Project description:The cell transition from an inflammatory phase to a subsequent proliferative phase is crucial for wound healing, yet the driving mechanism remains unclear. By profiling lncRNA expression changes during human skin wound healing and screening lncRNA functions, we identified SNHG26 as a pivotal regulator in keratinocyte progenitors underpinning this phase transition. To study the proteins interact with SNHG26, we performed RNA pull-down assay in human keratinocyte progenitors. The mass spectrometry (MS) analysis was performed to identify the proteins interacted with SNHG26.
Project description:Recent studies have revealed the importance of long noncoding RNAs (lncRNAs) as tissue-specific regulators of gene expression. There is ample evidence that distinct types of vasculature undergo tight transcriptional control to preserve their structure, identity, and functions. We determined, for the first time, the global lineage-specific lncRNAome of human dermal blood and lymphatic endothelial cells (BECs and LECs), combining RNA-Seq and CAGE-Seq. A subsequent genome-wide antisense oligonucleotide-knockdown profiling of two BEC- and two LEC-specific lncRNAs identified LETR1 as a critical gatekeeper of the global LEC transcriptome. Deep RNA-DNA and RNA-protein interaction studies, and phenotype rescue analyses revealed that LETR1 is a nuclear trans-acting lncRNA modulating, via key epigenetic factors, the expression of essential target genes governing the growth and migratory ability of LECs. Together, our study provides new evidence supporting the intriguing concept that every cell type expresses precise lncRNA signatures to control lineage-specific regulatory programs.
Project description:In pursuit of a biological role of Salmonella 3' UTR derived sRNA NarS ,we sought to determine potential target mRNAs of NarS under anaerobic conditions. To this end, we compared gene expression in NarS-deficient and NarS overexpression (from plasmid pPL-NarS) strains following a 30-minute anaerobic shock by RNA-seq.
Project description:The black-footed ferret (Mustela nigripes) is a star example of the efforts of conservation programs in bringing endangered species back from the brink of extinction. As one of the world’s most endangered mammals, the vast majority of black-footed ferrets living in the wild today are the offspring of a founding captive population. The success of this ongoing breeding program, however, is threatened by inbreeding depression and the observed decline in pregnancy rates since its founding. As the wild and modern captive populations share a genetic history, the greatest difference between the two groups is the captive environment of the breeding program. In this study, we used RNA sequencing and proteomics for the first time in black-footed ferrets to explore whether the diet of wild ferrets versus captive diet variants could explain the differences in fertility and sperm characteristics observed between each population. We find that changes in both the transcriptional and proteomic profile of black-footed ferret ejaculate are strongly associated with differences in fertility, especially in pathways associated with innate immunity and metabolism; that transcriptional changes are further exacerbated by diet. Overall, our results support the hypothesis of ongoing environmental-dependent inbreeding depression in the black-footed ferret, with a need to re-evaluate dietary and environmental parameters of the conservation program; and also illustrates the value of multi-level genomics for conservation management programs.
Project description:Molecular profiling of breast cancer has achieved great depth in defining the mutational landscapes and molecular profiles of primary tumors, though little is still known regarding cancer evolution into a recurrence. Proteogenomic workflows are particularly useful in defining the multi-layered biology of complex diseases by combining genomic, transcriptomic, and proteomic technologies so to inform not only on mutational processes, but also on their repercussion at the effector level, proteins. We employed our recently developed proteogenomic workflow to analyze a cohort of 27 primary breast cancers and their matched loco-regional recurrences by whole genome sequencing, RNA sequencing, and mass spectrometry.
Project description:In all domains of life, the catalysed degradation of RNA facilitates rapid adaption to changing environmental conditions. We identified a virus-encoded protein that directly binds and inhibits the RNA degradation machinery of its bacterial host, allowing efficient accumulation of viral RNA in the infected cell. Encoded by the giant phage фKZ, KZ37/Dip associates with two RNA binding sites of the RNase E component of the Pseudomonas aeruginosa RNA degradosome. Thereby, KZ37/Dip competes with the binding of RNA substrates, resulting in effective inhibition of RNA degradation. The crystal structure of KZ37/Dip (2.2 Å) reveals an unprecedented fold for which there are no identified structural homologues. The protein forms a homo-dimer that resembles a partially opened scroll and binds RNase E through exposed acidic patches on its convex outer surface. Through the activity of KZ37/Dip, фKZ has evolved a unique mechanism to down regulate a key process of its host.
Project description:Chagas disease is endemic in 22 Latin American countries, with approximately 8 million individuals infected worldwide and 10,000 deaths per year. Trypanosoma cruzi, the etiologic agent from Chagas disease, presents an intracellular life cycle in mammalian hosts to sustain infection. Parasite infection activates host cell responses, promoting an unbalance in reactive oxygen species (ROS) in the intracellular environment inducing genomic DNA lesions in the host cell during the early and late stages of infection. To further understand changes in host cell chromatin induced by parasite infection, we investigated proteomic alterations in chromatin caused by parasite infection at early and late infection phases by performing a quantitative proteomic analysis. Interestingly, we identified DNA Damage Repair (DDR) proteins recruited to the chromatin and changes in chromatin remodeling enzymes, suggesting that parasite infection may shape the epigenome of the host cells. Furthermore, the presence of Poly-ADP-ribose Polymerase 1 (PARP-1) and 8-oxoG Glycosylase (OGG1) in the host nucleus confirm the damaged cellular genome. Moreover, we observed that at 6 h post-infection, PARP-1 and X-Ray Repair Cross Complementing 6 (XRRC6) were upregulated in the chromatin of infected cells. Interestingly, mitochondrial proteins involved in oxidative phosphorylation and vesicle-mediated transport proteins were upregulated in the host chromatin at the final stages of infection. Additionally, we have observed that Apoptosis-inducing Factor (AIF) is translocated to the host cell nucleus upon infection, suggesting that cells enter parthanatos type of death. Finally, we also observed that T. cruzi induces changes in chromatin-modifying enzymes. Altogether, this work provides novel data reveals how parasites interfere in the host cells' responses at the chromatin level and important crosstalks that support and disseminate infection.
Project description:We report scRNA-seq data captured from 9,410 cells obtained from the skin of K14E7 transgenic and wildtype C57/BL6 mice. The K14E7 mouse model harbors the HPV16 E7 oncogene driven from a Keratin 14 promoter for keratinocyte-specific expression. We used scRNA-seq to detect and measure E7 transcription with unprecedented accuracy and resolution. With these data, we uncovered transcriptional differences between the individual cells; demonstrated that increased HPV16 E7 copy number is associated with increased expression of E7-induced genes; and showed that E7 expression is predominantly associated with basal keratinocytes.