Neuronal specification occurs at the periventricular surface of the embryonic central nervous system. During early postnatal periods, radial glial cells in various ventricular zones of the brain differentiate into ependymal cells and astrocytes. However, mechanisms that drive this time-and cell-specific differentiation remain largely unknown. Here, we show that expression of the forkhead transcription factor FoxJ1 in mice is required for differentiation into ependymal cells and a small subset of FoxJ1 + astrocytes in the lateral ventricles, where these cells form a postnatal neural stem cell niche. Moreover, we show that a subset of FoxJ1 + cells harvested from the stem cell niche can self-renew and possess neurogenic potential. Using a transcriptome comparison of FoxJ1-null and wild-type microdissected tissue, we identified candidate genes regulated by FoxJ1 during early postnatal development. The list includes a significant number of microtubule-associated proteins, some of which form a protein complex that could regulate the transport of basal bodies to the ventricular surface of differentiating ependymal cells during FoxJ1-dependent ciliogenesis. Our results suggest that time-and cell-specific expression of FoxJ1 in the brain acts on an array of target genes to regulate the differentiation of ependymal cells and a small subset of astrocytes in the adult stem cell niche.

b Epstein-Barr virus (EBV) is an oncogenic human herpesvirus that dramatically reorganizes host gene expression to immortalize primary B cells. In this study, we analyzed EBV-regulated host gene expression changes following primary B-cell infection, both during initial proliferation and through transformation into lymphoblastoid cell lines (LCLs). While most EBV-regulated mRNAs were changed during the transition from resting, uninfected B cells through initial B-cell proliferation, a substantial number of mRNAs changed uniquely from early proliferation through LCL outgrowth. We identified constitutively and dynamically EBV-regulated biological processes, protein classes, and targets of specific transcription factors. Early after infection, genes associated with proliferation, stress responses, and the p53 pathway were highly enriched. However, the transition from early to long-term outgrowth was characterized by genes involved in the inhibition of apoptosis, the actin cytoskeleton, and NF-B activity. It was previously thought that the major viral protein responsible for NF-B activation, latent membrane protein 1 (LMP1), is expressed within 2 days after infection. Our data indicate that while this is true, LCL-level LMP1 expression and NF-B activity are not evident until 3 weeks after primary B-cell infection. Furthermore, heterologous NF-B activation during the first week after infection increased the transformation efficiency, while early NF-B inhibition had no effect on transformation. Rather, inhibition of NF-B was not toxic to EBV-infected cells until LMP1 levels and NF-B activity were high. These data collectively highlight the dynamic nature of EBV-regulated host gene expression and support the notion that early EBV-infected proliferating B cells have a fundamentally distinct growth and survival phenotype from that of LCLs.

Plant root growth is affected by both gravity and mechanical stimulation . A coordinated response to both stimuli requires specific and common elements. To delineate the transcriptional response mechanisms, we carried out whole-genome microarray analysis of Arabidopsis root apices after gravity stimulation (reorientation) and mechanical stimulation and monitored transcript levels of 22,744 genes in a time course during the first hour after either stimulus. Rapid, transient changes in the relative abundance of specific transcripts occurred in response to gravity or mechanical stimulation, and these transcript level changes reveal clusters of coordinated events. Transcriptional regulation occurs in the root apices within less than 2 min after either stimulus. We identified genes responding specifically to each stimulus as well as transcripts regulated in both signal transduction pathways. Several unknown genes were specifically induced only during gravitropic stimulation (gravity induced genes). We also analyzed the network of transcriptional regulation during the early stages of gravitropism and mechanical stimulation.Plants adapt their growth in response to environmental cues. Gravity is a constant force that guides the direction of plant growth. Mechanical stimuli such as wind, rain, and obstacles in the soil trigger changes in growth patterns (Braam and Davis, 1990;. Gravitropic and mechanical stimulation in the root are interactive processes, mutually influencing differential growth (Mullen et al., 2000;Fasano et al., 2002;. The mechanisms of sensing and signal transduction for either stimulus are not well understood, but it has been shown that the transcript levels of specific genes are regulated early during signal transduction after either stimulus Braam and Davis, 1990).It is widely accepted that gravitropic stimulation by reorientation is perceived by sedimentation of starchcontaining plastids (statoliths) in the columella cells of the root tip (Kiss et al., 1989(Kiss et al., , 1996Juniper et al., 1966;Blancaflor et al., 1998). Columella cells show differences in their contribution toward gravity perception and in the velocity of sedimentation of their statoliths (Blancaflor et al., 1998). While complete sedimentation of the statoliths requires at least 5 min (Blancaflor et al., 1998;MacCleery and Kiss, 1999), the presentation time (duration of the stimulus that is required to establish a response) was estimated at only approximately 1 min for wild-type Arabidopsis root tips (Blancaflor et al., 1998). Statolith sedimentation is postulated to disrupt the actin-based cytoskeletal network and its links to plasma membrane receptors in some regions of the cell cortex (Yoder et al., 2001). Other groups hypothesized that statoliths are directly connected to the cytoskeleton, activating membrane proteins anchored to the filaments upon dislocation or activation of mechanosensitive ion channels (Evans et al., 1986;Pickard and Ding, 1993;Collings et al., 2001;Blancaflor, 2002).The transduction of the physical alt...

SUMMARY PARAGRAPH Transcription factors (TF) recognize specific genomic sequences to regulate complex gene expression programs. Although it is well established that TFs bind specific DNA sequences using a combination of base readout and shape recognition, some fundamental aspects of protein-DNA binding remain poorly understood 1 , 2 . Many DNA-binding proteins induce changes in the DNA structure outside the intrinsic B-DNA envelope. However, how the energetic cost associated with distorting DNA contributes to recognition has proven difficult to study because the distorted DNA exists in low-abundance in the unbound ensemble 3 – 9 . Here, we use a novel high-throughput assay called SaMBA ( Sa turation M ismatch- B inding A ssay) to investigate the role of DNA conformational penalties in TF-DNA recognition. In SaMBA, mismatches are introduced to pre-induce DNA structural distortions much larger than those induced by changes in Watson-Crick sequence. Strikingly, approximately 10% of mismatches increased TF binding, and at least one mismatch was found that increased the binding affinity for each of 22 examined TFs. Mismatches also converted non-specific sites into high-affinity sites, and high-affinity sites into super-sites stronger than any known canonical binding site. Determination of high-resolution X-ray structures, combined with NMR measurements and structural analyses revealed that many of the mismatches that increase binding induce distortions similar to those induced by protein binding, thus pre-paying some of the energetic cost to deform the DNA. Our work indicates that conformational penalties are a major determinant of protein-DNA recognition, and reveals mechanisms by which mismatches can recruit TFs and thus modulate replication and repair activities in the cell 10 , 11 .