Nascent RNA profiling is growing in popularity; however, there is no standard analysis
pipeline to uniformly process the data and assess quality. Here, we introduce PEPPRO, a …

Precision genomic run-on assays (PRO-seq) quantify nascent RNA at single nucleotide
resolution with strand specificity. Here we deconstruct a recently published genomic nascent …

Conventional scRNA-seq expression analyses rely on the availability of a high quality
genome annotation. Yet, as we show here with scRNA-seq experiments and analyses …

Nascent RNA-sequencing tracks transcription at nucleotide resolution. The genomic
distribution of engaged transcription complexes, in turn, uncovers functional genomic …

Adipocytes contribute to metabolic disorders such as obesity, diabetes, and atherosclerosis.
Prior characterizations of the transcriptional network driving adipogenesis have overlooked …

Nascent RNA sequencing protocols, such as PRO-seq and NET-seq, are now widely used
in the study of eukaryotic transcription, and these experimental techniques have given rise to …

Motivation Quantification of isoform abundance has been extensively studied at the mature
RNA level using RNA-seq but not at the level of precursor RNAs using nascent RNA …

Transcription factors bind to sequence motifs and act as activators or repressors.
Transcription factors interface with a constellation of accessory cofactors to regulate distinct …

The promoter shift is a long known phenomenon which implies changes in the coordinates
of a transcription start site (TSS). Analysis of CAGE experiments allows one to assess the …

Single-cell RNA-sequencing (scRNA-seq) has accelerated discovery in biology. Yet, current
scRNA-seq methods miss potentially important transcriptional information due to limitations …