Didier Trono

Antigenic landscape of a highly mutated SARS-CoV-2 Spike in ongoing viral evolution

This study examines how mutations in the N-terminal domain of SARS-CoV-2 Spike affect antigenic properties and immune escape, finding that structural flexibility and loss of heme-metabolite interaction reduce antibody neutralization.

An overexpression platform reveals the functional diversity of human KRAB-Zinc Finger Proteins in maintaining cellular homeostasis

The paper identifies functional roles of human KZFPs through overexpression screening and integrative analysis, revealing diverse mechanisms in cellular homeostasis.

Identification of a Lipid Oxygen Radical Defense pathway and its epigenetic control

The paper identifies the Lipid Oxygen Radical Defense (LORD) pathway and shows it is epigenetically controlled, affecting oxidative stress and ferroptosis.

Cancer cells subvert the primate-specific KRAB zinc finger protein ZNF93 to control APOBEC3B

The paper shows ZNF93, a primate-specific protein, regulates APOBEC3B and influences cancer progression by affecting DNA synthesis and genomic stability.

Evolutionarily recent transcription factors partake in human cell cycle regulation

This study identifies evolutionarily recent transcription factors that influence human cell cycle regulation by affecting gene expression and replication timing.

Tissue-specific restriction of TE-derived regulatory elements safeguards cell-type identity

The paper identifies a noncanonical role for KZFPs in restricting TE-derived regulatory elements to maintain cell-type identity, independent of TRIM28.

Zinc-finger proteins with a co-opted capsid domain anchor nucleosomes over transposon sequences

This study shows that SCAN domain zinc-finger proteins bind transposon sequences and anchor nucleosomes, affecting chromatin structure and regulatory states.

Transposable element co-option drives transcription factor neofunctionalization

The paper shows that a transposable element-derived domain in KRAB zinc-finger proteins enables new transcription factor functions through trimerization and condensate formation.

Clusters of lineage-specific genes are anchored by ZNF274 in repressive perinucleolar compartments

This study identifies ZNF274's role in anchoring lineage-specific gene clusters within repressive perinucleolar compartments, revealing its impact on chromatin structure and gene regulation.

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

This study identifies degenerate transposable elements in the human genome using ancestral genome reconstruction, finding 1.45 million new elements and their regulatory roles.

Transposable elements mediate genetic effects altering the expression of nearby genes in colorectal cancer

The paper identifies TE-eQTLs in colorectal cancer and shows that tumor-specific TEs mediate genetic effects on gene expression, including cancer driver genes.

Statistical learning quantifies transposable element-mediated cis-regulation

The paper quantifies TE-mediated cis-regulation using statistical learning, showing TE-embedded CREs influence gene expression and can be predicted from RNA-seq data.

Genetic features and genomic targets of human KRAB-Zinc Finger Proteins

This study examines the genetic features and genomic targets of human KRAB-Zinc Finger Proteins, revealing their role in regulating transposable elements and their evolutionary significance.

Efficient and sensitive profiling of RNA-protein interactions using TLC-CLIP

This paper introduces TLC-CLIP, a method to profile RNA-protein interactions with increased sensitivity and efficiency by improving CLIP library preparation.

Profiling drug sensitivity of leukemic stem cells via bulk-to-single-cell deconvolution

The paper develops a machine learning framework to estimate cell subtype-specific drug sensitivity from bulk data, applying it to leukemia datasets to identify potential therapeutic targets.

Transposable elements contribute to the spatiotemporal microRNA landscape in human brain development

The paper identifies a dynamic TE-embedded miRNA expression landscape in human brain development and introduces a web tool for exploring these dynamics.

Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain

The paper identifies KZFP:TE transcriptional profiles and TE-derived promoters in the developing human brain, showing their role in neurogenesis.

Ongoing evolution of KRAB zinc finger protein-coding genes in modern humans

The paper analyzes the evolutionary dynamics of KRAB zinc finger protein-coding genes in humans, finding that older genes show stronger negative selection while younger genes exhibit more genetic variation and less constraint.

A human-specific structural variation at the ZNF558 locus controls a gene regulatory network during forebrain development

The paper identifies a human-specific structural variation at the ZNF558 locus that regulates a gene network involved in forebrain development by controlling SPATA18 expression through a VNTR contraction.

Non-essential function of KRAB zinc finger gene clusters in retrotransposon suppression

The paper shows that deleting large KRAB-ZFP gene clusters in mice leads to retrotransposon activation, indicating most KRAB-ZFPs are non-essential for transposon suppression.

DUX is a non-essential synchronizer of zygotic genome activation

This study shows that DUX regulates transcription during early embryonic cell divisions in mice but is not strictly essential for embryogenesis.

DPPA2 and DPPA4 are necessary to establish a totipotent state in mouse embryonic stem cells

This study identifies DPPA2 and DPPA4 as essential for activating Dux and LINE-1 transcription, which is critical for zygotic genome activation in mouse embryos.

The KZFP/KAP1 system controls transposable elements-embedded regulatory sequences in adult T cells

The paper shows that the KZFP/KAP1 system dynamically regulates TEeRS in adult human T cells, affecting gene expression and chromatin states.