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Analysis to evaluate the presence of 5’ cap in intragenic lncRNAs

ABSTRACT: RNA aliquots were digested with 5’-phosphate-dependent exonuclease (5'-exo) following pre-treatment with tobacco acid pyrophosphatase (TAP) to release the 5’ cap and render the RNA susceptible to 5’ exonuclease digestion (TAP+/5'-exo+). Two color array hybridizations were performed and TAP+/5'-exo+ samples were compared with TAP-/5'-exo+ control samples. Two-condition experiment, TAP+/5'-exo+ vs. TAP-/5'-exo+ treated total RNA samples. Biological replicates: 4 with dye swap

ORGANISM(S): Homo sapiens

SUBMITTER: Eduardo Reis

PROVIDER: E-GEOD-62984 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Analysis to evaluate the presence of 5’ cap in intragenic lncRNAs

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Project description:Heat shock protein 90 (HSP90) is a highly abundant molecular chaperone that interacts with many other intracellular proteins to regulate various cellular processes. However, compositions of the HSP90-interacting complex remain underinvestigated. This study thus aimed to characterize such complex in human embryonic kidney (HEK293T) cells under normal physiologic state using tandem affinity purification (TAP) followed by protein identification using an ultrahigh-resolution tandem mass spectrometer (Qq-TOF MS/MS). A total of 32 proteins, including four forms of HSP90 and 16 novel HSP90-interacting partners, were successfully identified from this complex using TAP control to subtract non-specific binders. Co-immunoprecipitation followed by immunoblotting and immunofluorescence co-staining confirmed the association of HSP90 with known (HSP70, α-tubulin, and β-actin) and novel (vimentin, calpain-1, and importin-β1) partners. Knockdown of HSP90 by small-interfering RNA (siHSP90) caused significant changes in levels of HSP70, α-tubulin, β-actin, vimentin, and calpain-1, all of which are calcium oxalate (CaOx) crystal-binding proteins that play significant roles in kidney stone formation. Moreover, crystal-binding capability was significantly decreased in siHSP90-transfected cells as compared to non-transfected control and siControl-transfected cells. In summary, we report herein a number of novel HSP90-interacting proteins in renal cells and demonstrate the potential role of HSP90-interacting complex in kidney stone formation.

2018-12-17 | PXD011432 | Pride

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