Genome-Wide Analysis of Nelf - Nelf Is Linked to Promoter Proximal Pausing Throughout the Drosophila Genome. (Paperback)

Negative elongation factor, NELF, has been shown to cause RNA polymerase II to pause in the promoter proximal region of the hsp70 gene in Drosophila and of several genes in human cells. To investigate the global role of NELF and promoter proximal pausing in transcription regulation, I determined the genome-wide distribution of NELF in Drosophila cells using ChIP-chip. NELF was detected at the promoter region of over 2,000 genes. I used these data to identify locations in the Drosophila genome where paused Pol II might reside. Using permanganate genomic footprinting for detection of transcriptionally engaged Pol II, I analyzed the association of Pol II with 61 genes where NELF was detected and 4 genes where NELF was not detected. Paused Pol II was detected at 51 genes associated with NELF, revealing that there is a good correlation of NELF and promoter proximal pausing. Based on these ChIP-chip and permanganate footprinting results, I estimated that at least 1,000 genes in Drosophila cells harbor paused Pol II. To determine if there are cis-DNA elements near such paused Pol II, I used the MEME algorithm to analyze the sequences of 51 promoter regions at which permanganate footprints had been detected. The search for conserved sequence elements identified a 35 nucleotide long motif with similarity to a combination of initiator element, DPE, and MTE. Each of these elements is reported to be recognized by TFIID. The 35 nucleotide long motif was enriched on genes associated with NELF and paused Pol II. This conserved promoter element might contribute to pausing by increasing the affinity of TFIID to the promoter and establishing a promoter architecture for pausing. Sequence analysis also showed that GAGA elements were enriched at genes with paused Pol II. This observation, together with previous studies suggesting that GAGA factor is involved in establishing paused Pol II on the hsp70 gene, led me to analyze the distribution of GAGA factor in the Drosophila genome. Using ChIP-chip analysis, I determined that GAGA factor was associated with the promoters of 1,566 genes in the entire genome. Comparison of the distribution of NELF and GAGA factor revealed that 832 of 2,111 genes with NELF associated with GAGA factor. This result suggests that GAGA factor is linked to NELF and promoter proximal pausing. To further investigate the mechanism of promoter proximal pausing, I analyzed the locations of permanganate footprints of 51 genes. A composite of all the permanganate footprints revealed that paused Pol II typically resided in the region 20 to 50 nucleotides downstream from an initiator element. This indicates that Pol II pauses after transcribing approximately 30 nucleotides, extruding at least a 10 nucleotide-long transcript from the elongation complex. The exposed nascent transcript might provide a possible site for NELF-E binding. Therefore, these results strongly support the proposed mechanism by which NELF mediates promoter proximal pausing by restricting the movement of Pol II through the association of NELF-E with the nascent transcript. Since NELF has been reported to repress expression of several genes in Drosophila and human cells, I determined if NELF correlates with transcription repression. Using the previously reported genome-wide expression data for Drosophila cells, I determined that many of genes associated with NELF are actively transcribed. This indicates that NELF is not necessarily acting as a repressor of transcription. Whereas NELF might serve to inhibit expression of some genes, in the majority of cases, NELF could generate a limiting-step during gene activation and function as a checkpoint for proper RNA...