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126 results for “Transcription”
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Blurred Boundaries: The RNA Binding Protein Lin28A Is Also an Epigenetic Regulator.
Molecular cell · 2016 · 61(1): 1-2
Lin28A is best known as a post-transcriptional regulator of gene expression. In this issue, Zeng et al. (2016) show that Lin28A has an unexpected role as an epigenetic regulator of DNA.
PMID 26748607 DOI ↗
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The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion.
Annual review of biochemistry · 2015 · 84: 325-54
Throughout their lifetimes, messenger RNAs (mRNAs) associate with proteins to form ribonucleoproteins (mRNPs). Since the discovery of the first mRNP component more than 40 years ago, what is known as the mRNA interactome now comprises >1,000 proteins. These proteins bind …
PMID 25784054 DOI ↗
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The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression.
Science (New York, N.Y.) · 2015 · 350(6259): 455-9
Autoantibodies target the RNA binding protein Ro60 in systemic lupus erythematosus (SLE) and Sjögren's syndrome. However, it is unclear whether Ro60 and its associated RNAs contribute to disease pathogenesis. We catalogued the Ro60-associated RNAs in human cell lines and found …
PMID 26382853 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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Applications of Cas9 as an RNA-programmed RNA-binding protein.
BioEssays : news and reviews in molecular, cellular and developmental biology · 2015 · 37(7): 732-9
The Streptococcus pyogenes CRISPR-Cas system has gained widespread application as a genome editing and gene regulation tool as simultaneous cellular delivery of the Cas9 protein and guide RNAs enables recognition of specific DNA sequences. The recent discovery that Cas9 can …
PMID 25880497 DOI ↗
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Regulation of asymmetric division and CD8+ T lymphocyte fate specification by protein kinase Cζ and protein kinase Cλ/ι.
Journal of immunology (Baltimore, Md. : 1950) · 2015 · 194(5): 2249-59
During an immune response against a microbial pathogen, activated naive T lymphocytes give rise to effector cells that provide acute host defense and memory cells that provide long-lived immunity. It has been shown that T lymphocytes can undergo asymmetric division, …
PMID 25617472 DOI ↗
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The Period protein homolog LIN-42 negatively regulates microRNA biogenesis in C. elegans.
Developmental biology · 2014 · 390(2): 126-35
MicroRNAs (miRNAs) are small RNAs that post-transcriptionally regulate gene expression in many multicellular organisms. They are encoded in the genome and transcribed into primary (pri-) miRNAs before two processing steps that ultimately produce the mature miRNA. In order to generate …
PMID 24699545 DOI ↗
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Early specification of CD8+ T lymphocyte fates during adaptive immunity revealed by single-cell gene-expression analyses.
Nature immunology · 2014 · 15(4): 365-372
T lymphocytes responding to microbial infection give rise to effector cells that mediate acute host defense and memory cells that provide long-lived immunity, but the fundamental question of when and how these cells arise remains unresolved. Here we combined single-cell …
PMID 24584088 DOI ↗
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The dsRBP and inactive editor ADR-1 utilizes dsRNA binding to regulate A-to-I RNA editing across the C. elegans transcriptome.
Cell reports · 2014 · 6(4): 599-607
Inadequate adenosine-to-inosine editing of noncoding regions occurs in disease but is often uncorrelated with ADAR levels, underscoring the need to study deaminase-independent control of editing. C. elegans have two ADAR proteins, ADR-2 and the theoretically catalytically inactive ADR-1. Using high-throughput …
PMID 24508457 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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Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs.
Nature neuroscience · 2012 · 15(11): 1488-97
FUS/TLS (fused in sarcoma/translocated in liposarcoma) and TDP-43 are integrally involved in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. We found that FUS/TLS binds to RNAs from >5,500 genes in mouse and human brain, primarily through a GUGGU-binding motif. We …
PMID 23023293 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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Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration.
