Search publications

Self-Transfecting Micellar RNA: Modulating Nanoparticle Cell Interactions via High Density Display of Small Molecule Ligands on Micelle Coronas.

Bioconjugate chemistry · 2018 · 29(1): 126-135

The intracellular delivery of synthetic nucleic acids represents a major challenge in biotechnology and in biomedicine. Methods to deliver short, double-stranded RNA to living cells are of particular interest because of the potential to engage the RNA interference machinery and …

PMID 29286237 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 ↗

NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing.

Nature structural & molecular biology · 2017 · 24(10): 816-824

MicroRNA (miRNA) biogenesis is known to be modulated by a variety of RNA-binding proteins (RBPs), but in most cases, individual RBPs appear to influence the processing of a small subset of target miRNAs. Here, we report that the RNA-binding NONO-PSF …

PMID 28846091 DOI ↗

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 ↗

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 ↗

Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions.

Advances in experimental medicine and biology · 2016 · 907: 1-28

After an RNA is transcribed, it undergoes a variety of processing steps that can change the encoded protein sequence (through alternative splicing and RNA editing), regulate the stability of the RNA, and control subcellular localization, timing, and rate of translation. …

PMID 27256380 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 ↗

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 ↗

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 ↗

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 ↗

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 ↗

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 ↗

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 ↗

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 ↗

RNA-seq analysis of gene expression and alternative splicing by double-random priming strategy.

Methods in molecular biology (Clifton, N.J.) · 2011 · 729: 247-55

Transcriptome analysis by deep sequencing, more commonly known as RNA-seq is, becoming the method of choice for gene discovery and quantitative splicing detection. We published a double-random priming RNA-seq approach capable of generating strand-specific information [Li et al., Proc Natl …

PMID 21365495 DOI ↗

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 ↗

Alternative splicing in stem cell self-renewal and diferentiation.

Advances in experimental medicine and biology · 2010 · 695: 92-104

This chapter provides a review of recent advances in understanding the importance of alternative pre-messenger RNA splicing in stem cell biology. The majority of transcribed pre-mRNAs undergo RNA splicing where introns are excised and exons are juxtaposed to form mature …

PMID 21222201 DOI ↗

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 ↗

A regulator of Dscam mutually exclusive splicing fidelity.

Nature structural & molecular biology · 2007 · 14(12): 1134-40

The Down syndrome cell adhesion molecule (Dscam) gene has essential roles in neural wiring and pathogen recognition in Drosophila melanogaster. Dscam encodes 38,016 distinct isoforms via extensive alternative splicing. The 95 alternative exons in Dscam are organized into clusters that …

PMID 21188797 DOI ↗

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 ↗

Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements.

PLoS genetics · 2007 · 3(5): e85

Knowledge of the functional cis-regulatory elements that regulate constitutive and alternative pre-mRNA splicing is fundamental for biology and medicine. Here we undertook a genome-wide comparative genomics approach using available mammalian genomes to identify conserved intronic splicing regulatory elements (ISREs). Our …

PMID 17530930 DOI ↗

Splicing regulators: targets and drugs.

Genome biology · 2005 · 6(12): 240

Silencing of splicing regulators by RNA interference, combined with splicing-specific microarrays, has revealed a complex network of distinct alternative splicing events in Drosophila, while a high-throughput screen of more than 6,000 compounds has identified drugs that interfere specifically and directly …

PMID 16356274 DOI ↗

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 ↗