Transcriptome innovations in primates revealed by single-molecule long-read sequencing
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion Lumos
ORGANISM(S): Pongo Pygmaeus (bornean Orangutan) Homo Sapiens (human) Pan Troglodytes (chimpanzee) Gorilla Gorilla Macaca Mulatta (rhesus Macaque)
TISSUE(S): B-lymphoblastoid Cell Line
SUBMITTER: 
Luis Ferrández
LAB HEAD: Tomàs Marquès Bonet
PROVIDER: PXD031213 | Pride | 2022-05-31
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| raw.rar | Other | |||
| reanalysis-feb21-all-pacbio-db-_1_.pdResult | Other |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:Existing methods to analyse RNA localisation are constrained to specific RNAs or subcellular niches, precluding the cell-wide mapping of RNA. We present Localisation of RNA (LoRNA), which maps, at once, RNAs to membranous (nucleus, ER and mitochondria) and membraneless compartments (cytosol, nucleolus and phase-separated granules). Simultaneous interrogation of all RNA locations allows the system-wide quantification of RNA proportional distribution and the comprehensive analysis of RNA subcellular dynamics. Moreover, we have re-engineered the LOPIT (Localisation Of Proteins by Isotope Tagging) method, enabling integration with LoRNA, to jointly map RNA and protein subcellular localisation. Applying this framework, we obtain a global re-localisation map for 31839 transcripts and 5314 proteins during the unfolded protein response, uncovering that ER-localised transcripts are more efficiently recruited to stress granules than cytosolic RNAs, and revealing eIF3d is key to sustain cytoskeletal function. Overall, we provide the most exhaustive map to date of RNA and protein subcellular dynamics.
2022-01-25 | PXD030456 | Pride
Project description:Notch signaling relies on ligand-induced proteolysis to liberate a nuclear effector that drives cell fate decisions. The location and timing of individual steps required for proteolysis and movement of Notch from membrane to nucleus, however, remain unclear. Here, we use proximity labeling with quantitative multiplexed mass spectrometry to monitor the microenvironment of endogenous Notch2 after ligand stimulation in the presence of a gamma secretase inhibitor and then as a function of time after inhibitor removal. Our studies show that gamma secretase cleavage of Notch2 occurs in an intracellular compartment and that formation of nuclear complexes and recruitment of chromatin-modifying enzymes occurs within 45 minutes of inhibitor washout. This work provides a spatiotemporal map of unprecedented detail tracking the itinerary of Notch from membrane to nucleus after activation and identifies molecular events in signal transmission that are potential targets for modulating Notch signaling activity.
2023-07-03 | PXD039008 | Pride
Project description:Notch signaling relies on ligand-induced proteolysis to liberate a nuclear effector that drives cell fate decisions. The location and timing of individual steps required for proteolysis and movement of Notch from membrane to nucleus, however, remain unclear. Here, we use proximity labeling with quantitative multiplexed mass spectrometry to monitor the microenvironment of endogenous Notch2 after ligand stimulation in the presence of a gamma secretase inhibitor and then as a function of time after inhibitor removal. Our studies show that gamma secretase cleavage of Notch2 occurs in an intracellular compartment and that formation of nuclear complexes and recruitment of chromatin-modifying enzymes occurs within 45 minutes of inhibitor washout. This work provides a spatiotemporal map of unprecedented detail tracking the itinerary of Notch from membrane to nucleus after activation and identifies molecular events in signal transmission that are potential targets for modulating Notch signaling activity.
2023-07-03 | PXD039010 | Pride
Project description:practipractical access to the portimines and analogs thereof simplified the development of photoaffinity analogs, which were used in chemical proteomic experiments to identify a primary target of portimine A as the 60S ribosomal export protein NMD3cal access to the portimines and analogs thereof simplified the development of photoaffinity analogs, which were used in chemical proteomic experiments to identify a primary target of portimine A as the 60S ribosomal export protein NMD3
2023-07-12 | PXD041911 | Pride
Project description:SLC15A4 is an endolysosome-resident transporter intimately linked with autoinflammation and autoimmunity. Specifically, SLC15A4 is critical for Toll-like receptor (TLR) 7-9 as well as the nucleotide-binding oligomerization domain-containing protein (NOD) signaling in several immune cell subsets. Notably, SLC15A4 is essential for the development of systemic lupus erythematosus in murine models and is associated with autoimmune conditions in humans. Despite its therapeutic potential, to our knowledge no chemical probes have been developed that target SLC15A4. Here, we use an integrated chemical proteomics approach to develop a suite of chemical tools, including first-in-class functional inhibitors, for SLC15A4. We demonstrate SLC15A4 inhibitors described herein suppress endolysosomal TLR and NOD functions in a variety of human and mouse immune cells, furnish evidence of their ability to suppress inflammation in vivo and in clinical settings, and provide insights into their mechanism of action. Our findings establish SLC15A4 as a druggable target for the treatment of autoimmune/autoinflammatory conditions.
