Enhancing Transcriptome Mapping with Rapid PRO-seq Profiling of Nascent RNA

Precision nuclear run-on (PRO) sequencing (PRO-seq) is a powerful technique for mapping transcriptomes with nucleotide resolution and measuring newly synthesized transcripts at both promoters and enhancer elements. The current PRO-seq protocol is time intensive, technically challenging, and requires a large amount of starting material. To overcome these limitations, we developed rapid PRO-seq (rPRO-seq), enabling efficient transcriptome mapping within a single day (∼12 h), increasing ligation efficiency, abolishing adapter dimers, and reducing sample loss and RNA degradation. Rapid PRO-seq allows for transcriptome mapping using 5,000 cells and is applicable to mouse hematopoietic progenitor cells (mHPCs) as well as mouse neurons. Using acute depletion of INTS11 in neuronal cells, we pinpoint a critical role for INTS11 as a regulator of genes in neurodevelopmental disorders. Taken together, rPRO-seq represents a significant advance in the field of nascent transcript analyses and will be a valuable tool for generating patient-specific genome-wide transcription profiles with minimal sample requirements. PRO-seq and rPRO-seq were conducted in duplicates using HeLa cells and mHPC cells. rPRO-seq were conducted in duplicates using HeLa cells and mouse neuronal differentiated (ND) mESC cells.