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39 results for “transcription factor”
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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 ↗
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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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A protein-RNA interaction atlas of the ribosome biogenesis factor AATF.
Scientific reports · 2019 · 9(1): 11071
AATF is a central regulator of the cellular outcome upon p53 activation, a finding that has primarily been attributed to its function as a transcription factor. Recent data showed that AATF is essential for ribosome biogenesis and plays a role …
PMID 31363146 DOI ↗
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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 ↗
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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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Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9.
Nucleic acids research · 2018 · 46(14): 7323-7338
Adenosine DeAminases acting on RNA (ADAR) catalyzes adenosine-to-inosine (A-to-I) conversion within RNA duplex structures. While A-to-I editing is often dynamically regulated in a spatial-temporal manner, the mechanisms underlying its tissue-selective restriction remain elusive. We have previously reported that transcripts of …
PMID 29733375 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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Biallelic mutations in the 3' exonuclease TOE1 cause pontocerebellar hypoplasia and uncover a role in snRNA processing.
Nature genetics · 2017 · 49(3): 457-464
Deadenylases are best known for degrading the poly(A) tail during mRNA decay. The deadenylase family has expanded throughout evolution and, in mammals, consists of 12 Mg<sup>2+</sup>-dependent 3'-end RNases with substrate specificity that is mostly unknown. Pontocerebellar hypoplasia type 7 (PCH7) …
PMID 28092684 DOI ↗
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Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model.
Genome medicine · 2016 · 8(1): 94
Tuberous sclerosis complex (TSC) is a genetic disease characterized by benign tumor growths in multiple organs and neurological symptoms induced by mTOR hyperfunction. Because the molecular pathology is highly complex and the etiology poorly understood, we employed a defined human …
PMID 27655340 DOI ↗
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Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells.
Nature · 2016 · 532(7600): 508-511
Umbilical cord blood-derived haematopoietic stem cells (HSCs) are essential for many life-saving regenerative therapies. However, despite their advantages for transplantation, their clinical use is restricted because HSCs in cord blood are found only in small numbers. Small molecules that enhance …
PMID 27121842 DOI ↗
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A Gene Regulatory Network Cooperatively Controlled by Pdx1 and Sox9 Governs Lineage Allocation of Foregut Progenitor Cells.
Cell reports · 2015 · 13(2): 326-36
The generation of pancreas, liver, and intestine from a common pool of progenitors in the foregut endoderm requires the establishment of organ boundaries. How dorsal foregut progenitors activate pancreatic genes and evade the intestinal lineage choice remains unclear. Here, we …
PMID 26440894 DOI ↗
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Coordinate Nodal and BMP inhibition directs Baf60c-dependent cardiomyocyte commitment.
Genes & development · 2013 · 27(21): 2332-44
A critical but molecularly uncharacterized step in heart formation and regeneration is the process that commits progenitor cells to differentiate into cardiomyocytes. Here, we show that the endoderm-derived dual Nodal/bone morphogenetic protein (BMP) antagonist Cerberus-1 (Cer1) in embryonic stem cell …
PMID 24186978 DOI ↗
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LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance.
Molecular cell · 2012 · 48(2): 195-206
LIN28 is a conserved RNA-binding protein implicated in pluripotency, reprogramming, and oncogenesis. It was previously shown to act primarily by blocking let-7 microRNA (miRNA) biogenesis, but here we elucidate distinct roles of LIN28 regulation via its direct messenger RNA (mRNA) …
PMID 22959275 DOI ↗
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Transcriptional signature and memory retention of human-induced pluripotent stem cells.
PloS one · 2009 · 4(9): e7076
Genetic reprogramming of somatic cells to a pluripotent state (induced pluripotent stem cells or iPSCs) by over-expression of specific genes has been accomplished using mouse and human cells. However, it is still unclear how similar human iPSCs are to human …
PMID 19763270 DOI ↗
Datasets 25+
Multi-Modal Comparison of human Hepatic Stellate Cells identifies novel therapeutic targets for Metabolic Dysfunction-Associated Steatotic Liver Disease
Homo sapiens · GPL24676, GPL37309
Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation
GPL17021
Foxo1 regulates intestinal tissue-resident memory CD8 T cell biology in an anatomic compartment- and context-specific manner
GPL24247
Densely interconnected transcriptional circuits control cell states in human hematopoiesis
Homo sapiens · GPL4685
Aging-dependent demethylation of regulatory elements correlates with chromatin state and improved insulin secretion by pancreatic β cells
Mus musculus · GPL13112
Defining memory-like CD8 T cells that respond to PD-1 therapy in chronic viral infection
Mus musculus · GPL1261
Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk
Mus musculus · GPL17021
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
Remodeling of oncogenic transcriptomes by small-molecules targeting the RNA-binding protein NONO
Homo sapiens · GPL24676
Next Generation Sequencing Investigation of altered transcripts in presence of dominant-negative transcription factor
Mus musculus · GPL13112
Small intestine and colon tissue-resident memory CD8+ T cells exhibit transcriptional, epigenetic, and functional heterogeneity in concert with differential dependence on Eomesodermin [CITE-seq]
Mus musculus · GPL24247
CRISPR/Cas9 screening of RNA binding proteins (RBPs) that regulate RUNX1 isoform production
Homo sapiens · GPL20301
Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [RNA-seq]
Homo sapiens · GPL24676
Pseudotemporal ordering of single cells reveals metabolic control of postnatal beta cell proliferation
Mus musculus · GPL17021
Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [RBNS]
synthetic construct · GPL34014
Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [SLAM-Seq]
Homo sapiens · GPL24676
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [ChIP-Seq]
Homo sapiens · GPL11154
Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [Cut&Run]
Homo sapiens · GPL24676
Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [eCLIP]
Homo sapiens · GPL24676
Showing first 25 dataset results.
Analyses 3
GSE72408 · 1 step · GSE · code_examples
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. (2022)
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)
GSE74583 · 5 steps · RNA-Seq · code_examples
PPAR-δ is repressed in Huntington's disease, is required for normal neuronal function and can be targeted therapeutically. (2016)