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107 results for “gene expression”
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Context-dependent functional compensation between Ythdf m<sup>6</sup>A reader proteins.
Genes & development · 2020 · 34(19-20): 1373-1391
The N6-methyladenosine (m<sup>6</sup>A) modification is the most prevalent post-transcriptional mRNA modification, regulating mRNA decay and splicing. It plays a major role during normal development, differentiation, and disease progression. The modification is regulated by a set of writer, eraser, and reader …
PMID 32943573 DOI ↗
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Transcriptome-wide analysis of PGC-1α-binding RNAs identifies genes linked to glucagon metabolic action.
Proceedings of the National Academy of Sciences of the United States of America · 2020 · 117(36): 22204-22213
The peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) is a transcriptional coactivator that controls expression of metabolic/energetic genes, programming cellular responses to nutrient and environmental adaptations such as fasting, cold, or exercise. Unlike other coactivators, PGC-1α contains protein domains involved …
PMID 32848060 DOI ↗
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Motoneuron expression profiling identifies an association between an axonal splice variant of HDGF-related protein 3 and peripheral myelination.
The Journal of biological chemistry · 2020 · 295(34): 12233-12246
Disorders that disrupt myelin formation during development or in adulthood, such as multiple sclerosis and peripheral neuropathies, lead to severe pathologies, illustrating myelin's crucial role in normal neural functioning. However, although our understanding of glial biology is increasing, the signals …
PMID 32647008 DOI ↗
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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 ↗
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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 ↗
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Heterogenous Populations of Tissue-Resident CD8<sup>+</sup> T Cells Are Generated in Response to Infection and Malignancy.
Immunity · 2020 · 52(5): 808-824.e7
Tissue-resident memory CD8<sup>+</sup> T cells (Trm) provide host protection through continuous surveillance of non-lymphoid tissues. Using single-cell RNA-sequencing (scRNA-seq) and genetic reporter mice, we identified discrete lineages of intestinal antigen-specific CD8<sup>+</sup> T cells, including a Blimp1<sup>hi</sup>Id3<sup>lo</sup> tissue-resident effector cell population …
PMID 32433949 DOI ↗
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Early precursors and molecular determinants of tissue-resident memory CD8<sup>+</sup> T lymphocytes revealed by single-cell RNA sequencing.
Science immunology · 2020 · 5(47)
During an immune response to microbial infection, CD8<sup>+</sup> T cells give rise to distinct classes of cellular progeny that coordinately mediate clearance of the pathogen and provide long-lasting protection against reinfection, including a subset of noncirculating tissue-resident memory (T<sub>RM</sub>) cells …
PMID 32414833 DOI ↗
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The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis.
Cell stem cell · 2019 · 25(5): 622-638.e13
Post-transcriptional mechanisms have the potential to influence complex changes in gene expression, yet their role in cell fate transitions remains largely unexplored. Here, we show that suppression of the RNA helicase DDX6 endows human and mouse primed embryonic stem cells …
PMID 31588046 DOI ↗
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Disruption in A-to-I Editing Levels Affects C. elegans Development More Than a Complete Lack of Editing.
Cell reports · 2019 · 27(4): 1244-1253.e4
A-to-I RNA editing, catalyzed by ADAR proteins, is widespread in eukaryotic transcriptomes. Studies showed that, in C. elegans, ADR-2 can actively deaminate dsRNA, whereas ADR-1 cannot. Therefore, we set out to study the effect of each of the ADAR genes …
PMID 31018137 DOI ↗
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Overriding FUS autoregulation in mice triggers gain-of-toxic dysfunctions in RNA metabolism and autophagy-lysosome axis.
eLife · 2019 · 8
Mutations in coding and non-coding regions of FUS cause amyotrophic lateral sclerosis (ALS). The latter mutations may exert toxicity by increasing FUS accumulation. We show here that broad expression within the nervous system of wild-type or either of two ALS-linked …
PMID 30747709 DOI ↗
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A Transcriptome-wide Translational Program Defined by LIN28B Expression Level.
Molecular cell · 2019 · 73(2): 304-313.e3
LIN28 RNA binding proteins are dynamically expressed throughout mammalian development and during disease. However, it remains unclear how changes in LIN28 expression define patterns of post-transcriptional gene regulation. Here we show that LIN28 expression level is a key variable that …
PMID 30527666 DOI ↗
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Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells.
Frontiers in molecular neuroscience · 2018 · 11: 261
The human brain is composed of a complex assembly of about 171 billion heterogeneous cellular units (86 billion neurons and 85 billion non-neuronal glia cells). A comprehensive description of brain cells is necessary to understand the nervous system in health …
PMID 30147644 DOI ↗
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An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys.
