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Ribosomal Pulldown Assays and Their Use to Analyze Gene Expression in Multiple Inner Ear Cell Types
Research of inner ear cell development and function has greatly benefited from the advent of next-generation sequencing. Cell type-specific analysis of gene expression by RNA sequencing (RNA-seq) has mediated ...
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Article
Open AccessA CRISPR knockout screen reveals new regulators of canonical Wnt signaling
The Wnt signaling pathways play fundamental roles during both development and adult homeostasis. Aberrant activation of the canonical Wnt signal transduction pathway is involved in many diseases including canc...
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Article
Open AccessExpression pattern of cochlear microRNAs in the mammalian auditory hindbrain
The auditory system comprises the auditory periphery, engaged in sound transduction and the central auditory system, implicated in auditory information processing and perception. Recently, evidence mounted tha...
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Open AccessA comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis
Frequent activation of the co-transcriptional factor YAP is observed in a large number of solid tumors. Activated YAP associates with enhancer loci via TEAD4-DNA-binding protein and stimulates cancer aggressiv...
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Activity-dependent neuroprotective protein (ADNP) is an alcohol-responsive gene and negative regulator of alcohol consumption in female mice
Neuroadaptations in the brain reward system caused by excessive alcohol intake, lead to drinking escalation and alcohol use disorder phenotypes. Activity-dependent neuroprotective protein (ADNP) is crucial for...
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Helios is a key transcriptional regulator of outer hair cell maturation
The sensory cells that are responsible for hearing include the cochlear inner hair cells (IHCs) and outer hair cells (OHCs), with the OHCs being necessary for sound sensitivity and tuning1. Both cell types are th...
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Open AccessGenomic meta-analysis of the interplay between 3D chromatin organization and gene expression programs under basal and stress conditions
Our appreciation of the critical role of the genome’s 3D organization in gene regulation is steadily increasing. Recent 3C-based deep sequencing techniques elucidated a hierarchy of structures that underlie th...
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Open AccessFunctional CRISPR screen identifies AP1-associated enhancer regulating FOXF1 to modulate oncogene-induced senescence
Functional characterization of non-coding elements in the human genome is a major genomic challenge and the maturation of genome-editing technologies is revolutionizing our ability to achieve this task. Oncoge...
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Open AccessFOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map
Recent sequencing technologies enable joint quantification of promoters and their enhancer regions, allowing inference of enhancer–promoter links. We show that current enhancer–promoter inference methods produ...
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Characterization of noncoding regulatory DNA in the human genome
Genome-wide map** of regulatory elements will improve our understanding of how genetic variation in the noncoding genome affects disease phenotypes.
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Open AccessGfi1Cre mice have early onset progressive hearing loss and induce recombination in numerous inner ear non-hair cells
Studies of developmental and functional biology largely rely on conditional expression of genes in a cell type-specific manner. Therefore, the importance of specificity and lack of inherent phenotypes for Cre-dri...
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Open AccessRedifferentiation of expanded human islet β cells by inhibition of ARX
Ex-vivo expansion of adult human islet β cells has been evaluated for generation of abundant insulin-producing cells for transplantation; however, lineage-tracing has demonstrated that this process results in β-c...
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Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9
CRISPR-Cas9 is used for both enrichment and dropout screens of functional enhancers in human cells.
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Open AccessRFX transcription factors are essential for hearing in mice
Sensorineural hearing loss is a common and currently irreversible disorder, because mammalian hair cells (HCs) do not regenerate and current stem cell and gene delivery protocols result only in immature HC-lik...
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Alternative cleavage and polyadenylation: extent, regulation and function
Recent advances in technologies for global map** of alternative polyadenylation (APA) have allowed unprecedented investigation of alternative polyadenylation...
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Open Accessp53 induces transcriptional and translational programs to suppress cell proliferation and growth
Cell growth and proliferation are tightly connected to ensure that appropriately sized daughter cells are generated following mitosis. Energy stress blocks cell growth and proliferation, a critical response fo...
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Open AccessE2F mediates enhanced alternative polyadenylation in proliferation
The majority of mammalian genes contain multiple poly(A) sites in their 3' UTRs. Alternative cleavage and polyadenylation are emerging as an important layer of gene regulation as they generate transcript isofo...
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Open AccessSelective inhibition of microRNA accessibility by RBM38 is required for p53 activity
MicroRNAs (miRNAs) interact with 3′-untranslated regions of messenger RNAs to restrict expression of most protein-coding genes during normal development and cancer. RNA-binding proteins (RBPs) can control the ...
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A Pumilio-induced RNA structure switch in p27-3′ UTR controls miR-221 and miR-222 accessibility
Quiescent cells contain high levels of both the cell cycle inhibitor p27, and the miRNAs that should negatively regulate it. In response to growth factor, the RNA-binding protein PUM1 interacts with the 3′UTR ...
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Open AccessMajor role for mRNA stability in sha** the kinetics of gene induction
mRNA levels in cells are determined by the relative rates of RNA production and degradation. Yet, to date, most analyses of gene expression profiles were focused on mechanisms which regulate transcription, whi...
