Edward J. Rice

A comparative analysis of promoter-proximal pausing reveals kinetic and distributional dimensions of variation

The paper introduces a model-based framework to compare promoter-proximal pausing dynamics across biological contexts, revealing kinetic and distributional variations in pausing.

Functional and Computational Interrogation of the Juvenile Idiopathic Arthritis Risk Loci Identifies Candidate Causal SNPs and Target Genes in CD4+ T cells

The paper identifies candidate causal SNPs and target genes in CD4+ T cells for juvenile idiopathic arthritis using GWAS data, chromatin accessibility, and functional assays.

RNA polymerase II and PARP1 shape enhancer-promoter contacts

This study investigates enhancer-promoter contact architecture and communication, finding that RNA polymerase II and PARP1 activity stabilize these contacts.

GDNF-RET signaling and EGR1 form a positive feedback loop that promotes tamoxifen resistance via cyclin D1

This study identifies a GDNF-RET-EGR1 positive feedback loop that promotes tamoxifen resistance in breast cancer by upregulating cyclin D1.

Meiotic gene transcription programs are mediated by A-MYB and BRDT-dependent RNA polymerase II pause release during mammalian prophase I

The paper investigates how A-MYB and BRDT regulate RNA polymerase II pause release during meiotic prophase I, linking transcriptional bursts to chromatin changes and recombination.

Genetic Dissection of the RNA Polymerase II Transcription Cycle

This study uses genetic variation in mice to show how DNA sequence affects RNA Polymerase II positioning and transcription dynamics across the genome.

RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription

The paper shows that RNA Pol II pausing is essential for proper pluripotency transitions in mouse embryos by maintaining balance between gene expression states.

Multiple stages of evolutionary change in anthrax toxin receptor expression in humans

The paper examines evolutionary changes in ANTXR2 expression in humans, finding regulatory changes and recent positive selection linked to adaptation to anthrax disease.

Identification and prediction of developmental enhancers in sea urchin embryos

The paper predicts enhancer activity in sea urchin embryos using chromatin accessibility, transcription, and Pol II data, finding Pol II distribution is the best predictor for promoter-overlapping elements.

Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data

The paper introduces a method to estimate RNA half-lives using PRO-seq and RNA-seq data, finding correlations between RNA stability and splicing, miRNA binding, DNA methylation, and histone modifications.

A rapid, sensitive, scalable method for Precision Run-On sequencing (PRO-seq)

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.

Interdependence between histone marks and steps in Pol II transcription

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.

Chromatin run-on reveals the transcriptional etiology of glioblastoma multiforme

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

Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells

The paper compares nascent transcription in primates to identify evolutionary patterns in coding and non-coding transcription, finding that transcription factor binding sites and adaptive substitutions drive species-specific differences.

Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution

The paper uses deep sequencing to analyze mtDNA transcription in human and metazoan organisms, revealing conserved pausing sites and divergence across species.