Publications by Alexandre Coudray

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Background Transposable element-embedded regulatory sequences (TEeRS) and their KRAB-containing zinc finger protein (KZFP) controllers are increasingly recognized as modulators of gene expression. We aim to characterize the contribution of this system to g ...

Gene expression aberration is a hallmark of cancers, but the mechanisms underlying such aberrations remain unclear. Human endogenous retroviruses (HERVs) are genomic repetitive elements that potentially function as enhancers. Since numerous HERVs are epige ...

The cell cycle is a fundamental process in eukaryotic biology and is accordingly controlled by a highly conserved core signaling cascade. However, whether recently evolved proteins also influence this process is unclear. Here, we systematically map the inf ...

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

Transposable elements (TEs) account for more than 50% of the human genome and many have been co-opted throughout evolution to provide regulatory functions for gene expression networks. Several lines of evidence suggest that these networks are fine-tuned by ...

Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by ...

The treatment of colorectal cancer (CRC) is an unmet medical need in absence of early diagnosis. Here, upon characterizing cancer-specific transposable element-driven transpochimeric gene transcripts (TcGTs) produced by this tumor in the SYSCOL cohort, we ...

To detect functional somatic mutations in tumor samples, whole-exome sequencing (WES) is often used for its reliability and relative low cost. RNA-seq, while generally used to measure gene expression, can potentially also be used for identification of soma ...

Alexandre Coudray

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KRAB zinc finger protein ZNF676 controls the transcriptional influence of LTR12-related endogenous retrovirus sequences

Endogenous retroviruses drive KRAB zinc-finger protein family expression for tumor suppression

Evolutionarily recent transcription factors partake in human cell cycle regulation

Statistical learning quantifies transposable element-mediated cis-regulation

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

Genetic features and genomic targets of human KRAB-zinc finger proteins

Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis

DPPA2 and DPPA4 regulate expression of Dux in mouse embryonic stem cells

Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data

PAX5 as a model to study the evolution of transcription factors' regulatory networks

KRAB-ZFPs and transposable elements rewire early human embryonic development transcriptional networks

Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis