Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Widespread RNA Binding by Chromatin Associated Proteins

ABSTRACT: Recent evidence suggests that RNA interaction can regulate the activity and localization of DNA binding proteins, particularly chromatin-associated proteins. However, it is unknown if these observations are specialized instances for a few key RNAs and chromatin factors in specific contexts, or a general mechanism underlying the establishment of chromatin state and regulation of gene expression. Here, we introduce formaldehyde RNA ImmunoPrecipitation (fRIP-Seq), a sensitive method for cataloging RNA-protein interactions, to survey the RNA associated with a panel of 24 chromatin-associated and traditional RNA binding proteins. For each protein that reproducibly bound measurable quantities of bulk RNA (90% of the panel), we detected enrichment for hundreds to thousands of both noncoding and mRNA transcripts. We found that the enriched sets of RNA share biochemical, functional, and epigenetic properties. Thus, these data provide strong evidence that non-random RNA association is a common feature across diverse classes of chromatin modifying complexes. RNA associated with 24 different proteins using fRIP was compared to total RNA-seq

ORGANISM(S): Homo sapiens

SUBMITTER: David Kelley

PROVIDER: E-GEOD-67963 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Hepatocellular carcinoma (HCC) is the second prominent cause of cancer-associated death worldwide. Usually, HCC is diagnosed in advanced stages, where sorafenib, a multiple target ty-rosine kinase inhibitor, is used as the first line of treatment. Unfortunately, resistance to sorafenib is usually encountered within six months of the treatment. Therefore, there is a critical need to identify the underlying reasons for drug resistance. In the present study, we investigated the proteomic and metabolomics alterations accompanying to sorafenib resistance in hepatocellular carcinoma Hep3B cells by employing ultra-high-performance liquid chromatography quadrupole time of flight mass spectrometry (UHPLC-QTOF-MS). The Bruker Human Metabolome Database (HMDB) library was used to identify the differentially abundant metabolites through MetaboScape 4.0 software (Bruker). For protein annotation and identification, the Uniprot proteome for Homo sapiens (Human) da-tabase was utilised through MaxQuant. The results revealed that 27 metabolites and 18 proteins were significantly dysregulated due to sorafenib resistance in Hep3B cells compared to the parental phenotype. D-alanine, L-proline, o-tyrosine, succinic acid and phosphatidylcholine (PC, 16:0/16:0) were among the significantly altered metabolites. Ubiquitin carboxyl-terminal hydrolase isozyme L1, mitochondrial superoxide dismutase, UDP-glucose-6-dehydrogenase, sorbitol dehydrogenase and calpain small subunit 1 were among the significantly altered proteins. The findings revealed that resistant Hep3B cells demonstrated significant alterations in amino acid and nucleotide met-abolic pathways, energy production pathways and other pathways related to cancer aggressive-ness, migration, proliferation, and drug-resistance. Joint pathway enrichment analysis unveiled unique pathways, including the antifolate resistance pathway and other important pathways that maintain cancer cells' survival, growth, and proliferation. Collectively, the results identified po-tential biomarkers for sorafenib-resistant HCC and gave insights into their role in chemotherapeutic drug resistance, cancer initiation, progression, and aggressiveness, which may contribute to better prognosis and chemotherapeutic outcomes.

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Widespread RNA Binding by Chromatin Associated Proteins

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