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221 results for “T cell”
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Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis.
Acta neuropathologica · 2022 · 144(3): 413-435
Amyotrophic lateral sclerosis (ALS) is a fatal disease characterized by aberrant alternative splicing (AS). Nuclear loss and cytoplasmic accumulation of the splicing factor TDP-43 in motor neurons (MN) are hallmarks of ALS at late stages of the disease. However, it …
PMID 35778567 DOI ↗
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Engineered U1 snRNAs to modulate alternatively spliced exons.
Methods (San Diego, Calif.) · 2022 · 205: 140-148
Alternative splicing accounts for a considerable portion of transcriptomic diversity, as most protein-coding genes are spliced into multiple mRNA isoforms. However, errors in splicing patterns can give rise to mis-splicing with pathological consequences, such as the congenital diseases familial dysautonomia, …
PMID 35764245 DOI ↗
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AKT constitutes a signal-promoted alternative exon-junction complex that regulates nonsense-mediated mRNA decay.
Molecular cell · 2022 · 82(15): 2779-2796.e10
Despite a long appreciation for the role of nonsense-mediated mRNA decay (NMD) in destroying faulty, disease-causing mRNAs and maintaining normal, physiologic mRNA abundance, additional effectors that regulate NMD activity in mammalian cells continue to be identified. Here, we describe a …
PMID 35675814 DOI ↗
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Pre-existing adaptive immunity to the RNA-editing enzyme Cas13d in humans.
Nature medicine · 2022 · 28(7): 1372-1376
RNA-guided RNA-targeting nucleases, such as CRISPR-Cas13 proteins, have therapeutic potential for gene editing. Among Cas13d enzymes, Cas13d from the bacteria Ruminococcus flavefaciens (RfxCas13d) is of particular interest owing to its small size and high specificity. However, the existence of pre-existing …
PMID 35668177 DOI ↗
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The splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors.
Nature communications · 2022 · 13(1): 3833
Chemo-resistance in acute myeloid leukemia (AML) patients is driven by leukemic stem cells (LSCs) resulting in high rates of relapse and low overall survival. Here, we demonstrate that upregulation of the splicing factor, RBM17 preferentially marks and sustains LSCs and …
PMID 35781533 DOI ↗
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Illuminating RNA biology through imaging.
Nature cell biology · 2022 · 24(6): 815-824
RNA processing plays a central role in accurately transmitting genetic information into functional RNA and protein regulators. To fully appreciate the RNA life-cycle, tools to observe RNA with high spatial and temporal resolution are critical. Here we review recent advances …
PMID 35697782 DOI ↗
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MECP2-related pathways are dysregulated in a cortical organoid model of myotonic dystrophy.
Science translational medicine · 2022 · 14(651): eabn2375
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 the dystrophia myotonica-protein kinase (<i>DMPK</i>) gene. Despite its prominence as the most common adult-onset muscular dystrophy, …
PMID 35767654 DOI ↗
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The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression.
The Journal of experimental medicine · 2022 · 219(6)
During an immune response to microbial infection, CD8+ T cells give rise to short-lived effector cells and memory cells that provide sustained protection. Although the transcriptional programs regulating CD8+ T cell differentiation have been extensively characterized, the role of long …
PMID 35593887 DOI ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
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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 ↗
Datasets 25+
RNA secondary structome of different cell lines
Homo sapiens, Mus musculus · GPL20795, GPL21273
Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation
GPL17021
Single-cell and isoform-specific translational profiling of the mouse brain with long-read sequencing [scRNA-Seq, longread]
GPL34585
Single-cell and isoform-specific translational profiling of the mouse brain [scRNA-seq]
GPL34475
Foxo1 regulates intestinal tissue-resident memory CD8 T cell biology in an anatomic compartment- and context-specific manner
GPL24247
Comparing isogenic pairs of hESC and hiPSC lines reveals genetic background and reprogramming method as primary sources of transcriptional variation
Homo sapiens · GPL11154
scRNA-seq, bulk RNA-seq, and ATAC-seq data from progenitor exhausted and terminally exhausted CD8+ T cells from tumors and chronic viral infection
