PTEN, encoding a lipid phosphatase, is a tumor suppressor gene and is mutated in various types of cancers. It is reported to regulate G1 to S phase transition of the cell cycle by influencing the expression, protein stability and subcellular location of cyclin D1. Here, we provide evidence that PTEN modulates the transcription and protein stability of cyclin D2. Targeted deletion of Pten in mouse embryonic fibroblasts (MEFs) endowed cells with greater potential to overcome G1 arrest than wild-type MEFs and led to the elevated expression of cyclin D2, which was suppressed by the introduction of PTEN. We further defined a pathway involving GSK3b and b-catenin/TCF in PTEN-mediated suppression of cyclin D2 transcription. LiCl, an inhibitor of GSK3b, abolished inhibitory effect of PTEN on cyclin D2 expression, and TCF members could directly bind to the promoter of cyclin D2 and regulate its transcription in a CREB-dependent manner. Our results indicate that the downregulation of cyclin D2 expression by PTEN is mediated by the GSK3b/b-catenin/TCF pathway in cooperation with CREB, and suggest a convergence from the PI-3 kinase/PTEN pathway and the Wnt pathway in modulation of cyclin D2 expression.

Access to cis-regulatory elements packaged in chromatin is essential for directing gene expression and cell viability. Here, we report a super-resolution imaging strategy, 3D ATAC-PALM, that enables direct visualization of the entire accessible genome. We found that active chromosomal segments are organized into spatiallysegregated accessible chromatin domains (ACDs). Rapid depletion of CTCF or Cohesin (RAD21 subunit) induced enhanced ACD clustering, reduced physical separation between intrachromosomal ACDs, and differentially regulated ACD compaction. Experimental perturbations and polymer modeling suggest that dynamic proteinprotein and protein-DNA interactions within ACDs couple with loop extrusion to organize ACD topology. Dysorganization of ACDs upon CTCF or Cohesin loss alters transcription factor binding and target search dynamics in living cells. These results uncover fundamental mechanisms underpinning the formation of 3D genome architecture and its pivotal function in transcriptional regulation.

46Sepsis is a leading cause of death globally where neutrophils respond to pathogens via tightly 47 regulated antimicrobial effectors. Combining early neutrophilic responses and pathogen 48 detection may reveal insights for disease recognition. We performed ATAC-seq of human 49 neutrophils challenged with six toll-like receptor ligands and two organisms; and RNA-seq after 50Escherichia coli (EC) exposure for 1 and 4 hours along with ATAC-seq. ATAC-seq of 51 neurophils retains more pathogenic DNA reads than standard library preparation methods. Only 52 a fraction of differential chromatin regions overlap between challenges. Shared signatures exist 53for ligands but rest are unique in position, function, and challenge. Epigenomic changes are 54 plastic, only ~500 are shared by EC challenges over time, resulting in varied differential genes 55 and associated processes. We also identify three classes of chromatin mediated gene regulation 56based on their relative locations. These and transcription factor footprinting reveal timely and 57 challenge specific mechanisms of transcriptional regulation in neutrophils. 58 59

Over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation in health and disease. In one mechanism, disease-causing variants directly affect the activity of one or more cis-regulatory elements in specific cell types leading to dysregulation of gene expression. To identify such Our results provide insights into how genetic variants modulate cis-regulatory elements, in isolation or in concert, and influence gene expression in primary immune cells that play a key role in many human diseases.