Regulating the regulators: The pervasive effects of Pol II pausing on stimulus-responsive gene networks

Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA.
Genes & development (Impact Factor: 10.8). 05/2012; 26(9):933-44. DOI: 10.1101/gad.187781.112
Source: PubMed


The expression of many metazoan genes is regulated through controlled release of RNA polymerase II (Pol II) that has paused during early transcription elongation. Pausing is highly enriched at genes in stimulus-responsive pathways, where it has been proposed to poise downstream targets for rapid gene activation. However, whether this represents the major function of pausing in these pathways remains to be determined. To address this question, we analyzed pausing within several stimulus-responsive networks in Drosophila and discovered that paused Pol II is much more prevalent at genes encoding components and regulators of signal transduction cascades than at inducible downstream targets. Within immune-responsive pathways, we found that pausing maintains basal expression of critical network hubs, including the key NF-κB transcription factor that triggers gene activation. Accordingly, loss of pausing through knockdown of the pause-inducing factor NELF leads to broadly attenuated immune gene activation. Investigation of murine embryonic stem cells revealed that pausing is similarly widespread at genes encoding signaling components that regulate self-renewal, particularly within the MAPK/ERK pathway. We conclude that the role of pausing goes well beyond poising-inducible genes for activation and propose that the primary function of paused Pol II is to establish basal activity of signal-responsive networks.

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    • "Knockdown of eRNAs Causes NELF to Remain Bound to Target Gene Promoters Recent genome-wide studies unambiguously argue that proximal-promoter pausing of RNAPII is a widespread mechanism of transcriptional regulation for controlling expression of stimulus-responsive genes in higher eukaryotes (Adelman and Lis, 2012; Gilchrist et al., 2012). Because of the rapid induction kinetics of eRNAs (Figures 1B and 1E), we investigated whether eRNAs play a role in the early transcription elongation step that involves RNAPII pausing and release. "
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    ABSTRACT: Enhancer RNAs (eRNAs) are a class of long noncoding RNAs (lncRNA) expressed from active enhancers, whose function and action mechanism are yet to be firmly established. Here we show that eRNAs facilitate the transition of paused RNA polymerase II (RNAPII) into productive elongation by acting as a decoy for the negative elongation factor (NELF) complex upon induction of immediate early genes (IEGs) in neurons. eRNAs are synthesized prior to the culmination of target gene transcription and interact with the NELF complex. Knockdown of eRNAs expressed at neuronal enhancers impairs transient release of NELF from the specific target promoters during transcriptional activation, coinciding with a decrease in target mRNA induction. The enhancer-promoter interaction was unaffected by eRNA knockdown. Instead, chromatin looping might enable eRNAs to act locally at a specific promoter. Our findings highlight the spatiotemporally regulated action mechanism of eRNAs during early transcriptional elongation.
    Molecular Cell 09/2014; 56(1). DOI:10.1016/j.molcel.2014.08.023 · 14.02 Impact Factor
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    • "Heat shock genes are induced rapidly to protect cells under high temperatures, and thus it is often assumed that Pol II primes heat shock genes for rapid induction. Recent evidence, however, suggests that paused Pol II is not absolutely required for rapid gene induction since genes lacking Pol II occupancy can be induced just as quickly as, and perhaps to even higher levels than, paused genes (Lin et al., 2011; Gilchrist et al., 2012; Chen et al., 2013). Furthermore, a genome-wide analysis of transcription rates by GRO-seq in mammalian cells revealed that induction of paused genes in response to TNF-alpha treatment is associated with a slight delay (Danko et al., 2013). "
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    ABSTRACT: The rapid expansion of genomics methods has enabled developmental biologists to address fundamental questions of developmental gene regulation on a genome-wide scale. These efforts have demonstrated that transcription of developmental control genes by RNA polymerase II (Pol II) is commonly regulated at the transition to productive elongation, resulting in the promoter-proximal accumulation of transcriptionally engaged but paused Pol II prior to gene induction. Here we review the mechanisms and possible functions of Pol II pausing and their implications for development.
    Development 03/2014; 141(6):1179-83. DOI:10.1242/dev.088492 · 6.46 Impact Factor
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    • "At these genes, the major regulatory checkpoint is therefore the licensing of the polymerase to enter a productive elongation phase, as opposed to the recruitment of polymerase itself. Signal-dependent elongation is a well-conserved regulatory mechanism, having been well-documented at the heat-shock genes, and more recently at rapidly induced immune genes in Drosophila (69, 70). The inhibition of BRD4 by highly selective chemical compounds, however, revealed that such an inhibition can selectively inhibit low-CpG containing genes (71). "
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    ABSTRACT: The NF-κB family of transcription factors plays a central role in the inducible expression of inflammatory genes during the immune response, and the proper regulation of these genes is a critical factor in the maintenance of immune homeostasis. The chromatin environment at stimulus-responsive NF-κB sites is a major determinant in transcription factor binding, and dynamic alteration of the chromatin state to facilitate transcription factor binding is a key regulatory mechanism. NF-κB is in turn able to influence the chromatin state through a variety of mechanisms, including the recruitment of chromatin modifying co-activator complexes such as p300, the competitive eviction of negative chromatin modifications, and the recruitment of components of the general transcriptional machinery. Frequently, the selective interaction with these co-activators is dependent on specific post-translational modification of NF-κB subunits. Finally, the mechanisms of inducible NF-κB activity in different immune cell types seem to be largely conserved. The diversity of cell-specific NF-κB-mediated transcriptional programs is established at the chromatin level during cell differentiation by lineage-defining transcription factors. These factors generate and maintain a cell-specific chromatin landscape that is accessible to NF-κB, thus restricting the inducible transcriptional response to a cell-appropriate output.
    Frontiers in Immunology 02/2014; 5:71. DOI:10.3389/fimmu.2014.00071
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