Mus musculus · GPL19057
Chronic viral infection of naive, effector, memory and exhausted virus-specific CD8 T cells
Mus musculus · GPL81
Defining memory-like CD8 T cells that respond to PD-1 therapy in chronic viral infection
Mus musculus · GPL1261
Identifying differentially expressed genes in Zmat3 knockout cells
Mus musculus · GPL13112
Transactivation-deficient p53 Mutants in Ras-induced Cellular Senescence
Mus musculus · GPL1261
Aberrant splicing of U12-type introns is the hallmark of ZRSR2 mutant myelodysplastic syndrome
Homo sapiens · GPL11154
Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease
Homo sapiens · GPL15520
The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation
Mus musculus · GPL17543
Genome-wide maps of chromatin state and chromatin accessibility in CD8 T cell subsets
Mus musculus · GPL17021
RNA-Seq of CD8+ T cell subsets during LCMV infection III
Mus musculus · GPL17021
Transcriptional Survey of Ileal-Anal Pouch Immune Cells from Ulcerative Colitis
Homo sapiens · GPL20301
Single-cell analysis of Crohnâs disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy
Homo sapiens · GPL18573
Refined molecular taxonomy and treatment remodeling of pancreatic cancer using single-cell resolution
Homo sapiens · GPL20301
Exonuclease assisted mapping of protein-RNA interactions (ePRINT)
Homo sapiens · GPL24676
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP]
Mus musculus · GPL24247
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [eCLIP-seq ]
Mus musculus · GPL21103
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [isSTAMP]
Mus musculus · GPL30172
Single-cell transcriptomic atlas of the mouse regenerating muscle tissue
Mus musculus · GPL19057
Showing first 25 dataset results.
Analyses 25+
GSE145805 · 7 steps · SHAPE-seq · geo_data_processing
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data. (2025)
GSE247544 · 3 steps · scRNA-seq · geo_data_processing
Foxo1 regulates intestinal tissue-resident memory CD8 T cell biology in an anatomic compartment- and context-specific manner. (2025)
GSE279254 · 1 step · RNA-Seq · code_examples
Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted. (2025)
GSE279255 · 2 steps · OTHER · code_examples
Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted. (2025)
GSE280895 · 7 steps · GSE · code_examples
Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted. (2025)
GSE157259 · 22 steps · RIP-Seq · code_examples
RNA binding protein DDX5 restricts RORγt<sup>+</sup> T<sub>reg</sub> suppressor function to promote intestine inflammation. (2023)
GSE205549 · 3 steps · ATAC-seq · code_examples
Small intestine and colon tissue-resident memory CD8<sup>+</sup> T cells exhibit molecular heterogeneity and differential dependence on Eomes. (2023)
GSE205941 · 5 steps · OTHER · code_examples
Small intestine and colon tissue-resident memory CD8<sup>+</sup> T cells exhibit molecular heterogeneity and differential dependence on Eomes. (2023)
GSE205942 · 3 steps · GSE · code_examples
Small intestine and colon tissue-resident memory CD8<sup>+</sup> T cells exhibit molecular heterogeneity and differential dependence on Eomes. (2023)
GSE213467 · 11 steps · ChIP-Seq · code_examples
Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection. (2023)
GSE213469 · 2 steps · ATAC-seq · code_examples
Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection. (2023)
GSE213470 · 2 steps · RNA-Seq · code_examples
Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection. (2023)
GSE146014 · 3 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)
GSE157072 · 3 steps · RNA-Seq · code_examples
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. (2022)
GSE184564 · 3 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)
GSE195493 · 5 steps · RIP-Seq · code_examples
Nuclear and cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms. (2022)
GSE203086 · 10 steps · RNA-Seq · code_examples
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. (2022)
GSE203089 · 19 steps · OTHER · code_examples
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. (2022)
GSE203090 · 3 steps · ChIP-Seq · code_examples
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. (2022)
GSE203091 · 6 steps · OTHER · code_examples
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. (2022)
GSE203092 · 10 steps · GSE · code_examples
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. (2022)
GSE72408 · 1 step · GSE · code_examples
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. (2022)
GSE75214 · 1 step · GSE · code_examples
RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine. (2022)
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)
GSE157467 · 6 steps · RNA-Seq · code_examples
Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress. (2021)
Showing first 25 analysis results.