A nuclear run-on assay measures the amount of Pol II that is either actively transcribing or is “transcriptionally engaged,” tightly associated with DNA in preparation for transcription. We have recently expanded the power of these nuclear run-on assays with GRO-seq, an assay evaluates genome-wide the location, orientation, and density of transcriptionally-engage polymerases. A variation in this protocol, called PRO-seq, now allow Pol II to be mapped with base pair resolution.

Selected Papers:

  • Kwak H, Fuda NJ, Core LJ, Lis JT. (2013) “Precise maps of RNA polymerase reveal how promoters direct initiation and pausing.” Science. 339(6122):950-3. (PubMed)
  • Core LJ, Waterfall JJ, Gilchrist DA, Fargo DC, Kwak H, Adelman K, Lis JT. (2012) “Defining the Status of RNA Polymerase at Promoters.” Cell Reports.pii: S2211-1247(12)00274-4. [Epub ahead of print]. (PubMed)
  • Min IM , Waterfall JJ, CoreLJ, Munro RJ, SchimentiJ, and Lis JT (2011) “Regulating RNAPolymerase Pausing and Transcription Elongation in Embryonic Stem Cells.” Genes & Devel., 25: 742-754.(PubMed)
  • Hah N, Danko CG., Core LJ, Waterfall JJ, Siepel A, Lis, JT, and Kraus WL. (2011) “Global Analysis of the Immediate Transcriptional Effects of Estrogen Signaling Reveals a Rapid, Extensive, and Transient Response.” Cell 145: 622-34. (PubMed)
  • Core LJ, Waterfall JJ, and Lis JT (2008) “Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters.” Science 322: 1845-1848. (PubMed)
  • Rasmussen EB & Lis JT. (1993) “In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes.” Proc. Natl Acad. Sci. USA 90, 7923-7927. (PubMed)
    • Shows that capping predominantly occurs when the nascent mRNA is 20-30 nucleotides long.
  • Rougvie AE & Lis JT. (1988) “The RNA polymerase II molecule at the 5′ end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged.” Cell 54, 795–804 (PubMed)
    • Shows that Pol II present on the uninduced Hsp70 promoter is transcriptionally engaged and paused.