Histone demethylase KDM4B regulates otic vesicle invagination via epigenetic control of Dlx3 expression

In vertebrates, the inner ear arises from the otic placode, a thickened swathe of ectoderm that invaginates to form the otic vesicle. We report that histone demethylase KDM4B is dynamically expressed during early stages of chick inner ear formation. A loss of KDM4B results in defective invagination and striking morphological changes in the otic epithelium, characterized by abnormal localization of adhesion and cytoskeletal molecules and reduced expression of several inner ear markers, including Dlx3. In vivo chromatin immunoprecipitation reveals direct and dynamic occupancy of KDM4B and its target, H3K9me3, at regulatory regions of the Dlx3 locus. