Project description:Rabies virus (RABV) is the causative agent of rabies, a severe neurological disease with a 100% fatality rate for symptomatic infection with no therapeutic options. After invading a cell, the rabies virus interacts extensively with host proteins to replicate within the host and circumvent antiviral defense mechanisms. As the RNA of this virus only encodes five proteins, many of the host-viral interactions are mediated by the multifunctional phosphoprotein (P-protein). The functional diversity of P-protein is in part due to discrete functions of the individual domains (two regions of intrinsic disorder separated by a dimerization domain and an ordered C-terminal domain) but also through the expression of the five P-protein isoforms (P1-P5), that differ through N-terminal truncations. These isoforms have distinct phenotypes whereby they show differing organelle localization and interact with different cellular components. The cytosolic P1 is important for viral replication as a cofactor for the RNA polymerase (L protein) and a chaperon of the viral RNA binding N protein. P1 is also a known factor for binding and inhibiting the antiviral transcription factor, STAT1. P3, however, lacks the regions for binding L and N protein, and has gained new functions absent in P1, including microtubule association and bundling, accumulation in the nucleolus. We have also found that P3 binds RNA, whereas P1 does not. Both P1 and P3 have been shown to undergo liquid-liquid phase separation (LLPS), however it is unclear how this property impacts RNA binding. Here we have used crosslinking mass spectrometry method to characterize the structure of P1 and P3 by mapping the proximity between the domains of P-protein P1, P3 as well as P3 mutants P3-D289N and P3-K214A/R260A (called P3-KRm). We have measured abundances of individual crosslinks to determine conformational differences of the four proteins and uncover the structural and functional differences of P1 and P3.
Project description:Transcriptome profile was obtained from a set of human embryonic stem cell (hESCs) line (WA09: H9) with different passage numbers (P1: 40s, P2: 100s, P3: 200s, P4: 300s passage). Culture adaptation occurs in hESCs during repeated in vitro culture to acquire ‘survival advantage’ to be highly resistant to various stresses. In special, difference in gene expression profile of cell death or apoptotic gene signature was evident between P1/P2 and P3/P4 hESCs.
Project description:Purpose: we want to see gene expression changes during in vitro expansion of VM-derived NSCs (VM-NSCs) with cell passges in the absence or presence of Lin28a overexpression. changes upon Lin28 overexpression in P1 and P3 stages of Neural stem cells. RNA-seq, sRNA-seq, and Polysome-seq with/without Lin28 overexpression in P1 and P3 stages of Neural stem cells.
Project description:Expression arrays comparing Campylobacter jejuni 11168 before and after serial passage in C57 BL/6 IL-10 deficient mice. Gene expression was compared during exponential growth in Bolton broth. Unpassaged (p0) C. jejuni 11168 was compared to the same strain after 1 passage (p1) and after three passages (p3) through the mice. Biological replicates: 4 for p0 v. p1, 3 for p0 v. p3
Project description:TuBo cell line (E) was compared to passage 1 (P1), 2 (P2) and 3 (P3) mammospheres to detect specific transcription isoforms associated to cancer stem cell.
Project description:Chromatin accessibility change of chondrocytes in vitro remains unclear. We performed ATAC-seq of P1,P3, and P6 cells in vitro to explore chromatin accessibility change.
Project description:RNA viruses must achieve complex replication and immune evasion functions using limited coding capacity. The rabies virus P protein is a multifunctional viral protein expressed in multiple isoforms via alternative translation. In this study, we investigate how structural and functional diversity arises between two isoforms—P1 (full-length) and P3 (a naturally truncated form)—and how these differences influence host protein interactions. We used GFP-tagged P1 and P3 proteins expressed in HEK293T cells to perform quantitative immunoprecipitation-mass spectrometry (IP-MS) and define isoform-specific interactomes. This dataset includes raw and processed IP-MS data for GFP-P1, GFP-P3, and GFP control (each in quadruplicate), and supports the conclusion that conformational and functional diversification of viral proteins enables expanded host interface capacity. This study provides new mechanistic insights into how viruses exploit isoform diversity and RNA-driven interactions to overcome genome limitations.