Development, growth & differentiation · 2012 · 54(7): 673-85
Salamanders possess an extraordinary capacity for tissue and organ regeneration when compared to mammals. In our effort to characterize the unique transcriptional fingerprint emerging during the early phase of salamander limb regeneration, we identified transcriptional activation of some germline-specific genes …
PMID 22913491 DOI ↗
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Evidence for premature aging due to oxidative stress in iPSCs from Cockayne syndrome.
Human molecular genetics · 2012 · 21(17): 3825-34
Cockayne syndrome (CS) is a human premature aging disorder associated with neurological and developmental abnormalities, caused by mutations mainly in the CS group B gene (ERCC6). At the molecular level, CS is characterized by a deficiency in the transcription-couple DNA …
PMID 22661500 DOI ↗
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Comprehensive identification of miRNA target sites in live animals.
Methods in molecular biology (Clifton, N.J.) · 2011 · 732: 169-85
MicroRNAs (miRNAs) are small RNA molecules that posttranscriptionally regulate the expression of protein-coding genes. The mature miRNAs are loaded into Argonaute-containing protein complexes (miRISC, miRNA Induced S ilencing Complex), and guide these complexes to the 3' UTR of targeted mRNA …
PMID 21431713 DOI ↗
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Genome-wide approaches in the study of microRNA biology.
Wiley interdisciplinary reviews. Systems biology and medicine · 2011 · 3(5): 491-512
MicroRNAs (miRNAs), a class of ∼21-23 nucleotide long non-coding RNAs (ncRNAs), have critical roles in diverse biological processes that encompass development, proliferation, apoptosis, stress response, and fat metabolism. miRNAs recognize their target mRNA transcripts by partial sequence complementarity and collectively …
PMID 21197653 DOI ↗
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Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43.
Nature neuroscience · 2011 · 14(4): 459-68
We used cross-linking and immunoprecipitation coupled with high-throughput sequencing to identify binding sites in 6,304 genes as the brain RNA targets for TDP-43, an RNA binding protein that, when mutated, causes amyotrophic lateral sclerosis. Massively parallel sequencing and splicing-sensitive junction …
PMID 21358643 DOI ↗
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LIN-28 co-transcriptionally binds primary let-7 to regulate miRNA maturation in Caenorhabditis elegans.
Nature structural & molecular biology · 2011 · 18(3): 302-8
The highly conserved let-7 microRNA (miRNA) regulates developmental pathways across animal phyla. Mis-expression of let-7 causes lethality in C. elegans and has been associated with several human diseases. We show that timing of let-7 expression in developing worms is under …
PMID 21297634 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 ↗
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An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells.
Nature structural & molecular biology · 2009 · 16(2): 130-7
The elucidation of a code for regulated splicing has been a long-standing goal in understanding the control of post-transcriptional gene expression events that are crucial for cell survival, differentiation and development. We decoded functional RNA elements in vivo by constructing …
PMID 19136955 DOI ↗
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Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model.
Proceedings of the National Academy of Sciences of the United States of America · 2008 · 105(51): 20179-84
High-throughput sequencing has rapidly gained popularity for transcriptome analysis in mammalian cells because of its ability to generate digital and quantitative information on annotated genes and to detect transcripts and mRNA isoforms. Here, we described a double-random priming method for …
PMID 19088194 DOI ↗
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Divergent transcription from active promoters.
Science (New York, N.Y.) · 2008 · 322(5909): 1849-51
Transcription initiation by RNA polymerase II (RNAPII) is thought to occur unidirectionally from most genes. Here, we present evidence of widespread divergent transcription at protein-encoding gene promoters. Transcription start site-associated RNAs (TSSa-RNAs) nonrandomly flank active promoters, with peaks of antisense …
PMID 19056940 DOI ↗
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The PIWI proteins SMEDWI-2 and SMEDWI-3 are required for stem cell function and piRNA expression in planarians.
