drosophila neuronal Arc proteins

The paper reports the structure of virus-like capsids formed by Drosophila Arc proteins and shows their similarity to retroviral and retrotransposon capsids.

Diverse endogenous retroviruses generate structural variation between human genomes via LTR recombination

The paper identifies and validates structural variation in human genomes caused by LTR recombination of endogenous retroviruses, revealing previously unrecognized interindividual diversity.

The impact of endogenous retroviruses on nuclear organization and gene expression

The paper introduces 4Tran, a method to study transposon interactions in the genome, revealing their role in chromatin organization and gene regulation.

Cross-species transmission and differential fate of an endogenous retrovirus in three mammal lineages

The paper investigates cross-species transmission of a gammaretrovirus in bats, cats, and pangolins, showing different amplification dynamics in bat and cat lineages.