PRO-cap[1,2] is a nascent RNA run-on assay that measures transcription initiation events. PRO-cap data is strand-specific and base-resolution, so each PRO-cap read captures the exact 5' end or start of a nascent RNA transcript. Unlike RNA-seq or CAGE/RAMPAGE experiments, PRO-cap uniquely measures both stable and unstable RNAs, including transcription at enhancers.
Each track shows PRO-cap wiggle data for a specific cell type. As PRO-cap data is strand-specific, each track is an overlay of the data across both DNA strands: forward-strand reads are depicted as positive values, while reverse-strand reads are depicted as negative values. The y-axis shows the number of TSSs measured at each base. Cell types are color-coded and ordered alphabetically.
The full PRO-cap (CoPRO) experimental protocol is described in Tome et al. 2018[2]. Briefly, the PRO-cap protocol involves permeabilizing cells and performing a run-on reaction with biotin NTPs (which RNA polymerase incorporates into nascent transcripts), followed by selection for capped RNAs, and finally reverse transcription and paired-end sequencing.
The tracks hosted here are the merged (summed) bigWigs of all experimental replicates available for each cell type.
These PRO-cap datasets were generated as part of ENCODE[3] by Sagar Shah and the Yu and Lis Labs at Cornell.
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All PRO-cap data hosted through this track is freely available through the ENCODE portal at accession IDs ENCSR046BCI, ENCSR100LIJ, ENCSR935RNW, ENCSR261KBX, ENCSR098LLB, and ENCSR799DGV for cell types A673, Caco-2, Calu3, K562, HUVEC, and MCF10A, respectively.
[1] Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Kwak, H., Fuda, N.J., Core, L.J., & Lis, J.T. 2013. Science 339(6122): pp. 950-953. doi: 10.1126/science.122938
[2] Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers. Tome, J.M., Tippens, N.D., & Lis, J.T. 2018. Nature Genetics 50: pp. 1533-1541. doi: 10.1038/s41588-018-0234-5
[3] New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. Luo, Y., Hitz, B.C., Gabdank, I., Hilton, J.A., Kagda, M.S., Lam, B., Myers, Z., Sud, P., Jou, J., Lin, K., Baymuradov, U.K., Graham, K., Litton, C., Miyasato, S.R., Strattan, J.S., Jolanki, O., Lee, J., Tanaka, F.Y., Adenekan, P., O’Neill, E., & Cherry, J.M. 2020. Nucleic Acids Research 48(D1): pp. D882-D889. doi: 10.1093/nar/gkz1062