NELF and GAGA factor are linked to promoter proximal pausing at many genes in Drosophila

Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802; Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; Center for Integrative Genomics, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720

^* To whom correspondence should be addressed. Email: dsg11{at}psu.edu.

	Abstract

Recent analyses of RNA polymerase II (Pol II) reveals that Pol II is concentrated at the promoters of many active and inactive genes. NELF causes Pol II to pause in the promoter proximal region of the hsp70 gene in Drosophila. Here, genome-wide location analysis (ChIP-chip) reveals that NELF is concentrated at the 5' ends of 2111 genes in Drosophila cells. Permanganate genomic footprinting was used to determine if paused Pol II co-localized with NELF. Forty-six of 56 genes with NELF are found to have paused Pol II. Pol II pauses 30 to 50 nucleotides downstream from transcription start sites. Analysis of DNA sequences in the vicinity of paused Pol II identifies a conserved DNA sequence that probably associates with TFIID, but detects no evidence of RNA secondary structures or other conserved sequences that might directly control elongation. ChIP-chip experiments indicate that GAGA factor associates with 39% of the genes that have NELF. Surprisingly, NELF associates with almost half of the most highly expressed genes indicating that NELF is not necessarily a repressor of gene expression. NELF-associated pausing of Pol II might be an obligatory but sometimes transient checkpoint during the transcription cycle.