Shashank Sathe
A5060615493- RNA Research and Splicing
- Circular RNAs in diseases
- RNA modifications and cancer
- SARS-CoV-2 detection and testing
- SARS-CoV-2 and COVID-19 Research
- Infection Control and Ventilation
- COVID-19 epidemiological studies
- RNA and protein synthesis mechanisms
- RNA regulation and disease
- Biosensors and Analytical Detection
- COVID-19 Clinical Research Studies
- Neurogenetic and Muscular Disorders Research
- Protein Degradation and Inhibitors
- Animal Virus Infections Studies
- COVID-19 and healthcare impacts
- Cancer-related molecular mechanisms research
- Amyotrophic Lateral Sclerosis Research
- MicroRNA in disease regulation
- Chromosomal and Genetic Variations
- Viral Infections and Outbreaks Research
- Cancer-related gene regulation
- Mobile Crowdsensing and Crowdsourcing
- HVDC Systems and Fault Protection
- Data-Driven Disease Surveillance
- Clostridium difficile and Clostridium perfringens research
University of California, San Diego
2016-2025
Sanford Consortium for Regenerative Medicine
2016-2025
Abstract Many proteins regulate the expression of genes by binding to specific regions encoded in genome 1 . Here we introduce a new data set RNA elements human that are recognized RNA-binding (RBPs), generated as part Encyclopedia DNA Elements (ENCODE) project phase III. This class regulatory functions only when transcribed into RNA, they serve sites for RBPs control post-transcriptional processes such splicing, cleavage and polyadenylation, editing, localization, stability translation...
Abstract As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing infeasible at scale, especially in areas with limited resources, participation, or and/or sequencing capacity, which can also introduce biases 1–3 . RNA concentration wastewater successfully tracks regional infection dynamics provides less biased abundance estimates than 4,5 Tracking virus genomic sequences...
Direct RNA sequencing holds great promise for the de novo identification of modifications at single-coordinate resolution; however, interpretation raw output to discover modified bases remains a challenge. Using Oxford Nanopore's direct technology, we developed random forest classifier trained using experimentally detected N 6 -methyladenosine (m A) sites within DRACH motifs. Our software MINES A Identification Nanopore Sequencing) assigned m methylation status more than 13,000 previously...
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...
Circular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown bind RNA-binding proteins (RBPs); however, little is known about the prevalence and distribution of these interactions in different biological contexts.We conduct an extensive screen circRNA-RBP ENCODE cell lines HepG2 K562. We profile deep-sequenced total samples analyze using a large set eCLIP data binding sites 150 RBPs. validate for...
Summary As of January 2021, the highly transmissible B.1.1.7 variant SARS-CoV-2, which was first identified in United Kingdom (U.K.), has gained a strong foothold across world. Because sudden and rapid rise B.1.1.7, we investigated prevalence growth dynamics this States (U.S.), tracking it back to its early emergence onward local transmission. We found that RT-qPCR testing anomaly S gene target failure (SGTF), observed U.K., reliable proxy for detection. sequenced 212 SARS-CoV-2 genomes...
Schools are high-risk settings for SARS-CoV-2 transmission, but necessary children's educational and social-emotional wellbeing. Previous research suggests that wastewater monitoring can detect infections in controlled residential with high levels of accuracy. However, its effective accuracy, cost, feasibility non-residential community is unknown.The objective this study was to determine the effectiveness accuracy community-based passive surface (environmental) surveillance infection...
Abstract Mutations in the cardiac splicing factor RBM20 lead to malignant dilated cardiomyopathy (DCM). To understand mechanism of RBM20-associated DCM, we engineered isogenic iPSCs with DCM-associated missense mutations as well knockout (KO) iPSCs. iPSC-derived heart tissues made from these cell lines recapitulate contractile dysfunction DCM and reveal greater than KO. Analysis RNA binding by eCLIP reveals a gain-of-function preference mutant for 3′ UTR sequences that are shared amyotrophic...
Persistent cytoplasmic aggregates containing RNA binding proteins (RBPs) are central to the pathogenesis of late-onset neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS). These share components, molecular mechanisms, and cellular protein quality control pathways with stress-induced granules (SGs). Here, we assess impact stress on global mRNA localization landscape human pluripotent stem cell-derived motor neurons (PSC-MNs) using subcellular fractionation sequencing...
Abstract Background Infection prevention (IP) measures are designed to mitigate the transmission of pathogens in healthcare. Using large-scale viral genomic and social network analyses, we determined if IP used during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic were adequate protecting healthcare workers (HCWs) patients from acquiring SARS-CoV-2. Methods We performed retrospective cross-sectional analyses genomics all available SARS-CoV-2 samples collected at UC San...
Significance Glucagon action in liver is a central response to fasting and type 2 diabetes. has been delineated through regulatory mechanisms involving signaling, transcription factor/coactivator-based gluconeogenic gene expression, metabolic enzyme activity. Understanding the molecular whereby glucagon controls energy metabolism will define new strategies potential therapies treat diseases. Here, we have identified mechanism PGC-1α, known transcriptional regulator of action, binds RNAs...
Abstract Chemo-resistance in acute myeloid leukemia (AML) patients is driven by leukemic stem cells (LSCs) resulting high rates of relapse and low overall survival. Here, we demonstrate that upregulation the splicing factor, RBM17 preferentially marks sustains LSCs directly correlates with shorten patient knockdown primary AML leads to differentiation impaired colony formation vivo engraftment. Integrative multi-omics analyses show repression inclusion poison exons production...
Summary As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. RNA concentration wastewater successfully tracks regional infection dynamics provides less biased abundance estimates than testing. Tracking virus genomic sequences...
Environmental monitoring in public spaces can be used to identify surfaces contaminated by persons with coronavirus disease 2019 (COVID-19) and inform appropriate infection mitigation responses. Research groups have reported detection of severe acute respiratory syndrome 2 (SARS-CoV-2) on days or weeks after the virus has been deposited, making it difficult estimate when an infected individual may shed onto a SARS-CoV-2-positive surface, which turn complicates process establishing effective...
Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our work demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from can identify when infected have touched and they been present in hospital rooms or schools. However, the sensitivity specificity of surface sampling a method detecting presence positive individual, well guidance...