Comparision of La-RNA-binding between wild type La and sumoylation deficient La mutant (K41/200R) in HEK293 cells.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE102842 | GEO | 2017/11/22
SECONDARY ACCESSION(S): PRJNA399094
REPOSITORIES: GEO
Similar Datasets
Project description:Comparision of La-RNA-binding between wild type La and sumoylation deficient La mutant (K41/200R) in HEK293 cells.
| PRJNA399094 | ENA
Project description:To identify SmaugM-bM-^@M-^Ys target mRNAs on a genome-wide scale we used ribonucleoprotein (RNP) co-immunoprecipitation followed by microarray analysis of the co-purifying mRNAs (RIP-Chip). Extracts, prepared from wild-type embryos collected 0-3 hours post-egglaying, were immunoprecipitated with an anti-Smaug antibody (Smaug RIPs) while control immunoprecipitations using non-immune serum served as a negative control (control RIPs). Genome-wide transcript expression in wild-type embryos were also assessed and used as reference. There are 11 array experiments presented here: 1. gene expression profiling of total mRNA sample extracted from wild-type 0-3 hour embryos (3 technical replicates performed using a pooled input reference sample); 2. RNA co-immunoprecipitations of endogenous Smaug (Smaug RIPs) from wild-type 0-3 hour embryos (3 biological replicates and 1 technical replicates); 3. control RNA co-immunoprecipitations (control RIPs) from wild-type 0-3 hour embryos (3 biological replicates and 1 technical replicates).
2013-12-03 | E-GEOD-49943 | biostudies-arrayexpress
Project description:To identify Smaug’s target mRNAs on a genome-wide scale we used ribonucleoprotein (RNP) co-immunoprecipitation followed by microarray analysis of the co-purifying mRNAs (RIP-Chip). Extracts, prepared from wild-type embryos collected 0-3 hours post-egglaying, were immunoprecipitated with an anti-Smaug antibody (Smaug RIPs) while control immunoprecipitations using non-immune serum served as a negative control (control RIPs). Genome-wide transcript expression in wild-type embryos were also assessed and used as reference.
2013-12-03 | GSE49943 | GEO
Project description:We recently identified lysine L-lactylation (KL-la) on histones that can be labelled by L-lactate, the end-product of glycolysis. KL-la has two structural isomers, namely N--(carboxyethyl) lysine (Kce) and lysine D-lactylation (KD-la), which can also be caused by metabolites associated with glycolysis. It is unknown if perturbations of glycolysis can lead to dysregulation of KD-la and Kce, in addition to KL-la. Further, current methods have a difficulty to distinguish among these isomers in cellular contexts. To investigate these questions, we first generated specific antibodies against each one of these three modifications. These reagents enable us to distinguish these three isomers. We demonstrated that KL-la, but not KD-la and Kce, is dynamically regulated by glycolysis. KD-la and Kce occur mainly when the major glycolytic pathway is blocked downstream or when the glyoxalase system is incomplete. This result was also independently confirmed by orthogonal HPLC-mass spectrometry, showing that KL-la is the predominant isomer of lactylation on cellular histones. Finally, we demonstrated that lactyl-CoA, an intermediate between L-lactate and lactylation, is dynamically regulated by glycolysis and is positively correlated with KL-la. Thus, our study clearly shows that KL-la, but not KD-la and Kce, is the major glycolytic- and the Warburg-effect associated responsive modification in cells.
