Search publications
52 results for “differentiation”
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Zfp697/ZNF697 is an RNA-binding protein that modulates TGF-β1 signaling and hepatic inflammation in liver disease.
Molecular metabolism · 2026 : 102457
Liver diseases driven by metabolic dysfunction, inflammation, and fibrosis such as metabolic dysfunction-associated steatotic liver disease (MASLD), including metabolic dysfunction-associated steatohepatitis (MASH), and acute liver injury represent a growing global health burden. The zinc finger protein Zfp697 (ZNF697 in humans) …
PMID 42875003 DOI ↗
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The YTHDF proteins modulate Alzheimer's disease-associated brain gene signatures.
Molecular neurodegeneration · 2026 · 21(1)
Gene signatures of Alzheimer's disease (AD) brains reflect the output of a complex interplay of genetic, epigenetic, epi-transcriptomic, and post-transcriptional regulations. To nominate candidate factors modulating these signatures, we developed a machine learning model to integrate cellular and molecular features …
PMID 42811341 DOI ↗
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Localized regulation of cell junction mRNAs is required for epithelial cell integrity.
RNA (New York, N.Y.) · 2026 · 32(5): 635-653
Epithelial cells exhibit a highly polarized organization along their apico-basal axis, a feature that is critical to their function and is frequently perturbed in cancer. One less explored process modulating epithelial cell polarity is the subcellular localization of mRNA molecules. …
PMID 41535088 DOI ↗
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Flipper: An advanced framework for identifying differential RNA binding behavior with eCLIP data.
bioRxiv : the preprint server for biology · 2026
Crosslinking and immunoprecipitation (CLIP) methods remain the gold standard for characterizing RNA binding protein (RBP) behavior. As a result, many researchers rely on CLIP to assess how treatments targeting RBPs alter binding patterns and regulatory activity. However, current tools for …
PMID 41959526 DOI ↗
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Single-cell and isoform-specific translational profiling of the mouse brain.
Nature · 2026
The brain displays the richest repertoire of post-transcriptional mechanisms regulating mRNA translation<sup>1-11</sup>. Among these, alternative splicing has been shown to drive cell-type specificity and, when disrupted, is strongly linked to neurological disorders<sup>12-17</sup>. However, genome-wide measurements of mRNA translation with isoform …
PMID 41708856 DOI ↗
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MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy.
Neurobiology of disease · 2026 · 221: 107305
Myotonic dystrophy type 1 (DM1) arises from toxic CUG-expanded DMPK transcripts that sequester Muscleblind-like (MBNL) proteins, yet how this molecular lesion perturbs brain development in congenital DM1 (CDM) remains unknown. Here, we identify an unanticipated developmental role for MBNL2 in …
PMID 41644016 DOI ↗
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Dosage-sensitive <i>RBFOX2</i> autoregulation promotes cardiomyocyte differentiation by maturing the transcriptome.
bioRxiv : the preprint server for biology · 2025
Haploinsufficiency of the RNA splicing regulator, <i>RBFOX2</i> , is linked to congenital heart disease (CHD), yet its pathogenic mechanisms remain unclear. Here, we demonstrate that RBFOX2 is essential for progressing cardiomyocyte (CM) differentiation by shifting exon usage profiles to more …
PMID 41280054 DOI ↗
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Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted.
Nature · 2025 · 639(8054): 483-492
Tissue-resident memory CD8 T (T<sub>RM</sub>) cells provide protection from infection at barrier sites. In the small intestine, T<sub>RM</sub> cells are found in at least two distinct subpopulations: one with higher expression of effector molecules and another with greater memory potential<sup>1</sup>. …
PMID 39843748 DOI ↗
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ePRINT: exonuclease assisted mapping of protein-RNA interactions.
Genome biology · 2024 · 25(1): 140
RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactions, such as CLIP, rely on purifying single proteins at a time. Our new …
PMID 38807229 DOI ↗
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Functional Diversity of Memory CD8 T Cells is Spatiotemporally Imprinted.
bioRxiv : the preprint server for biology · 2024
Tissue-resident memory CD8 T cells (T<sub>RM</sub>) kill infected cells and recruit additional immune cells to limit pathogen invasion at barrier sites. Small intestinal (SI) T<sub>RM</sub> cells consist of distinct subpopulations with higher expression of effector molecules or greater memory potential. …
PMID 38585842 DOI ↗
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RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression.
Molecular cell · 2023 · 83(19): 3421-3437.e11
The nuclear receptor co-repressor (NCoR) complex mediates transcriptional repression dependent on histone deacetylation by histone deacetylase 3 (HDAC3) as a component of the complex. Unexpectedly, we found that signaling by the receptor activator of nuclear factor κB (RANK) converts the …
PMID 37751740 DOI ↗
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In Vivo Screening Unveils Pervasive RNA-Binding Protein Dependencies in Leukemic Stem Cells and Identifies ELAVL1 as a Therapeutic Target.
Blood cancer discovery · 2023 · 4(3): 180-207
Acute myeloid leukemia (AML) is fueled by leukemic stem cells (LSC) whose determinants are challenging to discern from hematopoietic stem cells (HSC) or uncover by approaches focused on general cell properties. We have identified a set of RNA-binding proteins (RBP) …
PMID 36763002 DOI ↗
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Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection.
PLoS biology · 2023 · 21(1): e3001983
During a microbial infection, responding CD8+ T cells give rise to effector cells that provide acute host defense and memory cells that provide sustained protection. An alternative outcome is exhaustion, a state of T cell dysfunction that occurs in the …
PMID 36716323 DOI ↗
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Small intestine and colon tissue-resident memory CD8<sup>+</sup> T cells exhibit molecular heterogeneity and differential dependence on Eomes.
