Wendy A. Bickmore

The paper identifies severe COVID-19 risk variants that modulate enhancer activity in lung cells using functional assays and deep learning.

The paper shows that loop extrusion and enhancer cooperativity independently affect enhancer-driven transcription through synthetic gene activation experiments.

This study benchmarks deconvolution methods for inferring tissue and cell type-of-origin from plasma cfRNA, showing method and reference variability impact performance.

The paper identifies H3K115ac enrichment at fragile nucleosomes in promoters and enhancers, suggesting its role in nucleosome destabilization and regulatory element identification.

The paper shows that disease-associated variants in alternative protein isoforms can cause structural mutations, emphasizing the need to consider tissue-specific expression and full-length transcripts in variant interpretation.

This study investigates the role of PRC2 in endodermal differentiation by analyzing its impact on gene repression and lineage fidelity in a stem cell model.

The paper shows TPR is required for early NF-κB activation during oncogene-induced senescence, leading to cytoplasmic chromatin fragment formation and SASP activation.

The paper shows that some Shh enhancers can activate transcription of both Shh and Mnx1 genes across a TAD boundary, supporting a cohesin-dependent hub model for enhancer function.

The paper investigates how estrogen receptor activation affects enhancer-promoter contact frequencies and spatial proximity, finding they change independently during gene activation.

The paper identifies functional non-coding genetic variants by combining DNase footprints and enhancer RNAs, introducing a framework called FINDER to prioritize variants for functional validation.

The paper identifies ultra-long-range chromatin interactions between active regulatory elements in vertebrate and invertebrate genomes, showing they are driven by three distinct mechanisms independent of RNA polymerase II and some cofactors.

The paper shows that disrupting PRC1 condensates with 1,6-hexandiol reversibly disrupts polycomb chromatin domains and loops in mouse embryonic stem cells.

The paper identifies distinct cell type-specific functions of two overlapping PAX6 retinal enhancers using live imaging and single-cell RNA sequencing in zebrafish.

The paper investigates oncogene expression from extrachromosomal DNA in glioblastoma and finds that copy number amplification, not spatial clustering, drives high transcriptional output.

The paper shows that cell proliferation in human embryonic stem cell-derived endodermal progenitors primes enhancer landscapes for organ-specific differentiation by modulating chromatin accessibility and enhancer decommissioning.

Q-STARZ assesses spatial and temporal activity of wild-type and mutant human CRE alleles in zebrafish using live imaging and transgenic reporters.

This study shows cohesin, but not CTCF, is required for activation of genes by distant enhancers, while close enhancers can function without cohesin.

This study identifies RIF1 as a molecular hub that co-regulates nuclear organisation and replication timing through its interaction with PP1, revealing distinct functional requirements for these processes.

This study shows Tex19.1 maintains acetylated SMC3 and sister chromatid cohesion in mouse oocytes, preventing aneuploidy.

Coolpup.py provides a versatile and efficient tool for pile-up analysis of Hi-C data, enabling robust detection of genomic loops and novel insights into 3D genome organization.

This study investigates the role of PRC1 in shaping 3D nuclear organization in mESCs, showing that PRC1-mediated interactions are independent of CTCF and can occur at a megabase scale.

The paper shows that Shh expression remains robust to TAD perturbations during development, except when enhancers are deleted.

The paper shows cohesin-dependent loop extrusion organizes zygotic chromatin into loops and domains, with distinct effects on maternal and paternal genomes.

The paper identifies PARP1-mediated chromatin unfolding as a mechanism for long-range enhancer activation at the Shh locus in neural progenitor cells.