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  1. Expanded encyclopaedias of DNA elements in the human and mouse genomes.

    Nature · 2020 · 583(7818): 699-710

    The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded …

    PMID 32728249 DOI ↗

  2. Suppression of Endothelial AGO1 Promotes Adipose Tissue Browning and Improves Metabolic Dysfunction.

    Circulation · 2020 · 142(4): 365-379

    Metabolic disorders such as obesity and diabetes mellitus can cause dysfunction of endothelial cells (ECs) and vascular rarefaction in adipose tissues. However, the modulatory role of ECs in adipose tissue function is not fully understood. Other than vascular endothelial growth …

    PMID 32393053 DOI ↗

  3. Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors.

    Nature methods · 2020 · 17(6): 636-642

    Genetic screens using pooled CRISPR-based approaches are scalable and inexpensive, but restricted to standard readouts, including survival, proliferation and sortable markers. However, many biologically relevant cell states involve cellular and subcellular changes that are only accessible by microscopic visualization, and …

    PMID 32393832 DOI ↗

  4. Heterogenous Populations of Tissue-Resident CD8<sup>+</sup> T Cells Are Generated in Response to Infection and Malignancy.

    Immunity · 2020 · 52(5): 808-824.e7

    Tissue-resident memory CD8<sup>+</sup> T cells (Trm) provide host protection through continuous surveillance of non-lymphoid tissues. Using single-cell RNA-sequencing (scRNA-seq) and genetic reporter mice, we identified discrete lineages of intestinal antigen-specific CD8<sup>+</sup> T cells, including a Blimp1<sup>hi</sup>Id3<sup>lo</sup> tissue-resident effector cell population …

    PMID 32433949 DOI ↗

  5. Early precursors and molecular determinants of tissue-resident memory CD8<sup>+</sup> T lymphocytes revealed by single-cell RNA sequencing.

    Science immunology · 2020 · 5(47)

    During an immune response to microbial infection, CD8<sup>+</sup> T cells give rise to distinct classes of cellular progeny that coordinately mediate clearance of the pathogen and provide long-lasting protection against reinfection, including a subset of noncirculating tissue-resident memory (T<sub>RM</sub>) cells …

    PMID 32414833 DOI ↗

  6. An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia.

    Nature cancer · 2020 · 1(4): 410-422

    Aggressive myeloid leukemias such as blast crisis chronic myeloid leukemia and acute myeloid leukemia remain highly lethal. Here we report a genome-wide in vivo CRISPR screen to identify new dependencies in this disease. Among these, RNA-binding proteins (RBPs) in general, …

    PMID 34109316 DOI ↗

  7. Author Correction: Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells.

    Nature communications · 2020 · 11(1): 1958

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    PMID 32312984 DOI ↗

  8. 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 ↗

  9. 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 ↗

  10. The mRNA Decay Factor CAR-1/LSM14 Regulates Axon Regeneration via Mitochondrial Calcium Dynamics.

    Current biology : CB · 2020 · 30(5): 865-876.e7

    mRNA decay factors regulate mRNA turnover by recruiting non-translating mRNAs and targeting them for translational repression and mRNA degradation. How mRNA decay pathways regulate cellular function in vivo with specificity is poorly understood. Here, we show that C. elegans mRNA …

    PMID 31983639 DOI ↗

  11. 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 ↗

  12. 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 ↗

  13. Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells.

    Nature communications · 2020 · 11(1): 550

    Many cellular models aimed at elucidating cancer biology do not recapitulate pathobiology including tumor heterogeneity, an inherent feature of cancer that underlies treatment resistance. Here we introduce a cancer modeling paradigm using genetically engineered human pluripotent stem cells (hiPSCs) that …

    PMID 31992716 DOI ↗

  14. Corrigendum: Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells.

    Frontiers in molecular neuroscience · 2019 · 12: 150

    [This corrects the article DOI: 10.3389/fnmol.2018.00261.].

    PMID 31244603 DOI ↗

  15. Regulation of RNA editing by RNA-binding proteins in human cells.

    Communications biology · 2019 · 2: 19

    Adenosine-to-inosine (A-to-I) editing, mediated by the ADAR enzymes, diversifies the transcriptome by altering RNA sequences. Recent studies reported global changes in RNA editing in disease and development. Such widespread editing variations necessitate an improved understanding of the regulatory mechanisms of …

    PMID 30652130 DOI ↗

  16. 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 ↗

  17. Peptide Brush Polymers for Efficient Delivery of a Gene Editing Protein to Stem Cells.

    Angewandte Chemie (International ed. in English) · 2019 · 58(44): 15646-15649

    The scarcity of effective means to deliver functional proteins to living cells is a central problem in biotechnology and medicine. Herein, we report the efficient delivery of an active DNA-modifying enzyme to human stem cells through high-density cell penetrating peptide …

    PMID 31404473 DOI ↗

  18. 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 ↗

  19. Small-Molecule Modulation of TDP-43 Recruitment to Stress Granules Prevents Persistent TDP-43 Accumulation in ALS/FTD.

    Neuron · 2019 · 103(5): 802-819.e11

    Stress granules (SGs) form during cellular stress and are implicated in neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). To yield insights into the role of SGs in pathophysiology, we performed a high-content screen to identify small …

    PMID 31272829 DOI ↗

  20. 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 ↗

  21. 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 ↗

  22. Th17 Lymphocytes Induce Neuronal Cell Death in a Human iPSC-Based Model of Parkinson's Disease.

    Cell stem cell · 2019 · 24(6): 1006

    PMID 31173705 DOI ↗

  23. Active Protein Neddylation or Ubiquitylation Is Dispensable for Stress Granule Dynamics.

    Cell reports · 2019 · 27(5): 1356-1363.e3

    Stress granule (SG) formation is frequently accompanied by ubiquitin proteasome system (UPS) impairment and ubiquitylated protein accumulation. SGs, ubiquitin, and UPS components co-localize, but the relationship between the ubiquitin pathway and SGs has not been systematically characterized. We utilize pharmacological …

    PMID 31042464 DOI ↗

  24. Disruption in A-to-I Editing Levels Affects C. elegans Development More Than a Complete Lack of Editing.

    Cell reports · 2019 · 27(4): 1244-1253.e4

    A-to-I RNA editing, catalyzed by ADAR proteins, is widespread in eukaryotic transcriptomes. Studies showed that, in C. elegans, ADR-2 can actively deaminate dsRNA, whereas ADR-1 cannot. Therefore, we set out to study the effect of each of the ADAR genes …

    PMID 31018137 DOI ↗

  25. Disruption of RNA Metabolism in Neurological Diseases and Emerging Therapeutic Interventions.

    Neuron · 2019 · 102(2): 294-320

    RNA binding proteins are critical to the maintenance of the transcriptome via controlled regulation of RNA processing and transport. Alterations of these proteins impact multiple steps of the RNA life cycle resulting in various molecular phenotypes such as aberrant RNA …

    PMID 30998900 DOI ↗