This is a PDF file of a peer-reviewed paper that has been accepted for publication. Although unedited, the content has been subjected to preliminary formatting. Nature is providing this early version of the typeset paper as a service to our authors and readers. The text and figures will undergo copyediting and a proof review before the paper is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers apply.

No abstract

SummaryDuring development, cells undergo dramatic changes in their morphology. By affecting contact geometry, these morphological changes could influence cellular communication. However, it has remained unclear whether and how signaling depends on contact geometry. This question is particularly relevant for Notch signaling, which coordinates neighboring cell fates through direct cell-cell signaling. Using micropatterning with a receptor trans-endocytosis assay, we show that signaling between pairs of cells correlates with their contact area. This relationship extends across contact diameters ranging from microns to tens of microns. Mathematical modeling predicts that dependence of signaling on contact area can bias cellular differentiation in Notch-mediated lateral inhibition processes, such that smaller cells are more likely to differentiate into signal-producing cells. Consistent with this prediction, analysis of developing chick inner ear revealed that ligand-producing hair cell precursors have smaller apical footprints than non-hair cells. Together, these results highlight the influence of cell morphology on fate determination processes.

SUMMARY Regulation of corticotropin-releasing hormone (CRH) activity is critical for the animal’s adaptation to stressful challenges, and its dysregulation is associated with psychiatric disorders in humans. However, the molecular mechanism underlying this transcriptional response to stress is not well understood. Using various stress paradigms in mouse and zebrafish, we show that the hypothalamic transcription factor Orthopedia modulates the expression of CRH as well as the splicing factor Ataxin 2-Binding Protein-1 (A2BP1/Rbfox-1). We further show that the G protein coupled receptor PAC1, which is a known A2BP1/Rbfox-1 splicing target and an important mediator of CRH activity, is alternatively spliced in response to a stressful challenge. The generation of PAC1-hop messenger RNA isoform by alternative splicing is required for termination of CRH transcription, normal activation of the hypothalamic-pituitary-adrenal axis and adaptive anxiety-like behavior. Our study identifies an evolutionarily conserved biochemical pathway that modulates the neuronal adaptation to stress through transcriptional activation and alternative splicing.

NF-B transcription factors activate genes important for immune response, inflammation, and cell survival. P-TEFb and DSIF, which are positive and negative transcription elongation factors, respectively, both regulate NF-B-induced transcription, but the mechanism underlying their recruitment to NF-B target genes is unknown. We show here that upon induction of NF-B, a subset of target genes is regulated differentially by either P-TEFb or DSIF. The regulation of these genes and their occupancy by these elongation factors are dependent on the NF-B enhancer and the core promoter type. Converting a TATA-less promoter to a TATA promoter switches the regulation of NF-B from DSIF to P-TEFb. Accumulation or displacement of DSIF and P-TEFb is dictated by the formation of distinct initiation complexes (TFIID dependent or independent) on the two types of core promoter. The underlying mechanism for the dissociation of DSIF from TATA promoters upon NF-B activation involves the phosphorylation of RNA polymerase II by P-TEFb. The results highlight a regulatory link between the initiation and the elongation phases of the transcription reaction and broaden our comprehension of the NF-B pathway.Transcription of protein-coding genes by RNA polymerase II (Pol II) is a multistep process, each step being a target for regulation and critical for the production of mature mRNA (27,29). A number of factors that control RNA Pol II elongation have been characterized in recent years. Among these are the positive elongation factor P-TEFb, which induces Pol II processivity by facilitating the transition from the early to the late elongation phase (24), and two negative elongation factors, DSIF (DRB sensitivity inducing factor) (31) and NELF (negative elongation factor) (37). In vitro, P-TEFb alleviates transcription inhibition by DSIF (25,32).NF-B is a transcription factor central to the cellular response to a broad range of extracellular signals, including inflammatory cytokines, tumor promoters, and chemotherapeutic agents. In response to these agents, NF-B induces the expression of cell cycle regulators, pro-and antiapoptotic factors, inflammatory cytokines, chemokines, adhesion molecules, and many other factors (22). In unstimulated cells, NF-B is retained in the cytoplasm by IB proteins. NF-B-activating signals trigger degradation of IB and nuclear translocation of NF-B, which result in activation of responsive genes (14). A subset of early response genes that includes IB␣ and A20 are themselves negative regulators of the NF-B pathway and so form a negative feedback loop. Transcriptional control of these genes is likely to influence the strength and the duration of the inflammatory signal.Induction of NF-B target genes is remarkably fast, and the mechanism underlying their rapid transcriptional activation was investigated previously. It was found that the promoters of NF-B-regulated genes are bound by the general transcription machinery prior to NF-B activation, and subsequent activation by NF-B increases the rate of the transcription cycl...