François Le Dily

Comparative cistromic analysis reveals a shift in tamoxifen-associated endometrial tumor ERα binding toward sites less frequently shared by progesterone receptors

The paper compares ERα cistromes in endometrial tumors from tamoxifen users and non-users to ERα and PR cistromes in Ishikawa cells, finding shifts in ERα binding patterns associated with tamoxifen exposure.

PARP1 Regulates 3D Structure and Function of Super-Enhancers and Hormone-Control Regions in Breast Cancer Cells

This paper shows PARP1 regulates 3D chromatin structure and gene expression at super-enhancers and hormone-control regions in breast cancer cells through chromatin looping and compartment organization.

EWS-FLI1 Expression in Human Embryonic MSCs Leads to Transcriptional Reprograming, Defective DNA Damage Repair and Ewing Sarcoma

This study shows that EWS-FLI1 expression in human embryonic mesenchymal stem cells leads to an ES-like transcriptome and tumor formation, despite not preferentially binding promoters.

The Hippo kinase LATS1 controls CTCF chromatin occupancy and the hormonal response of three-dimensionally grown breast cancer cells

This study shows that 3D culture of breast cancer cells alters chromatin structure and gene expression, with LATS1 kinase playing a key role in CTCF displacement and hormonal response.

Quantitative analysis of cellular morphology during in vitro decidualization

The paper develops a method to quantify morphological changes during in vitro decidualization using circularity analysis and a statistical model to compare hormonal effects.

Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion

The paper investigates how H1 depletion affects gene expression, H1 variant distribution, and genome 3D conformation in breast cancer cells.

Higher-order chromatin organization defines Progesterone Receptor and PAX2 binding to regulate estradiol-primed endometrial cancer gene expression

The paper identifies progestin control regions (PgCRs) where PR and PAX2 bind to regulate gene expression in endometrial cancer cells.

Hormone Control Regions mediate opposing steroid receptor-dependent genome organizations

The paper identifies Hormone-Control Regions (HCRs) that organize genome structure and mediate opposing transcriptional responses to steroid hormones in breast cancer cells.

Unliganded progesterone receptor governs estrogen receptor gene expression by regulating DNA methylation in breast cancer cells

The paper shows that the unliganded progesterone receptor (PR) maintains ESR1 expression and DNA methylation in hormone-deprived breast cancer cells, and that PR depletion leads to increased promoter methylation and reduced ESR1 expression.

Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization

This study investigates the distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization in non-transformed human cells, showing SA1 stabilizes TAD boundaries while SA2 facilitates enhancer-promoter interactions.

OneD: increasing reproducibility of Hi-C Samples with abnormal karyotypes

OneD improves Hi-C reproducibility for samples with abnormal karyotypes by addressing copy number variations, outperforming existing methods while maintaining performance on normal karyotypes.

Transcription Factors Orchestrate Dynamic Interplay Between Genome Topology And Gene Regulation During Cell Reprogramming

The paper shows transcription factors drive genome topology changes before gene expression during cell reprogramming.

Parallel sequencing lives, or what makes large sequencing projects successful

The paper compares two Hi-C samples, showing how adherence to FAIR principles leads to successful sequencing projects.

Hi-Cpipe: a pipeline for high-throughput chromosome capture

HiC-inspector provides a toolkit for analyzing and visualizing HiC data, including data formatting, alignment, quality control, interaction identification, and interactive visualization.

Distinct structural transitions of chromatin topological domains coordinate hormone-induced gene regulation

The paper examines how hormone-induced changes in gene regulation are coordinated by structural transitions of chromatin topological domains in breast cancer cells.