Uncaging promoter and enhancer dynamics: In order to understand cellular differentiation, it is important to understand the timing of the regulation of gene expression. Arner et al. used cap analysis of gene expression (CAGE) to analyze gene enhancer and promoter activities in a number of human and mouse cell types. The RNA of enhancers was transcribed first, followed by that of transcription factors, and finally by genes that are not transcription factors. Science , this issue p. 1010

A number of pathophysiologically relevant genes, including platelet-derived growth factor B-chain (PDGF-B), are induced in the vasculature after acute mechanical injury. In rat aorta, the activated expression of these genes was preceded by a marked increase in the amount of the early-growth-response gene product Egr-1 at the endothelial wound edge. Egr-1 interacts with a novel element in the proximal PDGF-B promoter, as well as with consensus elements in the promoters of other genes induced by endothelial injury. This interaction is crucial for injury-induced PDGF-B promoter-dependent expression. Sp1, whose binding site in the PDGF-B promoter overlaps that of Egr-1, occupies this element in unstimulated cells and is displaced by increasing amounts of Egr-1. These findings implicate Egr-1 in the up-regulated expression of PDGF-B and other potent mediators in mechanically injured arterial endothelial cells.

Sp1 is a ubiquitously expressed, prototypic C2H2-type zinc finger-containing DNA binding protein that can activate or repress transcription in response to physiologic and patholog- ical stimuli. It was originally found to selectively transactivate the early and late simian virus 40 promoters without influenc- ing numerous other promoters (16) and has since been shown to regulate the expression of thousands of genes implicated in the control of a diverse array of cellular processes, such as cell growth (26, 57), differentiation (48), apoptosis (26), angiogen- esis (43), and immune response (25), to name just a few. Sp1 is a 785-amino-acid, 100- to 110-kDa nuclear transcription factor which regulates gene expression via multiple mecha- nisms. It binds GC-rich motifs (such as 5-G/T-GGGCGG-G/ A-G/A-C/T-3 or 5-G/T-G/A-GGCG-G/T-G/A-G/A-C/T-3) with high affinity (4, 27, 28) and can regulate the expression of TATA-containing and TATA-less genes via protein-protein interactions or interplay with other transcription factors (47), such as Ets-1 (56), c-myc (51), c-Jun (44), Stat1 (6), and Egr-1 (31), and/or components of the basal transcriptional machin- ery. Sp1 has been linked to chromatin remodeling through interactions with chromatin-modifying factors such as p300 (62) and histone deacetylases (HDACs) (71). Sp1 was once thought to serve mainly as a constitutive acti- vator of housekeeping genes. However, growing evidence in- dicates that phosphorylation, acetylation, sumoylation, ubiqui- tylation, and glycosylation are among the posttranslational modifications that can influence the transcriptional activity and stability of Sp1. Here we will discuss recent developments in our understanding of the role of posttranslational modifica- tions influencing Sp1-dependent transcription, focusing mainly on phosphorylation.

In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.