Michaela Pagani

Activator-promoter compatibility in mammals: a CpG-Island-specific co-activator directly bridges transcription factors to TFIID

The paper identifies Hcfc1 as a CGI-specific co-activator that bridges transcription factors to TFIID, revealing a promoter-class-specific activation mechanism for CGI promoters.

Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila

The paper investigates enhancer-enhancer cooperativity in Drosophila, finding that housekeeping enhancers are additive while developmental enhancers are synergistic.

Proteome-scale tagging and functional screening in mammalian cells by ORFtag

ORFtag enables proteome-scale tagging and functional screening in mammalian cells, identifying known and novel regulators of transcription and post-transcriptional processes.

Widespread regulatory specificities between transcriptional corepressors and enhancers in Drosophila

This study identifies TF motifs that determine enhancer sensitivity or resistance to specific co-repressors in Drosophila, revealing regulatory rules for repression mechanisms.

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of enhancers

This paper introduces DeepSTARR, a deep learning model that predicts enhancer activity from DNA sequence and enables the de novo design of enhancers in Drosophila and human.

Resolving systematic errors in widely-used enhancer activity assays in human cells enables genome-wide functional enhancer characterization

The paper identifies and corrects systematic errors in enhancer activity assays, improving the reliability of genome-wide enhancer characterization in human cells.

Genome-wide Ultrabithorax binding analysis reveals highly targeted genomic loci at developmental regulators and a potential connection to Polycomb-mediated regulation

The paper presents a genome-wide Ubx binding map in Drosophila using ChIP-seq, showing clustered binding sites at developmental regulators and a potential link to Polycomb-mediated regulation.