Name: A U1-70K Protein Interaction Network Reveals a Functional Class of RNA Binding Proteins with Mixed Charge Domains
Keywords: U1-70k

Dataset Information

A U1-70K Protein Interaction Network Reveals a Functional Class of RNA Binding Proteins with Mixed Charge Domains

ABSTRACT: U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and other proteins of the spliceosome complex are mislocalized to cytoplasmic aggregates in Alzheimer’s disease (AD) brain, yet understanding of the specific mechanisms that cause their aggregation is limited. Many of the RNA binding proteins (RBPs) that aggregate in neurodegenerative diseases, including TDP-43 and FUS, self-assemble into RNA granules through disordered low complexity (LC) domains. We report here that a LC domain within U1-70K, that is comprised of tandem arrays of basic (R/K) and acidic (D/E) residues, shares many of the same properties of the Q/N-rich prion-like LC domains found in TDP-43 and FUS. These properties include the ability to self-assemble into oligomers, and to form nuclear granules in cells. To analyze the functional roles of the U1-70K LC domains, we performed co-immunoprecipitation of recombinant U1-70K and deletions lacking the C-terminal LC domain(s) followed by quantitative proteomics. Using a network-driven approach, functional classes of U1-70K interacting proteins were identified that showed a varying dependency on the U1-70K LC domain(s) for their interaction. We characterize a family of structurally homologous RBPs containing U1-70K LC1-like domains including LUC7L3 and RBM25, which require their respective LC1-like domains for reciprocal interactions with U1-70K and for participation in nuclear RNA granules. Finally, we also show that the LC1 domain of U1-70K can interact with Tau from AD brain supporting a hypothesis that mixed charge structural motifs on U1-70K and other RBPs could mediate cooperative interactions with pathological tau isoforms

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

DISEASE(S): Alzheimer's Disease

SUBMITTER: Eric Dammer

LAB HEAD: Nicholas T. Seyfried

PROVIDER: PXD008260 | Pride | 2018-06-21

REPOSITORIES: Pride

ACCESS DATA

Publications

RNA-binding proteins with basic-acidic dipeptide (BAD) domains self-assemble and aggregate in Alzheimer's disease.

Bishof Isaac I Dammer Eric B EB Duong Duc M DM Kundinger Sean R SR Gearing Marla M Lah James J JJ Levey Allan I AI Seyfried Nicholas T NT

The Journal of biological chemistry 20180525 28

The U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and other RNA-binding proteins (RBPs) are mislocalized to cytoplasmic neurofibrillary Tau aggregates in Alzheimer's disease (AD), yet the co-aggregation mechanisms are incompletely understood. U1-70K harbors two disordered low-complexity domains (LC1 and LC2) that are necessary for aggregation in AD brain extracts. The LC1 domain contains highly repetitive basic (Arg/Lys) and acidic (Asp/Glu) residues, referred to as a basic-acidic dipeptide ...[more]

PMID: 29802200

Similar Datasets

Project description:Evidence suggests that epigenetic perturbations are involved in the adverse effects associated with some drugs and toxicants, including certain classes of non-genotoxic carcinogens. Such epigenetic changes (altered DNA methylation and covalent histone modifications) may take place at the earliest stages of carcinogenesis and their identification holds great promise for biomedical research. Here, we evaluate the sensitivity and specificity of genome-wide epigenomic and transcriptomic profiling in phenobarbital (PB)-treated B6C3F1 mice, a well-characterized rodent model of non-genotoxic liver carcinogenesis. Methylated DNA Immunoprecipitation (MeDIP)-coupled microarray profiling of 17,967 promoter regions and 4,566 intergenic CpG islands was combined with genome-wide mRNA expression profiling to identify liver tissue-specific PB-mediated DNA methylation and transcriptional alterations. Only a limited number of significant anti-correlations were observed between PB-induced transcriptional and promoter-based DNA methylation perturbations. However, the constitutive androstane receptor (CAR) target gene Cyp2b10 was found to be concomitantly hypomethylated and transcriptionally activated in a liver tissue-specific manner following PB treatment. Furthermore, analysis of active and repressive histone modifications using chromatin immunoprecipitation revealed a strong PB-mediated epigenetic switch at the Cyp2b10 promoter. Our data reveal that PB-induced transcriptional perturbations are not generally associated with broad changes in the DNA methylation status at proximal promoters and suggest that the drug-inducible CAR pathway regulates an epigenetic switch from repressive to active chromatin at the target gene Cyp2b10. This study demonstrates the utility of integrated epigenomic and transcriptomic profiling for elucidating early mechanisms and biomarkers of non-genotoxic carcinogenesis. 29M-bM-^@M-^S32 days old male B6C3F1/Crl (C57BL/6 M-bM-^YM-^B x C3H/He M-bM-^YM-^@) mice were obtained from Charles River Laboratories (Germany). Animals were allowed to acclimatise for 5 days prior to being randomly divided into two treatment groups (n = 10) and phenobarbital (Sigma 04710, 0.05% (w/v) in drinking water) was administered to one group through ad libitum access to drinking water for 28 days. Mice were checked daily for activity and behavior and sacrificed on the last day of dosing (day 28). Blood was withdrawn for PK analysis and target (liver) and non-target (kidney) tissues removed, split into several sections, frozen in liquid nitrogen and stored at M-bM-^HM-^R80M-BM-0C for subsequent analyses. Total RNA from liver and kidney was purified and processed for Affymetrix gene expression profiling while genomic DNA was prepared for promoter array based methylome analysis using the Methylated DNA immunoprecipitation (MeDIP) procedure. Remaining tissue material was used for chromatin immunoprecipitation (ChIP) to analyze histone modifications at individual promoters. Plasma samples were also collected to evaluate phenobarbital exposure in individual animals by LC-MS.

Dataset Information

A U1-70K Protein Interaction Network Reveals a Functional Class of RNA Binding Proteins with Mixed Charge Domains

Publications

RNA-binding proteins with basic-acidic dipeptide (BAD) domains self-assemble and aggregate in Alzheimer's disease.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure