Jasmine R. Mueller
A5046814215- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- SARS-CoV-2 and COVID-19 Research
- Cancer-related gene regulation
- Animal Virus Infections Studies
- RNA regulation and disease
- COVID-19 Clinical Research Studies
- Viral gastroenteritis research and epidemiology
- Muscle Physiology and Disorders
- COVID-19 and healthcare impacts
- Genetics and Neurodevelopmental Disorders
- Data-Driven Disease Surveillance
- Bone Metabolism and Diseases
- Tuberculosis Research and Epidemiology
- COVID-19 epidemiological studies
- Amyotrophic Lateral Sclerosis Research
- CRISPR and Genetic Engineering
- Plant Virus Research Studies
- SARS-CoV-2 detection and testing
- NF-κB Signaling Pathways
- Epigenetics and DNA Methylation
- interferon and immune responses
- Genetic Neurodegenerative Diseases
- Neurogenetic and Muscular Disorders Research
University of California, San Diego
2019-2025
Sanford Consortium for Regenerative Medicine
2021-2022
Dermatology Specialists
2021
University of California San Diego Medical Center
2021
The N6-methyladenosine (m 6 A) modification is the most prevalent post-transcriptional mRNA modification, regulating decay and splicing. It plays a major role during normal development, differentiation, disease progression. regulated by set of writer, eraser, reader proteins. YTH domain family proteins consists three homologous m A-binding proteins, Ythdf1, Ythdf2, Ythdf3, which were suggested to have different cellular functions. However, their sequence similarity tendency bind same targets...
A critical step in uncovering rules of RNA processing is to study the vivo regulatory networks binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges large-scale analysis across datasets. The development enhanced CLIP (eCLIP) enabled for 150 RBPs K562 HepG2, creating a unique resource interactomes profiled with standardized methodology same cell types.
Abstract RNA binding proteins (RBPs) are key regulators of processing and cellular function. Technologies to discover targets RBPs such as TRIBE (targets identified by editing) STAMP (surveying APOBEC1 mediated profiling) utilize fusions base-editors (rBEs) circumvent the limitations immunoprecipitation (CLIP)-based methods that require enzymatic digestion large amounts input material. To broaden repertoire rBEs suitable for editing-based RBP-RNA interaction studies, we have devised...
Abstract Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy in need of new therapeutic options. Using unbiased analyses super-enhancers (SEs) as sentinels core genes involved cell-specific function, here we uncover druggable SE-mediated RNA-binding protein (RBP) cascade that supports PDAC growth through enhanced mRNA translation. This driven by SE associated with the RBP heterogeneous nuclear ribonucleoprotein F, which stabilizes arginine methyltransferase 1 (PRMT1) to, turn,...
Technology for crosslinking and immunoprecipitation (CLIP) followed by sequencing (CLIP-seq) has identified the transcriptomic targets of hundreds RNA-binding proteins in cells. To increase power existing future CLIP-seq datasets, we introduce Skipper, an end-to-end workflow that converts unprocessed reads into annotated binding sites using improved statistical framework. Compared with methods, Skipper on average calls 210%-320% more sometimes >1,000% sites, providing deeper insight...
RNA-binding proteins (RBPs) orchestrate post-transcriptional processes, including splicing, cleavage and polyadenylation, translation. We present an updated RBP resource, integrating data from 144 additional RBPs (376 total) profiled by eCLIP complementary knockdown (KD) RNA-seq datasets, comprehensively characterizing RNA elements within human K562 HepG2 cells. To decipher the "syntax" of binding, we trained deep learning models using data. These were employed in a linear mixed-effects...
The nuclear receptor co-repressor (NCoR) complex mediates transcriptional repression dependent on histone deacetylation by deacetylase 3 (HDAC3) as a component of the complex. Unexpectedly, we found that signaling activator factor κB (RANK) converts NCoR/HDAC3 to co-activator AP-1 and NF-κB target genes are required for mouse osteoclast differentiation. Accordingly, dominant function complexes in response RANK is activate, rather than repress, gene expression. Mechanistically, promotes...
Myotonic dystrophy type 1 (DM1) is a multisystem, autosomal-dominant inherited disorder caused by CTG microsatellite repeat expansions (MREs) in the 3′ untranslated region of dystrophia myotonica-protein kinase ( DMPK ) gene. Despite its prominence as most common adult-onset muscular dystrophy, patients with congenital to juvenile-onset forms DM1 can present debilitating neurocognitive symptoms along autism spectrum, characteristic possible utero cortical defects. However, molecular...
