Data were analyzed as previously described (44). Briefly, reads were aligned to the rat reference genome (Rnor_6.0) using Bowtie (v2.0.2) with default parameters allowing for two mismatches using seed alignment. Subsequently, aligned reads were filtered for high-quality, uniquely, and multimapped reads (MAPQ ! = [0, 2, 3, 4]). High-quality BAM files were merged for each condition using samtools (v0.1.18). Peak calling was performed using MACS2 (v2.1.2) with a minimum false discovery rate of 0.05. Peaks were assigned to the genes using PAVIS if they were located within 5 kb upstream of the TSS or in the transcribed region or within 1 kb downstream of the transcription end site.

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