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  1. 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 ↗

  2. 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 ↗

  3. 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 ↗

  4. 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 ↗

  5. 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 ↗

  6. Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for ALS and frontotemporal degeneration.

    Proceedings of the National Academy of Sciences of the United States of America · 2013 · 110(47): E4530-9

    Expanded hexanucleotide repeats in the chromosome 9 open reading frame 72 (C9orf72) gene are the most common genetic cause of ALS and frontotemporal degeneration (FTD). Here, we identify nuclear RNA foci containing the hexanucleotide expansion (GGGGCC) in patient cells, including …

    PMID 24170860 DOI ↗

  7. Coordinate Nodal and BMP inhibition directs Baf60c-dependent cardiomyocyte commitment.

    Genes & development · 2013 · 27(21): 2332-44

    A critical but molecularly uncharacterized step in heart formation and regeneration is the process that commits progenitor cells to differentiate into cardiomyocytes. Here, we show that the endoderm-derived dual Nodal/bone morphogenetic protein (BMP) antagonist Cerberus-1 (Cer1) in embryonic stem cell …

    PMID 24186978 DOI ↗

  8. 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 ↗

  9. ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43.

    Proceedings of the National Academy of Sciences of the United States of America · 2013 · 110(8): E736-45

    Transactivating response region DNA binding protein (TDP-43) is the major protein component of ubiquitinated inclusions found in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) with ubiquitinated inclusions. Two ALS-causing mutants (TDP-43(Q331K) and TDP-43(M337V)), but not wild-type human TDP-43, …

    PMID 23382207 DOI ↗

  10. 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 ↗

  11. Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs.

    Nature neuroscience · 2012 · 15(11): 1488-97

    FUS/TLS (fused in sarcoma/translocated in liposarcoma) and TDP-43 are integrally involved in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. We found that FUS/TLS binds to RNAs from >5,500 genes in mouse and human brain, primarily through a GUGGU-binding motif. We …

    PMID 23023293 DOI ↗

  12. 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 ↗

  13. Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration.

    Development, growth & differentiation · 2012 · 54(7): 673-85

    Salamanders possess an extraordinary capacity for tissue and organ regeneration when compared to mammals. In our effort to characterize the unique transcriptional fingerprint emerging during the early phase of salamander limb regeneration, we identified transcriptional activation of some germline-specific genes …

    PMID 22913491 DOI ↗

  14. 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 ↗

  15. 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 ↗

  16. 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 ↗

  17. 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 ↗

  18. 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 ↗

  19. 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 ↗

  20. Genome-wide approaches in the study of microRNA biology.

    Wiley interdisciplinary reviews. Systems biology and medicine · 2011 · 3(5): 491-512

    MicroRNAs (miRNAs), a class of ∼21-23 nucleotide long non-coding RNAs (ncRNAs), have critical roles in diverse biological processes that encompass development, proliferation, apoptosis, stress response, and fat metabolism. miRNAs recognize their target mRNA transcripts by partial sequence complementarity and collectively …

    PMID 21197653 DOI ↗

  21. 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 ↗

  22. LIN-28 co-transcriptionally binds primary let-7 to regulate miRNA maturation in Caenorhabditis elegans.

    Nature structural & molecular biology · 2011 · 18(3): 302-8

    The highly conserved let-7 microRNA (miRNA) regulates developmental pathways across animal phyla. Mis-expression of let-7 causes lethality in C. elegans and has been associated with several human diseases. We show that timing of let-7 expression in developing worms is under …

    PMID 21297634 DOI ↗

  23. 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 ↗

  24. A model for neural development and treatment of Rett syndrome using human induced pluripotent stem cells.

    Cell · 2010 · 143(4): 527-39

    Autism spectrum disorders (ASD) are complex neurodevelopmental diseases in which different combinations of genetic mutations may contribute to the phenotype. Using Rett syndrome (RTT) as an ASD genetic model, we developed a culture system using induced pluripotent stem cells (iPSCs) …

    PMID 21074045 DOI ↗

  25. A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells.

    Stem cells and development · 2010 · 19(6): 797-807

    Human embryonic stem cells (hESCs) have the potential to differentiate into many adult cell types, and they are being explored as a resource for cell replacement therapies for multiple diseases. In order to optimize in vitro differentiation protocols, it will …

    PMID 19807270 DOI ↗