Search publications
126 results for “Transcript”
-
How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms.
Molecular cell · 2020 · 78(1): 9-29
RNA-binding proteins (RBPs) comprise a large class of over 2,000 proteins that interact with transcripts in all manner of RNA-driven processes. The structures and mechanisms that RBPs use to bind and regulate RNA are incredibly diverse. In this review, we …
PMID 32243832 DOI ↗
-
Direct RNA sequencing enables m<sup>6</sup>A detection in endogenous transcript isoforms at base-specific resolution.
RNA (New York, N.Y.) · 2020 · 26(1): 19-28
Direct RNA sequencing holds great promise for the de novo identification of RNA modifications at single-coordinate resolution; however, interpretation of raw sequencing output to discover modified bases remains a challenge. Using Oxford Nanopore's direct RNA sequencing technology, we developed a …
PMID 31624092 DOI ↗
-
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 ↗
-
Complex Oscillatory Waves Emerging from Cortical Organoids Model Early Human Brain Network Development.
Cell stem cell · 2019 · 25(4): 558-569.e7
Structural and transcriptional changes during early brain maturation follow fixed developmental programs defined by genetics. However, whether this is true for functional network activity remains unknown, primarily due to experimental inaccessibility of the initial stages of the living human brain. …
PMID 31474560 DOI ↗
-
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 ↗
-
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 ↗
-
Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA.
Nature communications · 2019 · 10(1): 1338
Allele-specific protein-RNA binding is an essential aspect that may reveal functional genetic variants (GVs) mediating post-transcriptional regulation. Recently, genome-wide detection of in vivo binding of RNA-binding proteins is greatly facilitated by the enhanced crosslinking and immunoprecipitation (eCLIP) method. We developed …
PMID 30902979 DOI ↗
-
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 ↗
-
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 ↗
-
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 ↗
-
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 ↗
-
Sequence, Structure, and Context Preferences of Human RNA Binding Proteins.
Molecular cell · 2018 · 70(5): 854-867.e9
RNA binding proteins (RBPs) orchestrate the production, processing, and function of mRNAs. Here, we present the affinity landscapes of 78 human RBPs using an unbiased assay that determines the sequence, structure, and context preferences of these proteins in vitro by …
PMID 29883606 DOI ↗
-
Short poly(A) tails are a conserved feature of highly expressed genes.
Nature structural & molecular biology · 2017 · 24(12): 1057-1063
Poly(A) tails are important elements in mRNA translation and stability, although recent genome-wide studies have concluded that poly(A) tail length is generally not associated with translational efficiency in nonembryonic cells. To investigate whether poly(A) tail size might be coupled to …
PMID 29106412 DOI ↗
-
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 ↗
-
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 ↗
-
Early transcriptional and epigenetic regulation of CD8<sup>+</sup> T cell differentiation revealed by single-cell RNA sequencing.
Nature immunology · 2017 · 18(4): 422-432
During microbial infection, responding CD8<sup>+</sup> T lymphocytes differentiate into heterogeneous subsets that together provide immediate and durable protection. To elucidate the dynamic transcriptional changes that underlie this process, we applied a single-cell RNA-sequencing approach and analyzed individual CD8<sup>+</sup> T lymphocytes …
PMID 28218746 DOI ↗
-
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 ↗
-
RNA-binding protein CPEB1 remodels host and viral RNA landscapes.
Nature structural & molecular biology · 2016 · 23(12): 1101-1110
Host and virus interactions occurring at the post-transcriptional level are critical for infection but remain poorly understood. Here, we performed comprehensive transcriptome-wide analyses revealing that human cytomegalovirus (HCMV) infection results in widespread alternative splicing (AS), shortening of 3' untranslated regions …
PMID 27775709 DOI ↗
-
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 ↗
-
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 ↗
-
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 ↗
-
Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival.
Cell reports · 2016 · 15(3): 666-679
Human pluripotent stem cells (hPSCs) require precise control of post-transcriptional RNA networks to maintain proliferation and survival. Using enhanced UV crosslinking and immunoprecipitation (eCLIP), we identify RNA targets of the IMP/IGF2BP family of RNA-binding proteins in hPSCs. At the broad …
PMID 27068461 DOI ↗
-
Programmable RNA Tracking in Live Cells with CRISPR/Cas9.
Cell · 2016 · 165(2): 488-96
RNA-programmed genome editing using CRISPR/Cas9 from Streptococcus pyogenes has enabled rapid and accessible alteration of specific genomic loci in many organisms. A flexible means to target RNA would allow alteration and imaging of endogenous RNA transcripts analogous to CRISPR/Cas-based genomic …
PMID 26997482 DOI ↗
-
A Small RNA-Catalytic Argonaute Pathway Tunes Germline Transcript Levels to Ensure Embryonic Divisions.
Cell · 2016 · 165(2): 396-409
Multiple division cycles without growth are a characteristic feature of early embryogenesis. The female germline loads proteins and RNAs into oocytes to support these divisions, which lack many quality control mechanisms operating in somatic cells undergoing growth. Here, we describe …
PMID 27020753 DOI ↗
-
PPAR-δ is repressed in Huntington's disease, is required for normal neuronal function and can be targeted therapeutically.
Nature medicine · 2016 · 22(1): 37-45
Huntington's disease (HD) is a progressive neurodegenerative disorder caused by a CAG trinucleotide repeat expansion in the huntingtin (HTT) gene, which encodes a polyglutamine tract in the HTT protein. We found that peroxisome proliferator-activated receptor delta (PPAR-δ) interacts with HTT …
PMID 26642438 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
Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay
GPL18573
Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay [miRNA-Seq]
GPL18573
Mapping CCR4-NOT recruitment elements at high resolution reveals transcriptome-wide determinants of mRNA decay [RIP-Seq]
GPL18573
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
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
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [scRNA-Seq]
GPL24676
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
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [eCLIP]
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
Showing first 25 dataset results.
Analyses 25+
GSE299099 · 3 steps · RNA-Seq · code_examples
Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO. (2026)
GSE302648 · 3 steps · geo_data_processing
High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay. (2026)
GSE302649 · 11 steps · eCLIP · geo_data_processing
High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay. (2026)
GSE302651 · 3 steps · geo_data_processing
High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay. (2026)
GSE125970 · 4 steps · RNA-Seq · code_examples
Stratification of enterochromaffin cells by single-cell expression analysis. (2025)
GSE279255 · 2 steps · Spatial transcriptomics · geo_data_processing
Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted. (2025)
GSE280895 · 7 steps · Spatial transcriptomics · geo_data_processing
Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted. (2025)
GSE295421 · 3 steps · RNA-Seq · code_examples
Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs. (2025)
GSE104949 · 9 steps · RIP-Seq · code_examples
Transcriptome regulation by PARP13 in basal and antiviral states in human cells. (2024)
GSE106493 · 4 steps · RIP-Seq · code_examples
Transcriptome regulation by PARP13 in basal and antiviral states in human cells. (2024)
GSE107122 · 4 steps · RNA-Seq · code_examples
Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size. (2024)
GSE114820 · 4 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE143437 · 7 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE147127 · 5 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE210263 · 10 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE215251 · 5 steps · GSE · code_examples
Transcriptome regulation by PARP13 in basal and antiviral states in human cells. (2024)
GSE240014 · 6 steps · RNA-Seq · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
GSE240325 · 7 steps · RNA-Seq · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
GSE240326 · 6 steps · GSE · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
GSE240521 · 9 steps · RIP-Seq · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
GSE248461 · 6 steps · RNA-Seq · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
GSE255844 · 5 steps · RNA-Seq · code_examples
Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution. (2024)
GSE263371 · 6 steps · OTHER · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
GSE263870 · 9 steps · OTHER · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
GSE122425 · 5 steps · RNA-Seq · code_examples
Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP. (2023)
Showing first 25 analysis results.