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RNA-binding proteins control glycolysis via regulation of mRNA stability under chronic hypoxia

ABSTRACT: RBPs reliably binding to poly(A)-tailed RNAs were identified by comparing eRIC-MS data from same condition with irradiation (with UV) and without irradiation (without UV).

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: shungo adachi

PROVIDER: PXD051523 | JPOST Repository | Wed Oct 16 00:00:00 BST 2024

REPOSITORIES: jPOST

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	21a22301.raw	Raw
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RNA-Seq analysis to assess gene expression levels in MDA-MB-231 cells on treatment with (5-oxo-2-dibenzothienylmethyl)triphenylphosphonium (1-SO) and (2-dibenylthienylmethyl)triphenylphosphonium (1-S) under different UV-A irradiation conditions

Project description:We report the gene expression levels in MDA-MB-231 cells on treatment with (5-oxo-2-dibenzothienylmethyl)triphenylphosphonium (1-SO) and (2-dibenylthienylmethyl)triphenylphosphonium (1-S) irradiated with UV-A light. These gene expression levels were then compared to control conditions where the cells were treated with the compounds but were not irradiated with UV-A light. The samples were additionally compared to the cells treated with 1% DMSO in DMEM media (with and without UV-A irradiation). Results: From the first set of experiments, 30 minutes of UV-A irradiation upregulated 3 and downregulated 5 genes compared to cells with no UV-exposure. The experiments also indicated that 1-SO in UV-A irradiation significantly affected gene expression whereas 1-SO without UV-A did not have a notable effect on expression levels. However, 1-S affected gene expression levels significantly with or without UV-A irradiation.

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Solar UV-B regulation of high altitude maize

Project description:To initiate a genomic scale analysis of high altitude maize, we performed expression-profiling experiments using Unigene I cDNA arrays from the Maize Gene Discovery Project that contain 5664 cDNAs printed in triplicate spots; a triplicate set for nearly all cDNAs was printed in at least one additional location on each slide, thus there is a minimum of 6 spots for each cDNA per slide. Four-week-old maize plants grown in the field under the three irradiation regimes no UV-B, solar UV-B or UV-B supplemental were used for the experiments. Samples were collected from adult leaves 9 and 10; samples from 6 plants were pooled for preparation of poly(A)+ RNA. Keywords: parallel sample

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UPA-Seq: Prediction of functional lncRNAs using the sensitivities to UV-crosslinking

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Identification of mRNA processing complexes bound to histone H2A.2 3’ untranslated region

Project description:Processing of 3’ untranslated region (3’-UTR) of precursor messenger RNAs (pre-mRNA) is a fundamental step in mRNA maturation, where the mRNA transcript is cleaved at a specific site, located downstream the open reading frame of the encoded gene. The position of the cleavage site is determined by cis-acting RNA sequence elements, which are recognized with high specificity by large 3’ end processing multiprotein complexes. Two main categories of metazoan 3’ pre-mRNA processing have been identified so far, describing elaboration of either canonical mRNAs – occurring during all phases of the cell cycle and containing a characteristic Poly-Adenylation Signal (PAS) element – or histone mRNAs – prevalently occurring during the S phase and containing a Histone Downstream Element (HDE). In this work, we isolate both human endogenous canonical and histone 3’ pre-mRNA processing complexes from human nuclear extracts by using a pre-mRNA containing the 3’UTR sequence of replication-dependent histone H2A.2. This H2A.2 pre-mRNA (H2A_4m), containing both an HDE sequence and a PAS element in a native overlaid position, was modified with a 5’ photocleavable biotin tag, and with modification of few bases to allow complex assembly and purification by affinity chromatography on streptavidin-agarose beads, elution by UV irradiation and subsequent mass spectrometric identification of bound 3’ mRNA processing factors.

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Identification of human mRNA processing complexes bound to histone H2A.2 3’ untranslated region

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Revealing disulfide bond formation in GSDME upon UVC irradiation under non-reducing conditions

Project description:It is widely acknowledged that gasdermin family proteins, which are known as the executors of pyroptosis, undergo protease-mediated cleavage prior to inducing pyroptosis. Here, we unexpectedly discovered a non-canonical form of pyroptosis mediated by full-length GSDME (FL-GSDME) without any proteolytic cleavage. Upon intense ultraviolet (UV) irradiation-triggered DNA damage, hyperactivation of nuclear PARP1 led to extensive formation of poly(ADP-ribose) (PAR) polymers and then release to the cytoplasm.These PAR polymers activate PARP5 to catalyze GSDME PARylation, resulted in a conformational change in GSDME that relieved autoinhibition imposed by its C terminus on the N terminus. On the other hand, intense UV irradiation boosted mitochondrial fission-dependent generation of mitochondrial reactive oxygen species (mito-ROS), further promoting cytochrome c-catalyzed peroxidation of cardiolipin. This lipid-ROS signal was then sensed by PARylated-GSDME and then induced oxidative oligomerization of GSDME, which facilitated FL-GSDME plasma membrane targeting for perforation, eventually inducing pyroptosis. Reagents that concurrently stimulate PARPs activity and lipid-ROS also induced sequential modifications i.e., PARylation and oxidation of FL-GSDME and synergistically promoted pyroptotic cell death. Overall, our findings elucidate a novel mechanism underlying cleavage-independent function of GSDME in executing cell demise, further enriching the paradigms and cognition of FL-GSDME-mediated non-canonical pyroptosis.

2024-06-17 | PXD051840 | Pride

Transcription elongation rate affects nascent histone pre-mRNA folding and 3’ end processing

Project description:We report that slow transcription by mutant RNA pol II caused accumulation of polyadenylated histone mRNAs that extend past the stem loop processing site. UV irradiation, which decelerates pol II elongation, also induced long poly(A)+ histone transcripts. Inhibition of 3’ processing by slow pol II correlates with failure to recruit SLBP to histone genes. Chemical probing of nascent RNA structure showed that the stem loop fails to fold in transcripts made by slow pol II, thereby explaining the absence of SLBP and failure to process 3’ ends. These results show that regulation of transcription speed can modulate pre-mRNA processing by changing nascent RNA structure, and suggest a mechanism by which alternative processing could be controlled

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UV-B regulation of microRNAs in maize

Project description:Differential expression of microRNAs was studied in maize leaves after an 8-h-exposure under UV-B light. As a control, plants were kept in the greenhouse in the absence of UV-B 4-week maize plants were grown in the greenhouse in the absence of UV-B. Then, they were divided in two groups. One group was treated with UV-B lights provided once for 8 h, starting 3 h after the beginning of the light period, using fixtures mounted 30 cm above the plants (Phillips, F40UVB 40 W and TL 20 W/12) at a UV-B intensity of 2 W m-2, UV-A: 0.65 W m-2. The bulbs were covered with cellulose acetate to exclude wavelengths <280 nm. For the second control group, plants were exposed for 8 h under the same lamps covered with polyester film (no UV-B treatment, UV-B: 0.04 W m-2, UV-A: 0.4 W m-2). Lamp output was recorded using a UV-B/UV-A radiometer (UV203 A+B radiometer, Macam Photometrics, Ltd, Livingston, UK) to insure that both the bulbs and filters provided the designated UV dosage in all treatments. Leaf samples were collected immediately after irradiation. RNA was extracted immediately after the treatments, and used for the microRNA microarray experiments.

2013-10-31 | E-GEOD-19768 | biostudies-arrayexpress

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