Search publications

Engineered U1 snRNAs to modulate alternatively spliced exons.

Methods (San Diego, Calif.) · 2022 · 205: 140-148

Alternative splicing accounts for a considerable portion of transcriptomic diversity, as most protein-coding genes are spliced into multiple mRNA isoforms. However, errors in splicing patterns can give rise to mis-splicing with pathological consequences, such as the congenital diseases familial dysautonomia, …

PMID 35764245 DOI ↗

Pre-existing adaptive immunity to the RNA-editing enzyme Cas13d in humans.

Nature medicine · 2022 · 28(7): 1372-1376

RNA-guided RNA-targeting nucleases, such as CRISPR-Cas13 proteins, have therapeutic potential for gene editing. Among Cas13d enzymes, Cas13d from the bacteria Ruminococcus flavefaciens (RfxCas13d) is of particular interest owing to its small size and high specificity. However, the existence of pre-existing …

PMID 35668177 DOI ↗

Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq.

Nature protocols · 2022 · 17(5): 1223-1265

Discovery of interaction sites between RNA-binding proteins (RBPs) and their RNA targets plays a critical role in enabling our understanding of how these RBPs control RNA processing and regulation. Cross-linking and immunoprecipitation (CLIP) provides a generalizable, transcriptome-wide method by which …

PMID 35322209 DOI ↗

Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.

Research square · 2022

The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral …

PMID 35313591 DOI ↗

Integrative RNA-omics Discovers GNAS Alternative Splicing as a Phenotypic Driver of Splicing Factor-Mutant Neoplasms.

Cancer discovery · 2022 · 12(3): 836-855

Mutations in splicing factors (SF) are the predominant class of mutations in myelodysplastic syndrome (MDS), but convergent downstream disease drivers remain elusive. To identify common direct targets of missplicing by mutant U2AF1 and SRSF2, we performed RNA sequencing and enhanced …

PMID 34620690 DOI ↗

Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.

bioRxiv : the preprint server for biology · 2022

The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral …

PMID 35233578 DOI ↗

Global analysis of RNA-binding proteins identifies a positive feedback loop between LARP1 and MYC that promotes tumorigenesis.

Cellular and molecular life sciences : CMLS · 2022 · 79(3): 147

In addition to genomic alterations, aberrant changes in post-transcriptional regulation can modify gene function and drive cancer development. RNA-binding proteins (RBPs) are a large class of post-transcriptional regulators that have been increasingly implicated in carcinogenesis. By integrating multi-omics data, we …

PMID 35195778 DOI ↗

Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing.

Molecular cell · 2022 · 82(3): 645-659.e9

Pseudouridine is a modified nucleotide that is prevalent in human mRNAs and is dynamically regulated. Here, we investigate when in their life cycle mRNAs become pseudouridylated to illuminate the potential regulatory functions of endogenous mRNA pseudouridylation. Using single-nucleotide resolution pseudouridine …

PMID 35051350 DOI ↗

Non-microRNA binding competitively inhibits LIN28 regulation.

Cell reports · 2021 · 36(6): 109517

RNA binding protein (RBP) expression is finite. For RBPs that are vastly outnumbered by their potential target sites, a simple competition for binding can set the magnitude of post-transcriptional control. Here, we show that LIN28, best known for its direct …

PMID 34380031 DOI ↗

Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.

Nature methods · 2021 · 18(5): 507-519

RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets …

PMID 33963355 DOI ↗

A CRISPR RNA-binding protein screen reveals regulators of RUNX1 isoform generation.

Blood advances · 2021 · 5(5): 1310-1323

The proper balance of hematopoietic stem cell (HSC) self-renewal and differentiation is critical for normal hematopoiesis and is disrupted in hematologic malignancy. Among regulators of HSC fate, transcription factors have a well-defined central role, and mutations promote malignant transformation. More …

PMID 33656539 DOI ↗

Repeat RNA expansion disorders of the nervous system: post-transcriptional mechanisms and therapeutic strategies.

Critical reviews in biochemistry and molecular biology · 2021 · 56(1): 31-53

Dozens of incurable neurological disorders result from expansion of short repeat sequences in both coding and non-coding regions of the transcriptome. Short repeat expansions underlie microsatellite repeat expansion (MRE) disorders including myotonic dystrophy (DM1, CUG_50-3,500 in <i>DMPK</i>; DM2, CCTG_75-11,000 in …

PMID 33172304 DOI ↗

The sustained expression of Cas9 targeting toxic RNAs reverses disease phenotypes in mouse models of myotonic dystrophy type 1.

Nature biomedical engineering · 2021 · 5(2): 157-168

Myotonic dystrophy type I (DM1) is a multisystemic autosomal-dominant inherited human disorder that is caused by CTG microsatellite repeat expansions (MREs) in the 3' untranslated region of DMPK. Toxic RNAs expressed from such repetitive sequences can be eliminated using CRISPR-mediated …

PMID 32929188 DOI ↗

Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program.

Molecular cell · 2020 · 80(3): 452-469.e9

Although TP53 is the most commonly mutated gene in human cancers, the p53-dependent transcriptional programs mediating tumor suppression remain incompletely understood. Here, to uncover critical components downstream of p53 in tumor suppression, we perform unbiased RNAi and CRISPR-Cas9-based genetic screens …

PMID 33157015 DOI ↗

Evaluation of Engineered CRISPR-Cas-Mediated Systems for Site-Specific RNA Editing.

Cell reports · 2020 · 33(5): 108350

Site-directed RNA editing approaches offer great potential to correct genetic mutations in somatic cells while avoiding permanent off-target genomic edits. Nuclease-dead RNA-targeting CRISPR-Cas systems recruit functional effectors to RNA molecules in a programmable fashion. Here, we demonstrate a Streptococcus pyogenes …

PMID 33147453 DOI ↗

Large-scale tethered function assays identify factors that regulate mRNA stability and translation.

Nature structural & molecular biology · 2020 · 27(10): 989-1000

The molecular functions of the majority of RNA-binding proteins (RBPs) remain unclear, highlighting a major bottleneck to a full understanding of gene expression regulation. Here, we develop a plasmid resource of 690 human RBPs that we subject to luciferase-based 3'-untranslated-region …

PMID 32807991 DOI ↗

DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis.

Life science alliance · 2020 · 3(10)

Tumorigenesis in different segments of the intestinal tract involves tissue-specific oncogenic drivers. In the colon, complement component 3 (C3) activation is a major contributor to inflammation and malignancies. By contrast, tumorigenesis in the small intestine involves fatty acid-binding protein 1 …

PMID 32817263 DOI ↗

Transcriptome-wide analysis of PGC-1α-binding RNAs identifies genes linked to glucagon metabolic action.

Proceedings of the National Academy of Sciences of the United States of America · 2020 · 117(36): 22204-22213

The peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) is a transcriptional coactivator that controls expression of metabolic/energetic genes, programming cellular responses to nutrient and environmental adaptations such as fasting, cold, or exercise. Unlike other coactivators, PGC-1α contains protein domains involved …

PMID 32848060 DOI ↗

Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins.

Genome biology · 2020 · 21(1): 90

A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale analysis …

PMID 32252787 DOI ↗

RNA-targeting CRISPR systems from metagenomic discovery to transcriptomic engineering.

Nature cell biology · 2020 · 22(2): 143-150

Deployment of RNA-guided DNA endonuclease CRISPR-Cas technology has led to radical advances in biology. As the functional diversity of CRISPR-Cas and parallel systems is further explored, RNA manipulation is emerging as a powerful mode of CRISPR-based engineering. In this Perspective, …

PMID 32015437 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 ↗

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 ↗

Advances and challenges in the detection of transcriptome-wide protein-RNA interactions.

Wiley interdisciplinary reviews. RNA · 2018 · 9(1)

RNA binding proteins (RBPs) play key roles in determining cellular behavior by manipulating the processing of target RNAs. Robust methods are required to detect the numerous binding sites of RBPs across the transcriptome. RNA-immunoprecipitation followed by sequencing (RIP-seq) and crosslinking …

PMID 28853213 DOI ↗

Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP).

Methods in molecular biology (Clifton, N.J.) · 2017 · 1648: 177-200

Profiling of RNA binding protein targets in vivo provides critical insights into the mechanistic roles they play in regulating RNA processing. The enhanced crosslinking and immunoprecipitation (eCLIP) methodology provides a framework for robust, reproducible identification of transcriptome-wide protein-RNA interactions, with …

PMID 28766298 DOI ↗

Erratum to: Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP).

Methods in molecular biology (Clifton, N.J.) · 2017 · 1648: E1

PMID 29230720 DOI ↗