RNA (New York, N.Y.) · 2018 · 24(9): 1255-1265
During terminal erythropoiesis, the splicing machinery in differentiating erythroblasts executes a robust intron retention (IR) program that impacts expression of hundreds of genes. We studied IR mechanisms in the <i>SF3B1</i> splicing factor gene, which expresses ∼50% of its transcripts in …
PMID 29959282 DOI ↗
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Transcriptome-pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS.
Acta neuropathologica · 2018 · 136(3): 405-423
Sporadic amyotrophic lateral sclerosis (sALS) is the most common form of ALS, however, the molecular mechanisms underlying cellular damage and motor neuron degeneration remain elusive. To identify molecular signatures of sALS we performed genome-wide expression profiling in laser capture microdissection-enriched …
PMID 29881994 DOI ↗
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Short poly(A) tails are a conserved feature of highly expressed genes.
Nature structural & molecular biology · 2017 · 24(12): 1057-1063
Poly(A) tails are important elements in mRNA translation and stability, although recent genome-wide studies have concluded that poly(A) tail length is generally not associated with translational efficiency in nonembryonic cells. To investigate whether poly(A) tail size might be coupled to …
PMID 29106412 DOI ↗
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The <i>C. elegans</i> neural editome reveals an ADAR target mRNA required for proper chemotaxis.
eLife · 2017 · 6
ADAR proteins alter gene expression both by catalyzing adenosine (A) to inosine (I) RNA editing and binding to regulatory elements in target RNAs. Loss of ADARs affects neuronal function in all animals studied to date. <i>Caenorhabditis elegans</i> lacking ADARs exhibit …
PMID 28925356 DOI ↗
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Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation.
Molecular cell · 2017 · 67(1): 148-161.e5
Alternative splicing (AS) generates isoform diversity for cellular identity and homeostasis in multicellular life. Although AS variation has been observed among single cells, little is known about the biological or evolutionary significance of such variation. We developed Expedition, a computational …
PMID 28673540 DOI ↗
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Pseudotemporal Ordering of Single Cells Reveals Metabolic Control of Postnatal β Cell Proliferation.
Cell metabolism · 2017 · 25(5): 1160-1175.e11
Pancreatic β cell mass for appropriate blood glucose control is established during early postnatal life. β cell proliferative capacity declines postnatally, but the extrinsic cues and intracellular signals that cause this decline remain unknown. To obtain a high-resolution map of …
PMID 28467932 DOI ↗
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Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer.
Cancer discovery · 2017 · 7(4): 410-423
Recent studies have characterized the extensive somatic alterations that arise during cancer. However, the somatic evolution of a tumor may be significantly affected by inherited polymorphisms carried in the germline. Here, we analyze genomic data for 5,954 tumors to reveal …
PMID 28188128 DOI ↗
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High-Throughput and Cost-Effective Characterization of Induced Pluripotent Stem Cells.
Stem cell reports · 2017 · 8(4): 1101-1111
Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) offers the possibility of studying the molecular mechanisms underlying human diseases in cell types difficult to extract from living patients, such as neurons and cardiomyocytes. To date, studies have been published …
PMID 28410643 DOI ↗
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iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types.
Stem cell reports · 2017 · 8(4): 1086-1100
Large-scale collections of induced pluripotent stem cells (iPSCs) could serve as powerful model systems for examining how genetic variation affects biology and disease. Here we describe the iPSCORE resource: a collection of systematically derived and characterized iPSC lines from 222 …
PMID 28410642 DOI ↗
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RNA-binding protein CPEB1 remodels host and viral RNA landscapes.
Nature structural & molecular biology · 2016 · 23(12): 1101-1110
Host and virus interactions occurring at the post-transcriptional level are critical for infection but remain poorly understood. Here, we performed comprehensive transcriptome-wide analyses revealing that human cytomegalovirus (HCMV) infection results in widespread alternative splicing (AS), shortening of 3' untranslated regions …
PMID 27775709 DOI ↗
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Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology.
Molecular psychiatry · 2016 · 21(11): 1573-1588
Human neural progenitors derived from pluripotent stem cells develop into electrophysiologically active neurons at heterogeneous rates, which can confound disease-relevant discoveries in neurology and psychiatry. By combining patch clamping, morphological and transcriptome analysis on single-human neurons in vitro, we defined …
PMID 27698428 DOI ↗
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Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.
