Eileen E. M. Furlong

Genomic G quadruplexes regulate mRNA splicing

The paper shows that genomic G quadruplexes regulate mRNA splicing by recruiting RNA-binding proteins, with implications for cardiac function.

Heterotypic directional motifs contribute to TAD boundary function in Drosophila

The paper identifies directional motif pairs that determine TAD boundary compatibility in Drosophila, showing conservation from flies to mammals.

SPT5 regulates Pol II pausing and elongation in different ways at early versus late embryonic stages

This study shows SPT5 regulates Pol II pausing and elongation differently in early and late Drosophila embryogenesis, affecting gene expression dynamics.

Chip (Ldb1) is a new cofactor of Zelda forming a functional bridge to CBP during zygotic genome activation

The paper shows that Ldb1 (Chip) is a cofactor of Zelda that bridges to CBP to regulate gene expression during zygotic genome activation in Drosophila.

A function of Spalt proteins in heterochromatin organization and maintenance of genomic DNA integrity

This study investigates the role of Spalt proteins in Drosophila cells, showing their involvement in heterochromatin organization and genomic DNA integrity through chromatin accessibility changes, DNA damage, and transposable element misexpression.

Contextualising transcription factor binding during embryogenesis using natural sequence variation

The paper identifies genetic variants affecting TF binding during Drosophila embryogenesis and uses a CNN to predict functional variants.

In vivo silencing of regulatory elements using a single AAV-CRISPRi vector

This paper develops an AAV-based CRISPRi system to silence gene expression in cardiac myocytes, showing dose-dependent reduction of Nppa expression in vitro and in vivo.

CTCF, BEAF-32 and CP190 are not required for the initial establishment of TADs in early Drosophila embryos, but have locus specific roles

The paper shows TADs form during zygotic genome activation in Drosophila embryos without CTCF, BEAF-32, or CP190, but these factors have locus-specific roles in boundary insulation.

New enhancer-promoter interactions are gained during tissue differentiation and reflect changes in E/P activity

The paper identifies new enhancer-promoter interactions gained during tissue differentiation in Drosophila embryos, showing that E/P proximity correlates with activation during terminal differentiation.

scDALI: Modelling allelic heterogeneity of DNA accessibility in single-cells reveals context-specific genetic regulation

scDALI models allelic heterogeneity in single-cell chromatin accessibility to identify context-specific genetic regulation.

Cis acting variation is common, can propagates across multiple regulatory layers, but is often buffered in developmental programs

The paper quantifies how cis-acting genetic variation affects chromatin accessibility, histone modifications, and gene expression in Drosophila embryos, finding that much of this variation does not propagate to gene expression.

Predictive features of gene expression variation reveal a mechanistic link between expression variation and differential expression

The paper identifies genomic features predictive of gene expression variation across individuals and shows these features also predict differential expression under stress in Drosophila and humans.

The cis-regulatory dynamics of embryonic development at single cell resolution

The paper profiles chromatin accessibility in Drosophila embryos to uncover cis-regulatory programs and cell fate determinants during development.

The Drosophila Dosage Compensation Complex activates target genes by chromosome looping within the active compartment

The paper investigates how the Drosophila dosage compensation complex activates X chromosome genes through chromosome looping within the active compartment.

FourCSeq: Analysis of 4C sequencing data

FourCSeq identifies specific genomic interactions in 4C sequencing data and detects changes across conditions using statistical methods.