Immunity · 2023 · 56(1): 207-223.e8
Tissue-resident memory CD8<sup>+</sup> T (T<sub>RM</sub>) cells are a subset of memory T cells that play a critical role in limiting early pathogen spread and controlling infection. T<sub>RM</sub> cells exhibit differences across tissues, but their potential heterogeneity among distinct anatomic compartments …
PMID 36580919 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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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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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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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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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 ↗
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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 ↗
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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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Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses.
Science immunology · 2020 · 5(50)
Inflammatory bowel disease (IBD) encompasses a spectrum of gastrointestinal disorders driven by dysregulated immune responses against gut microbiota. We integrated single-cell RNA and antigen receptor sequencing to elucidate key components, cellular states, and clonal relationships of the peripheral and gastrointestinal …
PMID 32826341 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 mRNA Decay Factor CAR-1/LSM14 Regulates Axon Regeneration via Mitochondrial Calcium Dynamics.
Current biology : CB · 2020 · 30(5): 865-876.e7
mRNA decay factors regulate mRNA turnover by recruiting non-translating mRNAs and targeting them for translational repression and mRNA degradation. How mRNA decay pathways regulate cellular function in vivo with specificity is poorly understood. Here, we show that C. elegans mRNA …
PMID 31983639 DOI ↗
Datasets 25+
Zfp697/ZNF697 is an RNA-binding protein that modulates TGF-β1 2 signaling and hepatic inflammation in liver disease
Mus musculus · GPL30172
Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation
GPL17021
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [scRNA-Seq]
GPL24676
Densely interconnected transcriptional circuits control cell states in human hematopoiesis
Homo sapiens · GPL4685
Aberrant splicing of U12-type introns is the hallmark of ZRSR2 mutant myelodysplastic syndrome
Homo sapiens · GPL11154
Definition of a Small Core Transcriptional Circuit Regulated by AML1-ETO [ChIP-seq, Cut&Run]
Homo sapiens · GPL24676
Definition of a Small Core Transcriptional Circuit Regulated by AML1-ETO [RNA-seq]
Homo sapiens · GPL18573
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
In vivo CRISPR screening unveils RNA binding protein dependencies for leukemic stem cells and identifies ELAVL1 as a potential therapeutic target [eCLIPseq]
Mus musculus · GPL21103
In vivo CRISPR screening unveils RNA binding protein dependencies for leukemic stem cells and identifies ELAVL1 as a potential therapeutic target [RNA-seq]
Mus musculus · GPL18480
Exonuclease assisted mapping of protein-RNA interactions (ePRINT)
Homo sapiens · GPL30173
Mitochondrial double-stranded RNA triggers chronic stress in aged neurons
Homo sapiens · GPL24676, GPL30173
Tissue-resident memory CD8 T Cell Diversity is Spatiotemporally Imprinted
Mus musculus · GPL24247
The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [polysome RNA-seq]
Homo sapiens · GPL20301
The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RRBS]
Homo sapiens · GPL16791
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression (ChIP-Seq)
Mus musculus · GPL21103
CRISPR/Cas9 screening of RNA binding proteins (RBPs) that regulate RUNX1 isoform production
Homo sapiens · GPL20301
The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [ATAC-Seq]
Homo sapiens · GPL11154
Tissue-resident memory CD8 T Cell Diversity is Spatiotemporally Imprinted [snRNA-Seq]
Mus musculus · GPL24247
The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [CLIP-Seq]
Homo sapiens · GPL20301
RBM17 Mediates Evasion of Pro-Leukemic Factors from Splicing-coupled NMD to Enforce Leukemic Stem Cell Maintenance
Homo sapiens · GPL20301
Global Identification of the miR-130a targetome in human HSPC Reveals a Novel Role for TBL1XR1 in Hematopoietic Stem Cell Self-Renewal and t(8;21) AML [CUT&RUN]
Homo sapiens · GPL18573
Showing first 25 dataset results.
Analyses 25
GSE157072 · 3 steps · RNA-Seq · code_examples
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. (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)
GSE112383 · 3 steps · RNA-Seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE112439 · 4 steps · Bisulfite-Seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE112479 · 3 steps · GSE · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE112782 · 5 steps · RIP-Seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE124071 · 3 steps · ATAC-seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE124072 · 3 steps · RNA-Seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE125808 · 4 steps · RNA-Seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE125954 · 4 steps · ChIP-Seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE134164 · 3 steps · RNA-Seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE85908 · 11 steps · RNA-Seq · code_examples
Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation. (2017)
GSE89036 · 3 steps · ChIP-Seq · code_examples
Early transcriptional and epigenetic regulation of CD8<sup>+</sup> T cell differentiation revealed by single-cell RNA sequencing. (2017)
GSE89405 · 39 steps · RNA-Seq · code_examples
Early transcriptional and epigenetic regulation of CD8<sup>+</sup> T cell differentiation revealed by single-cell RNA sequencing. (2017)
GSE95237 · 3 steps · ChIP-Seq · code_examples
Early transcriptional and epigenetic regulation of CD8<sup>+</sup> T cell differentiation revealed by single-cell RNA sequencing. (2017)
GSE95238 · 3 steps · geo_data_processing
Early transcriptional and epigenetic regulation of CD8<sup>+</sup> T cell differentiation revealed by single-cell RNA sequencing. (2017)
GSE16678 · 7 steps · GSE · code_examples
A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells. (2010)
GSE16681 · 1 step · GSE · code_examples
A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells. (2010)
GSE16687 · 7 steps · GSE · code_examples
A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells. (2010)
GSE16689 · 7 steps · GSE · code_examples
A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells. (2010)