Search publications
15 results for “high-throughput sequencing”
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Variation in single-nucleotide sensitivity of eCLIP derived from reverse transcription conditions.
Methods (San Diego, Calif.) · 2017 · 126: 29-37
Crosslinking and immunoprecipitation (CLIP) followed by high-throughput sequencing identifies the binding sites of RNA binding proteins on RNAs. The covalent RNA-amino acid adducts produced by UV irradiation can cause premature reverse transcription termination and deletions (referred to as crosslink-induced mutation …
PMID 28790018 DOI ↗
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CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins.
Methods (San Diego, Calif.) · 2017 · 118-119: 50-59
Identification of in vivo direct RNA targets for RNA binding proteins (RBPs) provides critical insight into their regulatory activities and mechanisms. Recently, we described a methodology for enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP) using antibodies against endogenous …
PMID 28003131 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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Tethered Function Assays as Tools to Elucidate the Molecular Roles of RNA-Binding Proteins.
Advances in experimental medicine and biology · 2016 · 907: 61-88
Dynamic regulation of RNA molecules is critical to the survival and development of cells. Messenger RNAs are transcribed in the nucleus as intron-containing pre-mRNAs and bound by RNA-binding proteins, which control their fate by regulating RNA stability, splicing, polyadenylation, translation, …
PMID 27256382 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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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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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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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 ↗
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High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection.
Journal of virology · 2012 · 86(1): 226-35
Human cytomegalovirus (HCMV) contributes its own set of microRNAs (miRNAs) during lytic infection of cells, likely fine-tuning conditions important for viral replication. To enhance our understanding of this component of the HCMV-host transcriptome, we have conducted deep-sequencing analysis of small …
PMID 22013051 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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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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Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans.
Nature structural & molecular biology · 2010 · 17(2): 173-9
MicroRNAs (miRNAs) regulate gene expression by guiding Argonaute proteins to specific target mRNA sequences. Identification of bona fide miRNA target sites in animals is challenging because of uncertainties regarding the base-pairing requirements between miRNA and target as well as the …
PMID 20062054 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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RNA sequence analysis defines Dicer's role in mouse embryonic stem cells.
Proceedings of the National Academy of Sciences of the United States of America · 2007 · 104(46): 18097-102
Short RNA expression was analyzed from Dicer-positive and Dicer-knockout mouse embryonic [corrected] stem (ES) cells, using high-throughput pyrosequencing. A correlation of miRNA quantification with sequencing frequency estimates that there are 110,000 miRNAs per ES cell, the majority of which can …
PMID 17989215 DOI ↗
Datasets 17
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
Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease
Homo sapiens · GPL15520
RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination
Homo sapiens · GPL15520
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (splicing arrays)
Homo sapiens · GPL15106
High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection
Homo sapiens · GPL10999
Epigenetics CRISPRi screen in mouse neuronal progenitor cells (NPCs)
Mus musculus · GPL21626
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (CLIP-Seq)
Homo sapiens · GPL9052
Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (Affymetrix)
Mus musculus · GPL13185
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (RNA-Seq)
Homo sapiens · GPL9115
Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (CLIP)
Mus musculus · GPL9250
Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (RNA-seq)
Mus musculus · GPL9250
Variation in single-nucleotide sensitivity of eCLIP derived from reverse transcription conditions
Homo sapiens · GPL20301
LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance (splicing array)
Homo sapiens · GPL15106
CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins
Homo sapiens · GPL20301
LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance (HTS)
Homo sapiens · GPL9052
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