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88 results for “Genomics”

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  1. Nuclear and cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms.

    Nucleic acids research · 2022 · 50(8): 4685-4702

    The poly(A)-tail appended to the 3'-end of most eukaryotic transcripts plays a key role in their stability, nuclear transport, and translation. These roles are largely mediated by Poly(A) Binding Proteins (PABPs) that coat poly(A)-tails and interact with various proteins involved …

    PMID 35438785 DOI ↗

  2. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission.

    medRxiv : the preprint server for health sciences · 2022

    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 is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also …

    PMID 35411350 DOI ↗

  3. 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 ↗

  4. 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 ↗

  5. 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 ↗

  6. 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 ↗

  7. 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 ↗

  8. 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 ↗

  9. 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 ↗

  10. Reintroduction of the archaic variant of <i>NOVA1</i> in cortical organoids alters neurodevelopment.

    Science (New York, N.Y.) · 2021 · 371(6530)

    The evolutionarily conserved splicing regulator neuro-oncological ventral antigen 1 (<i>NOVA1</i>) plays a key role in neural development and function. <i>NOVA1</i> also includes a protein-coding difference between the modern human genome and Neanderthal and Denisovan genomes. To investigate the functional importance …

    PMID 33574182 DOI ↗

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

    medRxiv : the preprint server for health sciences · 2021

    The emergence of the early COVID-19 epidemic in the United States (U.S.) went largely undetected, due to a lack of adequate testing and mitigation efforts. The city of New Orleans, Louisiana experienced one of the earliest and fastest accelerating outbreaks, …

    PMID 33564781 DOI ↗

  12. Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States.

    medRxiv : the preprint server for health sciences · 2021

    As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first identified in the United Kingdom (U.K.), has gained a strong foothold across the world. Because of the sudden and rapid rise of B.1.1.7, we investigated …

    PMID 33564780 DOI ↗

  13. Base editing: advances and therapeutic opportunities.

    Nature reviews. Drug discovery · 2020 · 19(12): 839-859

    Base editing - the introduction of single-nucleotide variants (SNVs) into DNA or RNA in living cells - is one of the most recent advances in the field of genome editing. As around half of known pathogenic genetic variants are due …

    PMID 33077937 DOI ↗

  14. Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression.

    Genome medicine · 2020 · 12(1): 112

    Circular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA-binding proteins (RBPs); however, little is known about the prevalence and distribution of these interactions …

    PMID 33287884 DOI ↗

  15. Evaluation of Engineered CRISPR-Cas-Mediated Systems for Site-Specific RNA Editing.

    Cell reports · 2020 · 33(5): 108350

    Site-directed RNA editing approaches offer great potential to correct genetic mutations in somatic cells while avoiding permanent off-target genomic edits. Nuclease-dead RNA-targeting CRISPR-Cas systems recruit functional effectors to RNA molecules in a programmable fashion. Here, we demonstrate a Streptococcus pyogenes …

    PMID 33147453 DOI ↗

  16. A role for alternative splicing in circadian control of exocytosis and glucose homeostasis.

    Genes & development · 2020 · 34(15-16): 1089-1105

    The circadian clock is encoded by a negative transcriptional feedback loop that coordinates physiology and behavior through molecular programs that remain incompletely understood. Here, we reveal rhythmic genome-wide alternative splicing (AS) of pre-mRNAs encoding regulators of peptidergic secretion within pancreatic …

    PMID 32616519 DOI ↗

  17. Expanded encyclopaedias of DNA elements in the human and mouse genomes.

    Nature · 2020 · 583(7818): 699-710

    The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded …

    PMID 32728249 DOI ↗

  18. A large-scale binding and functional map of human RNA-binding proteins.

    Nature · 2020 · 583(7818): 711-719

    Many proteins regulate the expression of genes by binding to specific regions encoded in the genome<sup>1</sup>. Here we introduce a new data set of RNA elements in the human genome that are recognized by RNA-binding proteins (RBPs), generated as part …

    PMID 32728246 DOI ↗

  19. An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia.

    Nature cancer · 2020 · 1(4): 410-422

    Aggressive myeloid leukemias such as blast crisis chronic myeloid leukemia and acute myeloid leukemia remain highly lethal. Here we report a genome-wide in vivo CRISPR screen to identify new dependencies in this disease. Among these, RNA-binding proteins (RBPs) in general, …

    PMID 34109316 DOI ↗

  20. Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins.

