Genetic Dissection of the RNA Polymerase II Transcription Cycle with ChRO-seq from F1 hybrid mice

How DNA sequence affects the dynamics and position of RNA Polymerase II during transcription remains poorly understood. Here we used naturally occurring genetic variation in F1 hybrid mice to explore how DNA sequence differences affect the genome-wide distribution of Pol II. We measured the position and orientation of Pol II in eight organs collected from heterozygous F1 hybrid mice using ChRO-seq. Our data revealed a strong genetic basis for the precise coordinates of transcription initiation and promoter proximal pause, which was composed of both existing and novel DNA sequence motifs, allowing us to redefine molecular models of both core transcriptional processes. Our results implicate the strength of base pairing between A-T or G-C dinucleotides as key determinants to the position of Pol II initiation and pause. We reveal substantial and heritable differences in the position of transcription termination, which frequently do not affect the composition of the mature mRNA. Finally, we identified frequent, organ-specific changes in transcription that affect mRNA and ncRNA expression across broad genomic domains. Collectively, we reveal how DNA sequences shape core transcriptional processes at single nucleotide resolution in mammals. Overall design: We analyzed ChRO-seq data from eight organs from 7 independent reciprocal crosss of C57BL/6 (B6) and Castaneus F1 hybrid mices. We analyzed RNA-seq data from brain and liver from C57BL/6 (B6) and Castaneus F1 hybrid mices.