2023-11-29 | PXD045715 | Pride
Project description:Lamins are intermediate filament proteins responsible for nuclear mechanical integrity. Though linked to multiple heritable diseases, lamin structure and that of other intermediate filaments remains elusive. We employed cross-linking mass spectrometry to gain structural insights into lamin A dimer and tetramer structure. While confirming the parallel coiled-coil rod, we report that, contrary to prediction, rod linker regions are highly flexible and compressible. This explains the recently reported rod shortening in the assembled polymer and aspects of intermediate filament stretch properties. We further elucidate an extended interface in lamin A tetramers where both head and tail unstructured regions flanking the rod of each dimer act as polar bridges to stabilize lamin head-to-tail assembly. Furthermore, changes in these regions between dimer and tetramer forms suggest an ordered polymer assembly. Importantly, several residues mutated in laminopathies disrupt this interface and impair assembly, potentially explaining their role in disease.
2019-07-12 | PXD008337 | Pride
Project description:The nucleosome acidic patch is a major interaction hub for chromatin, providing a platform for enzymes to dock and orient for nucleosome-targeted activities. In order to define the molecular basis of acidic patch recognition proteome-wide, we performed an amino acid resolution acidic patch interactome screen. We discovered that the histone H3 lysine 36 (H3K36) demethylase KDM2A, but not its closely related paralog, KDM2B, requires the acidic patch for nucleosome binding. These KDM2 family JumonjiC (JmjC) domain lysine demethylases are critical to heterochromatin formation and are commonly misregulated in cancer. Despite fundamental roles in transcriptional regulation in health and disease, the molecular mechanisms governing nucleosome substrate specificity of KDM2A/B, or any other JmjC lysine demethylases, remain unclear. We used a covalent JmjC inhibitor to solve cryo-EM structures of KDM2A and KDM2B trapped in action on the nucleosome. Our structures show that KDM2-nucleosome binding is paralog-specific and facilitated by dynamic nucleosomal DNA unwrapping and histone charge shielding that mobilize the H3K36 sequence for demethylation.
2023-02-14 | PXD032791 | Pride
Project description:Streptococcus suis serotype 2 (SS2), a major swine pathogen and an emerging zoonotic agent, has greatly challenged global public health. Systematical information about host immune response to the infection is important for understanding the molecular mechanism of diseases. Here, we investigated the global expression changes in spleen following SS2 infection using the Affymetrix Porcine Genechip. Our findings indicate previously unrecognized gene transcription changes in case of SS infection in vivo. Our data should provide new clues for immune response in mammals and identification of candidate genes related to SS resistance. All animal tissue collection procedures were performed according to protocols approved by The Hubei Province, PR China for Biological Studies Animal Care and Use Committee. Piglets at 35 days old were determined to be S.suis 2-free by antibody-based ELISA before artificial bacterial challenges. Each piglet was intranasally challenged with 2×106 colony-forming units (CFU) per millilitre of SS2 strain 05ZY or ΔHP0197. A total of 4 piglets were challenged with 05ZY, 4 were challenged with ΔHP0197, and 4 pigs were used as controls. These three groups were raised in isolated facilities. Nine microarrays were used in the experiment, corresponding to the RNAs from spleen tissues of piglets with arthritis after SS2 infection and spleen tissues of piglets with no clinical signs and three controls.
2010-11-24 | E-GEOD-23596 | biostudies-arrayexpress
Project description:Investigation of whole genome expression pattern of 60 and 72 hours post fertilization Danio Rerio embryos exposed to TMT and vehicle control Embryos were exposed to 10uM TMT or control from 48hpf to 60 or 72 hpf. Three replicates were collected for each time point. 40 embryos were pooled to comprise a replicate.
2011-03-23 | E-GEOD-28131 | biostudies-arrayexpress
Project description:The rat pheochromocytoma cell line PC12 cells were cultured in complete DMEM till 80% confluence, then placed at 5000 cells per squared cm. Cells were then plated in 24-well plates for cell viability assay and in T75 flasks for RNA isolation. Medium was replaced with serum-free fresh medium for 12 hours prior to TMT treatment. Gene expression patterns were then analysed using Rat Expression Array 230A Experiment Overall Design: In this study we analize gene expression patterns in PC12 cells treated with Trimethyltin (TMT). We utilized control cells (untreated) and two different concentration (1 and 5) Experiment Overall Design: We used three biological replicates, for the three concentration tested, according to MIAME guidelines Experiment Overall Design: (total 9 chips were used in this study).
2009-04-29 | E-GEOD-5073 | biostudies-arrayexpress