Whereas traditional models for gene regulation posit that recruitment of Pol II to the promoter is both necessary and sufficient for gene expression, we have found that release of paused Pol II from the promoter-proximal region is rate-limiting for expression of a large number of genes. Our initial work investigated the prevalence of paused Pol II in Drosophila, employing a combination of global location analysis (using techniques called ChIP-chip and ChIP-seq) as well as in vivo footprinting assays. Surprisingly, these data showed that Pol II pausing is much more widespread than previously appreciated, occurring at thousands of promoters genome-wide. We and others have recently extended these findings to mammalian systems (mouse and human), demonstrating that pausing a prevalent gene regulatory strategy in higher organisms. Moreover, our results reveal that Pol II is constitutively present at many genes in environmentally- or developmentally-responsive gene networks, suggesting that the presence of Pol II facilitates efficient, integrated responses to a dynamically changing environment. Understanding the fundamental properties of paused Pol II, and the factors that govern maintenance vs. release of promoter-proximal Pol II into productive elongation are specific aims of research in the Adelman laboratory. In addition to providing crucial insight into stress-responses, this work is anticipated to elucidate gene expression during the development of cancer and AIDS, since similarly paused Pol II are observed at the mammalian promoters of proto-oncogenes like c-myc, c-fos and junB, as well as at the HIV promoter. As part of our efforts to better define the mechanisms underlying pausing, we have recently developed a novel technique for isolating the short RNA transcripts generated by paused Pol II, and analyzed them through massively-parallel sequencing of individual RNA molecules. This strategy allowed us to pinpoint both the locations of transcription initiation and pausing, at single-nucleotide resolution. Notably, this exciting new technique revealed a role for the DNA sequence within the initially transcribed region in specifying the efficiency of early elongation, providing insights into why polymerase pausing is more prominent at some genes than at others. In probing the molecular mechanisms governing Pol II stalling, the Negative ELongation Factor, or NELF complex, is of particular interest to the laboratory. NELF has been shown to establish paused Pol II at several genes to date, including the junB and HIV promoters. To globally identify targets of NELF, we have performed a microarray analysis on Drosophila cells that were depleted of NELF using RNA interference. We found that many NELF target genes are involved in stimulus-responsive pathways, with a particular enrichment in the innate immune response. To evaluate the physiological relevance of this finding, we have recently performed NELF depletion in the Drosophila fat body (the main immune responsive tissue), followed by microarray analysis of RNA levels to identify NELF target genes. This work confirms that NELF plays a key role in vivo in regulating expression of components of the innate immune system. Follow-up studies in both cells and flies revealed that NELF-mediated Pol II pausing is essential for an optimal immune response to bacterial challenge and indicated that polymerase pausing tunes the basal expression level of critical immune regulators such as the NF-kB transcription factor Relish (Rel). In addition to our work in Drosophila, we are studying the role of polymerase pausing in the mammalian inflammatory response, using primary macrophages derived from mouse. These investigations reveal that several genes that play critical roles in the response to bacterial infection, like TNF-alpha and junB, possess paused Pol II, waiting in their promoter regions in resting, uninduced cells. However, many other bacterially-induced genes do not harbor paused Pol II, and are regulated primarily by Pol II recruitment during gene activation. Interestingly, we find that there is a relationship between the presence of paused Pol II and the kinetics of the immune response, in that paused genes exhibit more finely-tuned bursts of transcription activity than do genes regulated through Pol II recruitment, which often exhibit a more sustained response. This suggests that there could be a fundamental link between gene regulatory strategy (i.e. the step in the transcription cycle that is rate-limiting for gene expression) and the kinetics or magnitude of gene expression. In this way, pausing might allow for fine tuning of both basal gene expression and activation, to enable precise, balanced responses to environmental or developmental cues.

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Rogatsky, Inez; Adelman, Karen (2014) Preparing the first responders: building the inflammatory transcriptome from the ground up. Mol Cell 54:245-54
Henriques, Telmo; Adelman, Karen (2013) Catching the waves: following the leading edge of elongating RNA polymerase II. Mol Cell 50:159-60
Gupte, Rebecca; Muse, Ginger W; Chinenov, Yurii et al. (2013) Glucocorticoid receptor represses proinflammatory genes at distinct steps of the transcription cycle. Proc Natl Acad Sci U S A 110:14616-21
Nechaev, Sergei; Adelman, Karen (2011) Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation. Biochim Biophys Acta 1809:34-45
Ardehali, M Behfar; Yao, Jie; Adelman, Karen et al. (2009) Spt6 enhances the elongation rate of RNA polymerase II in vivo. EMBO J 28:1067-77
Gilchrist, Daniel A; Fargo, David C; Adelman, Karen (2009) Using ChIP-chip and ChIP-seq to study the regulation of gene expression: genome-wide localization studies reveal widespread regulation of transcription elongation. Methods 48:398-408
Nechaev, Sergei; Adelman, Karen (2008) Promoter-proximal Pol II: when stalling speeds things up. Cell Cycle 7:1539-44
Gilchrist, Daniel A; Nechaev, Sergei; Lee, Chanhyo et al. (2008) NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly. Genes Dev 22:1921-33