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  1. The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction.

    Scientific reports · 2022 · 12(1): 5077

    Throughout the COVID-19 pandemic, massive sequencing and data sharing efforts enabled the real-time surveillance of novel SARS-CoV-2 strains throughout the world, the results of which provided public health officials with actionable information to prevent the spread of the virus. However, …

    PMID 35332213 DOI ↗

  2. Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.

    Research square · 2022

    The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral …

    PMID 35313591 DOI ↗

  3. Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML.

    Cell reports · 2022 · 38(10): 110481

    Gene expression profiling and proteome analysis of normal and malignant hematopoietic stem cells (HSCs) point to shared core stemness properties. However, discordance between mRNA and protein signatures highlights an important role for post-transcriptional regulation by microRNAs (miRNAs) in governing this …

    PMID 35263585 DOI ↗

  4. Crosstalk between CRISPR-Cas9 and the human transcriptome.

    Nature communications · 2022 · 13(1): 1125

    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 human RNA transcripts independent of its guide, we perform eCLIP (enhanced CLIP) of Cas9 …

    PMID 35236841 DOI ↗

  5. Integrative RNA-omics Discovers GNAS Alternative Splicing as a Phenotypic Driver of Splicing Factor-Mutant Neoplasms.

    Cancer discovery · 2022 · 12(3): 836-855

    Mutations in splicing factors (SF) are the predominant class of mutations in myelodysplastic syndrome (MDS), but convergent downstream disease drivers remain elusive. To identify common direct targets of missplicing by mutant U2AF1 and SRSF2, we performed RNA sequencing and enhanced …

    PMID 34620690 DOI ↗

  6. Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.

    bioRxiv : the preprint server for biology · 2022

    The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral …

    PMID 35233578 DOI ↗

  7. Global analysis of RNA-binding proteins identifies a positive feedback loop between LARP1 and MYC that promotes tumorigenesis.

    Cellular and molecular life sciences : CMLS · 2022 · 79(3): 147

    In addition to genomic alterations, aberrant changes in post-transcriptional regulation can modify gene function and drive cancer development. RNA-binding proteins (RBPs) are a large class of post-transcriptional regulators that have been increasingly implicated in carcinogenesis. By integrating multi-omics data, we …

    PMID 35195778 DOI ↗

  8. Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing.

    Molecular cell · 2022 · 82(3): 645-659.e9

    Pseudouridine is a modified nucleotide that is prevalent in human mRNAs and is dynamically regulated. Here, we investigate when in their life cycle mRNAs become pseudouridylated to illuminate the potential regulatory functions of endogenous mRNA pseudouridylation. Using single-nucleotide resolution pseudouridine …

    PMID 35051350 DOI ↗

  9. A multi-scale map of cell structure fusing protein images and interactions.

    Nature · 2021 · 600(7889): 536-542

    The cell is a multi-scale structure with modular organization across at least four orders of magnitude<sup>1</sup>. Two central approaches for mapping this structure-protein fluorescent imaging and protein biophysical association-each generate extensive datasets, but of distinct qualities and resolutions that are …

    PMID 34819669 DOI ↗

  10. Analysis of SARS-CoV-2 RNA Persistence across Indoor Surface Materials Reveals Best Practices for Environmental Monitoring Programs.

    mSystems · 2021 · 6(6): e0113621

    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 coronavirus 2 (SARS-CoV-2) on surfaces …

    PMID 34726486 DOI ↗

  11. SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with <i>Rothia</i> sp.

    medRxiv : the preprint server for health sciences · 2021

    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 past work has demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can …

    PMID 34909793 DOI ↗

  12. Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies.

    Nature communications · 2021 · 12(1): 6324

    Mutations in the cardiac splicing factor RBM20 lead to malignant dilated cardiomyopathy (DCM). To understand the mechanism of RBM20-associated DCM, we engineered isogenic iPSCs with DCM-associated missense mutations in RBM20 as well as RBM20 knockout (KO) iPSCs. iPSC-derived engineered heart …

    PMID 34732726 DOI ↗

  13. fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins.

    STAR protocols · 2021 · 2(3): 100762

    Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) structure probing techniques characterize the secondary structure of RNA molecules, which influence their functions and interactions. A variation of SHAPE, footprinting SHAPE (fSHAPE), probes RNA in the presence and absence of protein …

    PMID 34485935 DOI ↗

  14. Emergence of an early SARS-CoV-2 epidemic in the United States.

    Cell · 2021 · 184(19): 4939-4952.e15

    The emergence of the COVID-19 epidemic in the United States (U.S.) went largely undetected due to inadequate testing. New Orleans experienced one of the earliest and fastest accelerating outbreaks, coinciding with Mardi Gras. To gain insight into the emergence of …

    PMID 34508652 DOI ↗

  15. Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress.