Abstract CRISPR-Cas9 expression independent of its cognate synthetic guide RNA (gRNA) causes widespread genomic DNA damage in human cells. To investigate whether Cas9 can interact with endogenous transcripts guide, we perform eCLIP (enhanced CLIP) cells and find that reproducibly interacts hundreds transcripts. This association be partially explained by a model built on gRNA secondary structure sequence. Critically, transcriptome-wide binding sites do not appear to correlate published...
Amyotrophic lateral sclerosis (ALS) is linked to the reduction of certain nucleoporins in neurons. Increased nuclear localization charged multivesicular body protein 7 (CHMP7), a involved pore surveillance, has been identified as key factor damaging pores and disrupting transport. Using CRISPR-based microRaft, followed by gRNA identification (CRaft-ID), we discovered 55 RNA-binding proteins (RBPs) that influence CHMP7 localization, including SmD1, survival motor neuron (SMN) complex...
Abstract The N6-methyladenosine (m 6 A) modification is the most prevalent post-transcriptional mRNA modification, regulating decay, translation and splicing. It plays a major role during normal development, differentiation, disease progression. dynamically regulated by set of writer, eraser reader proteins. YTH-domain family proteins: Ythdf1, Ythdf2, Ythdf3, are three homologous m A binding proteins, which have different cellular functions. However, their sequence similarity tendency to...
Abstract A critical step in uncovering rules of RNA processing is to study the vivo regulatory networks binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enabled mapping RBP targets transcriptome-wide, but methodological differences present challenges large-scale integrated analysis across datasets. The development enhanced CLIP (eCLIP) for 150 RBPs K562 HepG2, creating a unique resource interactomes profiled with standardized methodology same cell types. Here we...
The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). betacoronvirus has a positive sense RNA genome which encodes for several binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral host RNAs in authentic virus-infected cells. proteins, NSP8, NSP12, nucleocapsid display distinct preferences specific regions the genome, providing evidence their shared separate roles...
Abstract Technology for crosslinking and immunoprecipitation followed by sequencing (CLIP-seq) has identified the transcriptomic targets of hundreds RNA-binding proteins in cells. To increase power existing future CLIP-seq datasets, we introduce Skipper, an end-to-end workflow that converts unprocessed reads into annotated binding sites using improved statistical framework. Compared to methods, Skipper on average calls 3.1-4.2 times more sometimes >10 sites, providing deeper insight...
Abstract RNA binding proteins (RBPs) are key regulators of processing and cellular function. Technologies to discover targets RBPs such as TRIBE (targets identified by editing) STAMP (surveying APOBEC1 mediated profiling) utilize fusions base-editors (rBEs) circumvent the limitations immunoprecipitation (CLIP)-based methods that require enzymatic digestion large amounts input material. To broaden repertoire rBEs suitable for editing-based RBP-RNA interaction studies, we have devised...
The COVID-19 pandemic was caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral host RNAs. proteins, NSP8 NSP12, bind specific regions in the RNA genome, providing evidence for their central potential roles replication, transcription genome recombination. proteins expressed human lung epithelial cells 4,821 unique Nine upregulate target gene expression,...
The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). betacoronvirus has a positive sense RNA genome which encodes for several binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral host RNAs in authentic virus-infected cells. proteins, NSP8, NSP12, nucleocapsid display distinct preferences specific regions the genome, providing evidence their shared separate roles...
Abstract Background Successful containment strategies for SARS-CoV-2, the causative virus of COVID-19 pandemic, have involved widespread population testing that identifies infections early and enables rapid contact tracing. In this study, we developed a inexpensive RT- qPCR pipeline population-level SARS-CoV-2 detection, used to establish clinical laboratory dedicated at University California San Diego (UCSD) with processing capacity 6,000 samples per day next-day result turnaround times....
Background: Successful containment strategies for SARS-CoV-2, the causative virus of COVID-19 pandemic, have involved widespread population testing that identifies infections early and enables rapid contact tracing.In this study, we developed a inexpensive RT-qPCR pipeline population-level SARS-CoV-2 detection, used to establish clinical laboratory dedicated at University California San Diego (UCSD) with processing capacity 6,000 samples per day next-day result turnaround times.Methods...