    Genome biology · 2020 · 21(1): 90

    A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale analysis …

    PMID 32252787 DOI ↗

  21. Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells.

    Nature communications · 2020 · 11(1): 550

    Many cellular models aimed at elucidating cancer biology do not recapitulate pathobiology including tumor heterogeneity, an inherent feature of cancer that underlies treatment resistance. Here we introduce a cancer modeling paradigm using genetically engineered human pluripotent stem cells (hiPSCs) that …

    PMID 31992716 DOI ↗

  22. Peptide Brush Polymers for Efficient Delivery of a Gene Editing Protein to Stem Cells.

    Angewandte Chemie (International ed. in English) · 2019 · 58(44): 15646-15649

    The scarcity of effective means to deliver functional proteins to living cells is a central problem in biotechnology and medicine. Herein, we report the efficient delivery of an active DNA-modifying enzyme to human stem cells through high-density cell penetrating peptide …

    PMID 31404473 DOI ↗

  23. Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription.

    Cell · 2019 · 178(1): 107-121.e18

    Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA-binding proteins (RBPs). Although multiple RBPs have been implicated in transcription control, it has remained unclear how extensively RBPs directly act on …

    PMID 31251911 DOI ↗

  24. Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA.

    Nature communications · 2019 · 10(1): 1338

    Allele-specific protein-RNA binding is an essential aspect that may reveal functional genetic variants (GVs) mediating post-transcriptional regulation. Recently, genome-wide detection of in vivo binding of RNA-binding proteins is greatly facilitated by the enhanced crosslinking and immunoprecipitation (eCLIP) method. We developed …

    PMID 30902979 DOI ↗

  25. RBP-Maps enables robust generation of splicing regulatory maps.

    RNA (New York, N.Y.) · 2019 · 25(2): 193-204

    Alternative splicing of pre-messenger RNA transcripts enables the generation of multiple protein isoforms from the same gene locus, providing a major source of protein diversity in mammalian genomes. RNA binding proteins (RBPs) bind to RNA to control splice site choice …

    PMID 30413564 DOI ↗

Datasets 11

GSE315443 GSE · GEO

MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [scRNA-Seq]

GPL24676

GSE247544 GSE · GEO

Foxo1 regulates intestinal tissue-resident memory CD8 T cell biology in an anatomic compartment- and context-specific manner

GPL24247

GSE5851 GSE · GEO

Phase II exploratory pharmacogenomics study of cetuximab monotherapy in patients with advanced metastatic CRC

Homo sapiens · GPL571

GSE17536 GSE · GEO

Metastasis Gene Expression Profile Predicts Recurrence and Death in Colon Cancer Patients (Moffitt Samples)

Homo sapiens · GPL570

GSE83687 GSE · GEO

A functional genomics predictive network model identifies regulators of inflammatory bowel disease: Mount Sinai Hospital (MSH) Population Specimen Collection and Profiling of Inflammatory Bowel Disease

Homo sapiens · GPL16791

GSE18920 GSE · GEO

Sporadic ALS has compartment-specific aberrant exon splicing and altered cell-matrix adhesion biology

Homo sapiens · GPL5188

GSE154778 GSE · GEO

Single-cell transcriptomics analysis of pancreatic primary tumor and metastatic biopsy tissues

Homo sapiens · GPL20301

GSE155726 GSE · GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [scRNA-seq]

Homo sapiens · GPL24676

GSE66696 GSE · GEO

Whole brain RNA from congenic littermates does not support a general effect of Nxf1 CAST alleles on alternative pre-mRNA processing

Mus musculus · GPL13185

GSE27371 GSE · GEO

Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (Affymetrix)

Mus musculus · GPL13185

GSE40649 GSE · GEO

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs (microarray)

Mus musculus · GPL13185

Analyses 2

GSE83687 Processing Pipeline

GSE83687 · 4 steps · RNA-Seq · code_examples

RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine. (2022)

GSE5851 Processing Pipeline

GSE5851 · 1 step · GSE · code_examples

DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)