    Cell reports · 2021 · 36(10): 109685

    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 aggregates share components, molecular mechanisms, and cellular protein quality control pathways with stress-induced RNA granules (SGs). …

    PMID 34496257 DOI ↗

  16. ADAR and hnRNPC deficiency synergize in activating endogenous dsRNA-induced type I IFN responses.

    The Journal of experimental medicine · 2021 · 218(9)

    Cytosolic double-stranded RNA (dsRNA) initiates type I IFN responses. Endogenous retroelements, notably Alu elements, constitute a source of dsRNA. Adenosine-to-inosine (A-to-I) editing by ADAR induces mismatches in dsRNA and prevents recognition by MDA5 and autoinflammation. To identify additional endogenous dsRNA …

    PMID 34297039 DOI ↗

  17. Non-microRNA binding competitively inhibits LIN28 regulation.

    Cell reports · 2021 · 36(6): 109517

    RNA binding protein (RBP) expression is finite. For RBPs that are vastly outnumbered by their potential target sites, a simple competition for binding can set the magnitude of post-transcriptional control. Here, we show that LIN28, best known for its direct …

    PMID 34380031 DOI ↗

  18. Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer.

    Molecular cell · 2021 · 81(15): 3048-3064.e9

    RNA-binding proteins (RBPs) are critical regulators of post-transcriptional gene expression, and aberrant RBP-RNA interactions can promote cancer progression. Here, we interrogate the function of RBPs in cancer using pooled CRISPR-Cas9 screening and identify 57 RBP candidates with distinct roles in …

    PMID 34216543 DOI ↗

  19. Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence.

    bioRxiv : the preprint server for biology · 2021

    Environmental monitoring in public spaces can be used to identify surfaces contaminated by persons with COVID-19 and inform appropriate infection mitigation responses. Research groups have reported detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on surfaces days or weeks …

    PMID 34312621 DOI ↗

  20. Huntington's disease mice and human brain tissue exhibit increased G3BP1 granules and TDP43 mislocalization.

    The Journal of clinical investigation · 2021 · 131(12)

    Chronic cellular stress associated with neurodegenerative disease can result in the persistence of stress granule (SG) structures, membraneless organelles that form in response to cellular stress. In Huntington's disease (HD), chronic expression of mutant huntingtin generates various forms of cellular …

    PMID 33945510 DOI ↗

  21. Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.

    Nature methods · 2021 · 18(5): 507-519

    RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets …

    PMID 33963355 DOI ↗

  22. Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States.

    Cell · 2021 · 184(10): 2587-2594.e7

    The highly transmissible B.1.1.7 variant of SARS-CoV-2, first identified in the United Kingdom, has gained a foothold across the world. Using S gene target failure (SGTF) and SARS-CoV-2 genomic sequencing, we investigated the prevalence and dynamics of this variant in …

    PMID 33861950 DOI ↗

  23. Loss of LUC7L2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS.

    Molecular cell · 2021 · 81(9): 1905-1919.e12

    Oxidative phosphorylation (OXPHOS) and glycolysis are the two major pathways for ATP production. The reliance on each varies across tissues and cell states, and can influence susceptibility to disease. At present, the full set of molecular mechanisms governing the relative …

    PMID 33852893 DOI ↗

  24. S-nitrosylated TDP-43 triggers aggregation, cell-to-cell spread, and neurotoxicity in hiPSCs and in vivo models of ALS/FTD.

    Proceedings of the National Academy of Sciences of the United States of America · 2021 · 118(11)

    Rare genetic mutations result in aggregation and spreading of cognate proteins in neurodegenerative disorders; however, in the absence of mutation (i.e., in the vast majority of "sporadic" cases), mechanisms for protein misfolding/aggregation remain largely unknown. Here, we show environmentally induced …

    PMID 33692125 DOI ↗

  25. A CRISPR RNA-binding protein screen reveals regulators of RUNX1 isoform generation.

    Blood advances · 2021 · 5(5): 1310-1323

    The proper balance of hematopoietic stem cell (HSC) self-renewal and differentiation is critical for normal hematopoiesis and is disrupted in hematologic malignancy. Among regulators of HSC fate, transcription factors have a well-defined central role, and mutations promote malignant transformation. More …

    PMID 33656539 DOI ↗