Fangjie Zhu

The paper introduces Agro-STARR-seq, an in planta enhancer screening method, and uses AI to design synthetic enhancers, identifying 14,715 active sequences in Arabidopsis.

This study reveals how ELF2, a pioneer transcription factor, remodels nucleosomes near transcription start sites by unwrapping DNA and exposing chromatin, facilitating transcription initiation.

The paper identifies sequence determinants of human gene regulatory elements by analyzing transcriptional activity of long DNA sequences in three cell types, revealing distinct enhancer types and TF subtypes based on motif content and activity patterns.

The paper identifies binding specificities of human RNA-binding proteins using HTR-SELEX, revealing that 70% bind linear sequences and 30% bind structured motifs, with novel roles for ZC3H12A/B/C in viral transcript degradation.

The paper investigates how transcription factors interact with nucleosomal DNA, finding that most have less access to it than free DNA and that nucleosome structure affects motif positioning and orientation.

The paper introduces ATI, a method to measure TF DNA-binding activity, and finds that few TFs with strong binding activity determine open chromatin.