biostudies-literatureShamie INovo Nordisk FoundationNIDA NIH HHSCancer Research Institute Irvington Postdoctoral Fellowship ProgramNational Institutes of HealthNational Institute of General Medical SciencesNovo Nordisk FondenNIGMS NIH HHSlqab061https://www.ebi.ac.uk/biostudies/studies/S-EPMC8276764biostudies-literatureUnknown3(3)Chinese hamster ovary (CHO) cells are widely used for producing biopharmaceuticals, and engineering gene expression in CHO is key to improving drug quality and affordability. However, engineering gene expression or activating silent genes requires accurate annotation of the underlying regulatory elements and transcription start sites (TSSs). Unfortunately, most TSSs in the published Chinese hamster genome sequence were computationally predicted and are frequently inaccurate. Here, we use nascent transcription start site sequencing methods to revise TSS annotations for 15 308 Chinese hamster genes and 3034 non-coding RNAs based on experimental data from CHO-K1 cells and 10 hamster tissues. We further capture tens of thousands of putative transcribed enhancer regions with this method. Our reNAR genomics and bioinformaticsA Chinese hamster transcription start site atlas that enables targeted editing of CHO cells.PMC8276764GM134366AI135972NNF16OC0021638NNF20SA0066621K99 GM135515U01 DA051972R01 GM134366K99GM135515NNF10CC1016517R00 GM135515NNF21SA0066621Tao JXiong KDuttke SHHan CZShamie IBenner CKarottki KJCGlass CKKildegaard HFHefzi HLi SLewis NELee GMHansen AHRoth SJfalseA Chinese hamster transcription start site atlas that enables targeted editing of CHO cells.Chinese hamster ovary (CHO) cells are widely used for producing biopharmaceuticals, and engineering gene expression in CHO is key to improving drug quality and affordability. However, engineering gene expression or activating silent genes requires accurate annotation of the underlying regulatory elements and transcription start sites (TSSs). Unfortunately, most TSSs in the published Chinese hamster genome sequence were computationally predicted and are frequently inaccurate. Here, we use nascent transcription start site sequencing methods to revise TSS annotations for 15 308 Chinese hamster genes and 3034 non-coding RNAs based on experimental data from CHO-K1 cells and 10 hamster tissues. We further capture tens of thousands of putative transcribed enhancer regions with this method. Our re2021-01-01T00:00:00Z2021 Sep2026-04-08T06:54:55.079Z2022-02-10T20:45:38.284ZS-EPMC82767643426849410.1093/nargab/lqab061