RNA (New York, N.Y.) · 2008 · 14(6): 1174-86
PIWI proteins are expressed in germ cells in a wide variety of metazoans, where they participate in the synthesis and function of a novel class of small RNAs called PIWI associated RNAs (piRNAs). One function of piRNAs is to preserve …
PMID 18456843 DOI ↗
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Alternative splicing events identified in human embryonic stem cells and neural progenitors.
PLoS computational biology · 2007 · 3(10): 1951-67
Human embryonic stem cells (hESCs) and neural progenitor (NP) cells are excellent models for recapitulating early neuronal development in vitro, and are key to establishing strategies for the treatment of degenerative disorders. While much effort had been undertaken to analyze …
PMID 17967047 DOI ↗
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Identification and analysis of alternative splicing events conserved in human and mouse.
Proceedings of the National Academy of Sciences of the United States of America · 2005 · 102(8): 2850-5
Alternative pre-mRNA splicing affects a majority of human genes and plays important roles in development and disease. Alternative splicing (AS) events conserved since the divergence of human and mouse are likely of primary biological importance, but relatively few of such …
PMID 15708978 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
Investigating m6A-relevant gene function in neural progenitor cells using CRISPR-Cas9 genome editing and RNA-seq
Homo sapiens · GPL24676
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
Ythdf m6A readers compensate each other in a context dependent manner [3'UTR RNA-seq]
GPL13112
Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE) [dataset2]
GPL20301, GPL24676, GPL34284
Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE) [dataset1]
GPL20301, GPL24676
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
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
Single cell and isoform-specific translational profiling of the mouse brain [ribostamp]
GPL24247
Single cell and isoform-specific translational profiling of the mouse brain [Bulk RNA-seq]
GPL24247
Single cell and isoform-specific translational profiling of the mouse brain [Ribo-STAMP]
GPL24247
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
Comparing isogenic pairs of hESC and hiPSC lines reveals genetic background and reprogramming method as primary sources of transcriptional variation
Homo sapiens · GPL11154
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
Phase II exploratory pharmacogenomics study of cetuximab monotherapy in patients with advanced metastatic CRC
Homo sapiens · GPL571
Integrative Genomic Analysis Reveals Widespread Enhancer Regulation by p53 in Response to DNA Damage
Mus musculus · GPL9115
Showing first 25 dataset results.
Analyses 25+
GSE107122 · 4 steps · RNA-Seq · code_examples
Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size. (2024)
GSE147127 · 5 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE255844 · 5 steps · RNA-Seq · code_examples
Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution. (2024)
GSE162335 · 2 steps · GSE · 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)
GSE123613 · 9 steps · OTHER · code_examples
Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing. (2022)
GSE126263 · 25 steps · RIP-Seq · code_examples
Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma. (2022)
GSE126337 · 3 steps · RNA-Seq · code_examples
Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma. (2022)
GSE134597 · 4 steps · RNA-Seq · code_examples
Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma. (2022)
GSE153264 · 3 steps · RNA-Seq · code_examples
Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML. (2022)
GSE153279 · 13 steps · OTHER · code_examples
Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML. (2022)
GSE72408 · 1 step · GSE · code_examples
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. (2022)
GSE90963 · 35 steps · RNA-Seq · code_examples
Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing. (2022)
GSE157048 · 14 steps · RNA-Seq · code_examples
AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation. (2020)
GSE157049 · 14 steps · RNA-Seq · code_examples
AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation. (2020)
GSE157050 · 6 steps · RNA-Seq · code_examples
AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation. (2020)
GSE157051 · 14 steps · GSE · code_examples
AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation. (2020)
GSE69889 · 5 steps · RNA-Seq · code_examples
A role for alternative splicing in circadian control of exocytosis and glucose homeostasis. (2020)
GSE120023 · 5 steps · OTHER · code_examples
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription. (2019)
GSE120104 · 5 steps · ChIP-Seq · code_examples
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription. (2019)
Showing first 25 analysis results.