CAGE-seq Profiling of Transcription Start Site Usage in mock-infected and human cytomegalovirus (HCMV) infected human embryonic lung fibroblasts (HELF) cells (human)

CAGE-seq (Cap Analysis of Gene Expression coupled with deep sequencing) was used to map transcription start site (TSS) usage in human embryonic lung fibroblast (HELF) cells in response to infection with the human cytomegalovirus (HCMV) HAN strain. Total RNA from infected cells at 72 hours post-infection and mock-infected controls was profiled. The analysis detected 224,206 and 292,294 CAGE transcription start sites (CTSSs) in infected and mock samples, respectively, which grouped into 20,532 and 26,407 transcript clusters (TCs). Comparative analysis identified 3,302 consensus clusters with significant shifts in TSS positions, spanning 2,487 protein-coding genes and 134 non-coding RNAs. These findings reveal extensive infection-associated remodeling of promoter choice across the host transcriptome. This study profiled TSS usage by CAGE-seq in human embryonic lung fibroblast (HELF) cells under two conditions: cells infected with the HCMV HAN strain(moi=3) and harvested at 72 hours post-infection, and mock-treated controls. Total RNA from each condition was used to generate CAGE libraries that capture capped 5′ transcript ends, and sequencing was performed on an Illumina HiSeq X Ten with 150-bp paired-end reads. Infection status was the primary variable, with mock-infected HELF cells serving as the reference control, enabling direct comparison of genome-wide TSS usage between conditions and detection of infection-associated TSS shifts. Raw data uploaded to SRA under Bioprojects: PRJNA1299111 and PRJNA1291936