Search publications
88 results for “gene regulation”
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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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RBP-Maps enables robust generation of splicing regulatory maps.
RNA (New York, N.Y.) · 2019 · 25(2): 193-204
Alternative splicing of pre-messenger RNA transcripts enables the generation of multiple protein isoforms from the same gene locus, providing a major source of protein diversity in mammalian genomes. RNA binding proteins (RBPs) bind to RNA to control splice site choice …
PMID 30413564 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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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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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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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 ↗
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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 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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RNA-binding proteins in neurodegeneration: Seq and you shall receive.
Trends in neurosciences · 2015 · 38(4): 226-36
As critical players in gene regulation, RNA binding proteins (RBPs) are taking center stage in our understanding of cellular function and disease. In our era of bench-top sequencers and unprecedented computational power, biological questions can be addressed in a systematic, …
PMID 25765321 DOI ↗
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Identification of novel long noncoding RNAs underlying vertebrate cardiovascular development.
Circulation · 2015 · 131(14): 1278-1290
Long noncoding RNAs (lncRNAs) have emerged as critical epigenetic regulators with important functions in development and disease. Here, we sought to identify and functionally characterize novel lncRNAs critical for vertebrate development. By relying on human pluripotent stem cell differentiation models, …
PMID 25739401 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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Functional genomic analysis of the let-7 regulatory network in Caenorhabditis elegans.
PLoS genetics · 2013 · 9(3): e1003353
The let-7 microRNA (miRNA) regulates cellular differentiation across many animal species. Loss of let-7 activity causes abnormal development in Caenorhabditis elegans and unchecked cellular proliferation in human cells, which contributes to tumorigenesis. These defects are due to improper expression of …
PMID 23516374 DOI ↗
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Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges.
Nature structural & molecular biology · 2013 · 20(12): 1434-42
Alternative splicing (AS) enables programmed diversity of gene expression across tissues and development. We show here that binding in distal intronic regions (>500 nucleotides (nt) from any exon) by Rbfox splicing factors important in development is extensive and is an …
PMID 24213538 DOI ↗
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Reactivation of fetal splicing programs in diabetic hearts is mediated by protein kinase C signaling.
The Journal of biological chemistry · 2013 · 288(49): 35372-86
Diabetic cardiomyopathy is one of the complications of diabetes that eventually leads to heart failure and death. Aberrant activation of PKC signaling contributes to diabetic cardiomyopathy by mechanisms that are poorly understood. Previous reports indicate that PKC is implicated in …
PMID 24151077 DOI ↗
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Differential L1 regulation in pluripotent stem cells of humans and apes.
Nature · 2013 · 503(7477): 525-529
Identifying cellular and molecular differences between human and non-human primates (NHPs) is essential to the basic understanding of the evolution and diversity of our own species. Until now, preserved tissues have been the main source for most comparative studies between …
PMID 24153179 DOI ↗
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Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing.
Molecular cell · 2013 · 50(2): 223-35
SR proteins are well-characterized RNA binding proteins that promote exon inclusion by binding to exonic splicing enhancers (ESEs). However, it has been unclear whether regulatory rules deduced on model genes apply generally to activities of SR proteins in the cell. …
PMID 23562324 DOI ↗
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Genome-wide approaches to dissect the roles of RNA binding proteins in translational control: implications for neurological diseases.
Frontiers in neuroscience · 2012 · 6: 144
Translational control of messenger RNAs (mRNAs) is a key aspect of neurobiology, defects of which can lead to neurological diseases. In response to stimuli, local translation of mRNAs is activated at synapses to facilitate long-lasting forms of synaptic plasticity, the …
PMID 23060744 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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Misregulated RNA processing in amyotrophic lateral sclerosis.
Brain research · 2012 · 1462: 3-15
Amyotrophic lateral sclerosis (ALS) research is undergoing an era of unprecedented discoveries with the identification of new genes as major genetic causes of this disease. These discoveries reinforce the genetic, clinical and pathological overlap between ALS and frontotemporal lobar degeneration …
PMID 22444279 DOI ↗
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Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins.
Cell reports · 2012 · 1(2): 167-78
Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here, we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate …
PMID 22574288 DOI ↗
Datasets 14
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [PAS-seq]
Homo sapiens · Illumina
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [RNA-Seq]
Homo sapiens · Illumina
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [eCLIP]
Homo sapiens · Illumina
Loss of canonical splicing factor SRSF1 in hepatocytes results in acute liver injury and regeneration
Mus musculus · GPL21103
Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling
Homo sapiens · GPL24676
Exonuclease assisted mapping of protein-RNA interactions (ePRINT)
Homo sapiens · GPL30173
Exonuclease assisted mapping of protein-RNA interactions (ePRINT)
Homo sapiens · GPL24676
Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [RNA-seq]
Homo sapiens · GPL24676
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
Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [Cut&Run]
Homo sapiens · GPL24676
Skipper analysis of RNA-protein interactions highlights depletion of genetic variation in translation factor binding sites
Homo sapiens · GPL24676
Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [eCLIP]
Homo sapiens · GPL24676
Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [Ribo-STAMP cell lines]
Homo sapiens · GPL24676
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