John T. Lis

This study compares divergent and unidirectional transcriptional regulatory elements, finding that unidirectional elements are younger and less constrained, with some transcription factors modulating their directionality.

The paper investigates enhancer-promoter interactions in a native chromatin context, revealing transcription factor synergy and the role of facilitators and repressive promoters in regulating gene activation.

This paper introduces DeepDETAILS, a method to reconstruct cell-type-specific genomic signals from bulk data, outperforming traditional methods and providing insights into disease mechanisms.

The paper introduces CIERA-seq to study transcription regulatory element interactions and finds pdTREs and edTREs have distinct functional and chromatin features.

This study evaluates multiple MPRA and STARR-seq datasets to identify enhancers, finding inconsistencies due to technical factors and proposing a unified pipeline to improve cross-assay agreement.

The paper introduces PReCIS-seq, a nascent RNA assay, to study lineage-specific Pol II activity in mouse skin, revealing mechanisms of gene regulation in adult homeostasis.

The paper identifies human RNA Polymerase II interactors at early transcription stages using biochemical purification and mass spectrometry, revealing new factors involved in PIC assembly and promoter-proximal pausing.

The paper presents a high-resolution atlas of transcriptional regulatory elements in human tissues and disease states using PRO-cap and deep learning models to prioritize noncoding variants.

The paper develops a dual reporter assay to measure promoter and enhancer potential, finding that they share regulatory logic and can function reciprocally.

The paper identifies a novel lncRNA regulatory network at the BRCA1 locus that is activated during transcriptional stress induced by XPB inhibition.

The paper trains a deep learning model to predict transcription initiation from DNA sequences, revealing shared cis-regulatory logic and epistatic interactions across promoters and enhancers.

This study identifies cis-regulatory elements that control transcriptional timing and noise in response to estrogen using single-cell RNA-seq and machine learning.

Femto-seq enables targeted DNA sequencing from specific nuclear regions in individual cells using nanoscale photobiotinylation and sequencing.

The paper introduces PRO-IP-seq to track Pol II CTD phosphorylation at nucleotide resolution and reveals its dynamic regulation during transcription.

The paper compares RNA sequencing assays and introduces a tool to identify active enhancers, compiling a compendium of enhancer candidates across 120 cell types.

The paper shows CTCF suppresses antisense transcription at divergent promoters without affecting sense transcription, using a combination of genetic and molecular techniques.

This study investigates how the glucocorticoid receptor (GR) interacts with pioneer factors and AP-1 to regulate gene expression in human cancer cells through cell-type-specific binding and transcriptional changes.

This study shows GAF, a Drosophila pioneer factor, works with chromatin remodelers PBAP and NURF to activate transcription by opening chromatin and facilitating Pol II recruitment and elongation.

The paper identifies two types of eRNA QTLs associated with enhancer function and reveals a bipartite enhancer architecture through population-scale eRNA analysis.

The paper identifies fundamental enhancer units defined by transcription start sites and shows adjacent units operate non-cooperatively.

A precision run-on sequencing (PRO-seq) variant with one streptavidin bead binding and on-bead enzymatic steps yields adapter-ligated cDNA in about 10 h and libraries from 0.05–0.25 × 10^6 cells.

The paper identifies Psi as a repressor of developmental pathways that promotes Drosophila wing growth by both activating Myc and repressing growth inhibitors.

The paper uses machine learning to show that transcription predicts histone marks and chromatin states, and that transcription is required for maintaining active and repressive histone modifications.

This study shows that chromatin conformation remains stable during heat shock-induced transcriptional changes in human and Drosophila cells.

The paper predicts Xist-induced gene silencing kinetics using a Random Forest model based on epigenetic and genomic features, identifying key factors like distance to Xist and promoter pre-marking.

This study shows that heat shock induces transcriptional memory in cells, accelerating promoter-proximal pause-release and slowing termination over mitotic divisions.

The paper identifies enhancer regions in cassava using RNA polymerase mapping and shows they are enriched with causal variants affecting fitness and root composition.

The paper identifies a Cdk9-PP1 kinase-phosphatase switch that regulates the transition of RNA polymerase II from elongation to termination by modulating Spt5 phosphorylation.

This study introduces ChRO-seq to map nascent transcription in glioblastoma and identifies enhancers and transcription factors driving GBM subtypes and clinical outcomes.

This study investigates the role of Cdk9 in regulating RNA Polymerase II elongation rate using fission yeast and PRO-seq, finding that Cdk9 inhibition severely impairs early transcription but allows continued elongation.