ABSTRACT
Intrinsically disordered regions (IDRs) represent a large percentage of overall nuclear protein content. The prevailing dogma is that IDRs engage in non-specific interactions because they are poorly constrained by evolutionary selection. Here, we demonstrate that condensate formation and heterotypic interactions are distinct and separable features of an IDR within the ARID1A/B subunits of the mSWI/SNF chromatin remodeler, cBAF, and establish distinct "sequence grammars" underlying each contribution. Condensation is driven by uniformly distributed tyrosine residues, and partner interactions are mediated by non-random blocks rich in alanine, glycine, and glutamine residues. These features concentrate a specific cBAF protein-protein interaction network and are essential for chromatin localization and activity. Importantly, human disease-associated perturbations in ARID1B IDR sequence grammars disrupt cBAF function in cells. Together, these data identify IDR contributions to chromatin remodeling and explain how phase separation provides a mechanism through which both genomic localization and functional partner recruitment are achieved.
Subject(s)
Chromatin Assembly and Disassembly , Multiprotein Complexes , Nuclear Proteins , Humans , Chromatin , DNA-Binding Proteins/chemistry , Intrinsically Disordered Proteins/genetics , Nuclear Proteins/metabolism , Transcription Factors/metabolism , Multiprotein Complexes/chemistry , Multiprotein Complexes/metabolismABSTRACT
Identifying host genes essential for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has the potential to reveal novel drug targets and further our understanding of Coronavirus Disease 2019 (COVID-19). We previously performed a genome-wide CRISPR/Cas9 screen to identify proviral host factors for highly pathogenic human coronaviruses. Few host factors were required by diverse coronaviruses across multiple cell types, but DYRK1A was one such exception. Although its role in coronavirus infection was previously undescribed, DYRK1A encodes Dual Specificity Tyrosine Phosphorylation Regulated Kinase 1A and is known to regulate cell proliferation and neuronal development. Here, we demonstrate that DYRK1A regulates ACE2 and DPP4 transcription independent of its catalytic kinase function to support SARS-CoV, SARS-CoV-2, and Middle East Respiratory Syndrome Coronavirus (MERS-CoV) entry. We show that DYRK1A promotes DNA accessibility at the ACE2 promoter and a putative distal enhancer, facilitating transcription and gene expression. Finally, we validate that the proviral activity of DYRK1A is conserved across species using cells of nonhuman primate and human origin. In summary, we report that DYRK1A is a novel regulator of ACE2 and DPP4 expression that may dictate susceptibility to multiple highly pathogenic human coronaviruses.
Subject(s)
COVID-19 , Virus Internalization , Animals , Humans , Angiotensin-Converting Enzyme 2 , COVID-19/genetics , COVID-19/metabolism , Dipeptidyl Peptidase 4 , Middle East Respiratory Syndrome Coronavirus/genetics , SARS-CoV-2/genetics , Severe acute respiratory syndrome-related coronavirus/genetics , Dyrk KinasesABSTRACT
Highly coordinated changes in gene expression underlie T cell activation and exhaustion. However, the mechanisms by which such programs are regulated and how these may be targeted for therapeutic benefit remain poorly understood. Here, we comprehensively profile the genomic occupancy of mSWI/SNF chromatin remodeling complexes throughout acute and chronic T cell stimulation, finding that stepwise changes in localization over transcription factor binding sites direct site-specific chromatin accessibility and gene activation leading to distinct phenotypes. Notably, perturbation of mSWI/SNF complexes using genetic and clinically relevant chemical strategies enhances the persistence of T cells with attenuated exhaustion hallmarks and increased memory features in vitro and in vivo. Finally, pharmacologic mSWI/SNF inhibition improves CAR-T expansion and results in improved anti-tumor control in vivo. These findings reveal the central role of mSWI/SNF complexes in the coordination of T cell activation and exhaustion and nominate small-molecule-based strategies for the improvement of current immunotherapy protocols.
Subject(s)
Chromatin Assembly and Disassembly , Chromosomal Proteins, Non-Histone , Chromosomal Proteins, Non-Histone/genetics , Chromosomal Proteins, Non-Histone/metabolism , Transcription Factors/metabolism , Chromatin/genetics , Transcriptional ActivationABSTRACT
The marine bacterium Vibrio vulnificus infects humans via food or water contamination, leading to serious manifestations, including gastroenteritis, wound infections, and septic shock. Previous studies suggest phylogenetic Lineage 1 isolates with the vcgC allele of the vcg gene cause human infections, whereas Lineage 2 isolates with the vcgE allele are less pathogenic. Mouse studies suggest that some variants of the primary toxin could drive more serious infections. A collection of 109 V. vulnificus United States human clinical isolates from 2001 to 2019 with paired clinical outcome data were assembled. The isolates underwent whole-genome sequencing, multilocus-sequence phylogenetic analysis, and toxinotype analysis of the multifunctional autoprocessing repeats-in-toxin (MARTX) toxin. In contrast to prior reports, clinical isolates were equally distributed between lineages. We found no correlation between phylogenetic lineage or MARTX toxinotype and disease severity. Infections caused by isolates in Lineage 1 demonstrated a borderline statistically significant higher mortality. Lineage 1 isolates had a trend toward a higher proportion of M-type MARTX toxins compared with Lineage 2, although this was not statistically significant. IMPORTANCE Vibrio vulnificus is an aquatic pathogen that is capable of causing severe disease in humans. Previous studies have suggested that pathogenic isolates were restricted to certain phylogenetic lineages and possibly toxinotype. Our study demonstrated that phylogenetic lineage and multifunctional autoprocessing repeats-in-toxin (MARTX) toxinotype do not predict severity of infection. V. vulnificus strains capable of causing severe human disease are not concentrated in Lineage 1 but are genetically diverse. Thus, food surveillance based on lineage type or toxinotype may not be an appropriate intervention measure to control this rare but serious infection.