Neuron · 2016 · 92(4): 780-795
HnRNPA2B1 encodes an RNA binding protein associated with neurodegeneration. However, its function in the nervous system is unclear. Transcriptome-wide crosslinking and immunoprecipitation in mouse spinal cord discover UAGG motifs enriched within ∼2,500 hnRNP A2/B1 binding sites and an unexpected role …
PMID 27773581 DOI ↗
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Rbfox2 function in RNA metabolism is impaired in hypoplastic left heart syndrome patient hearts.
Scientific reports · 2016 · 6: 30896
Hypoplastic left heart syndrome (HLHS) is a fatal congenital heart disease in which the left side of the heart is underdeveloped, impairing the systemic circulation. Underdeveloped left ventricle exerts biomechanical stress on the right ventricle that can progress into heart …
PMID 27485310 DOI ↗
Datasets 25+
Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay [miRNA-Seq]
GPL18573
Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay [RIP-Seq]
GPL18573
Multi-Modal Comparison of human Hepatic Stellate Cells identifies novel therapeutic targets for Metabolic Dysfunction-Associated Steatotic Liver Disease
Homo sapiens · GPL24676, GPL37309
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [CRISPR]
GPL24676
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [eCLIP]
GPL24676
PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [RNA-seq]
GPL24676
Densely interconnected transcriptional circuits control cell states in human hematopoiesis
Homo sapiens · GPL4685
Expression data from reactive astrocytes acutely purified from young adult mouse brains
Mus musculus · GPL1261
Gene expression analysis of TSC-tubers reveals increased expression of adhesion and inflammatory factors
Homo sapiens · GPL570
Comparing isogenic pairs of hESC and hiPSC lines reveals genetic background and reprogramming method as primary sources of transcriptional variation
Homo sapiens · GPL11154
The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis
6239 · GPL19757
Disruption of human-specific synaptogenesis program in autism [RNA-seq]
9598 · GPL11154
Conserved expression of lincRNA during human and macaque prefrontal cortex development and maturation
9544 · GPL11154
Chronic viral infection of naive, effector, memory and exhausted virus-specific CD8 T cells
Mus musculus · GPL81
Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression
Mus musculus · GPL17021
A seven-gene signature aggregates a subgroup of stage II colon cancers with stage III.
Homo sapiens · GPL570
Colorectal cancer susceptibility loci as predictive markers of rectal cancer prognosis after surgery
Homo sapiens · GPL13497
Gene Expression Profiles in Stage II and III Colon Cancer. Application of a 128-gene signature
Homo sapiens · GPL570
Metastasis Gene Expression Profile Predicts Recurrence and Death in Colon Cancer Patients (Moffitt Samples)
Homo sapiens · GPL570
Experimentally Derived Metastasis Gene Expression Profile Predicts Recurrence and Death in Colon Cancer Patients
Mus musculus · GPL570
Transactivation-deficient p53 Mutants in Ras-induced Cellular Senescence
Mus musculus · GPL1261
RNA-targeting Cas9 corrects molecular and physiological features in pre-clinical model of myotonic dystrophy type 1
Mus musculus · GPL21103
The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation
Mus musculus · GPL17543
Expression data from human hematopoietic stem and progenitor compartments from patients with acute myeloid leukemia with normal karyotype and healthy controls
Homo sapiens · GPL6244
Showing first 25 dataset results.
Analyses 18
GSE237099 · 3 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE122425 · 5 steps · RNA-Seq · code_examples
Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP. (2023)
GSE138197 · 6 steps · RNA-Seq · code_examples
Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites. (2023)
GSE211676 · 10 steps · GSE · code_examples
RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression. (2023)
GSE213470 · 2 steps · RNA-Seq · code_examples
Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection. (2023)
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)
GSE17536 · 3 steps · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE17538 · 3 steps · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE31595 · 2 steps · GSE · code_examples
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. (2020)
GSE95156 · 7 steps · RNA-Seq · code_examples
A role for alternative splicing in circadian control of exocytosis and glucose homeostasis. (2020)
GSE76220 · 5 steps · RNA-Seq · code_examples
Transcriptome-pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS. (2018)
GSE16969 · 2 steps · GSE · code_examples
Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model. (2016)
GSE72420 · 3 steps · GSE · code_examples
The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. (2015)
GSE72500 · 3 steps · RIP-Seq · code_examples
The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. (2015)
GSE72501 · 5 steps · RNA-Seq · code_examples
The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. (2015)
GSE72502 · 5 steps · RNA-Seq · code_examples
The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. (2015)
GSE72509 · 5 steps · RNA-Seq · code_examples
The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. (2015)
GSE54321 · 3 steps · GSE · code_examples
Early specification of CD8+ T lymphocyte fates during adaptive immunity revealed by single-cell gene-expression analyses. (2014)