2023-03-13 | PXD040840 | iProX
Project description:In this study we investigated the steady-state growth of Methylotuvimicrobium alcaliphilum 20ZR in media containing calcium (Ca) or lanthanum (La, a REE element). RNA-seq profiling of Methylomicrobium alcaliphilum strain 20ZR in bioreactor on methane. Sample cultures, La-optimum, La-CH4 limited, Ca-optimum and Ca-CH4 limited, were collected and immediately transferred into tubes containing 5 ml of the stop solution (5% water-equilibrated phenol in ethanol). It was found, that cells supplemented with La show a higher growth rate compared to Ca-cultures; however, the efficiency of carbon conversion, estimated as biomass yield, is higher in cells grown with Ca. The study was financially supported by DOE under FOA DE-FOA-0001085 and by NSF-CBET award 1605031
2024-02-02 | GSE253414 | GEO
Project description:The Lupus autoantigen (La) is a single-stranded RNA-binding protein that stabilizes RNA polymerase III (pol III) transcripts and supports RNA folding. In addition, La has been implicated in different steps of the mammalian small RNA pathway. Here, we have analyzed effects of La depletion on the Argonaute (Ago)-bound small RNAs in human cells. We find that in the absence of La, distinct tRNA fragments are loaded into Ago protein complexes and our data suggests that La prevents the production and loading of such tRNA fragments. However, one specific isoleucine tRNA escapes this regulation and produces both a functional tRNA as well as a microRNA (miRNA). We demonstrate that fully complementary 5' leader and 3' trailer of the pre-tRNA-Ile form a double-stranded RNA molecule that has low affinity to La. Instead, Exportin 5 (Xpo5) recognizes it as miRNA precursor and transports it into the cytoplasm for Dicer processing and Ago loading. Thus, La functions as gatekeeper to ensure correct tRNA generation and to protect the miRNA pathway from potentially functional tRNA fragments.
2016-06-22 | GSE77897 | GEO
Project description:The Lupus autoantigen (La) is a single-stranded RNA-binding protein that stabilizes RNA polymerase III (pol III) transcripts and supports RNA folding. In addition, La has been implicated in different steps of the mammalian small RNA pathway. Here, we have analyzed effects of La depletion on the Argonaute (Ago)-bound small RNAs in human cells. We find that in the absence of La, distinct tRNA fragments are loaded into Ago protein complexes and our data suggests that La prevents the production and loading of such tRNA fragments. However, one specific isoleucine tRNA escapes this regulation and produces both a functional tRNA as well as a microRNA (miRNA). We demonstrate that fully complementary 5' leader and 3' trailer of the pre-tRNA-Ile form a double-stranded RNA molecule that has low affinity to La. Instead, Exportin 5 (Xpo5) recognizes it as miRNA precursor and transports it into the cytoplasm for Dicer processing and Ago loading. Thus, La functions as gatekeeper to ensure correct tRNA generation and to protect the miRNA pathway from potentially functional tRNA fragments.
2016-06-22 | GSE76676 | GEO
Project description:La proteins bind the UUU-3’OH sequence found at the 3’-end of nascent RNA polymerase III transcripts, including pre-tRNAs, using a tandem arrangement of a winged-helix fold La motif (LaM) and an adjacent RNA recognition motif (RRM). La binding in diverse species results in protection of the 3’-end from exonucleases, stabilization of the pre-tRNA species and promotion of pre-tRNA folding until the UUU-3’OH containing trailer is endonucleolytically cleaved. Based on sequence conservation in the LaM, the Tetrahymena thermophila protein MLP1 (and related factors in other alveolates) has been hypothesized to function as a genuine La protein, despite the absence of the adjacent RRM found in La proteins of all prior investigated species. We show that MLP1 functions as a genuine La protein in that it binds and affects the processing of pre-tRNAs in T. thermophila and when expressed as a heterologous factor in fission yeast, however, unlike in other examined eukaryotes, depletion of MLP1 results in 3’-trailer stabilization. We also observed that 3’-trailers in T. thermophila are uniquely shortened relative to other examined eukaryotes, and that 5’-leaders in this species have evolved to disfavour pre-tRNA leader/trailer pairing. Our data suggest that the variant MLP1 architecture relative to other genuine La proteins is linked to an altered mechanism of tRNA processing in T. thermophila.
2022-09-13 | GSE199642 | GEO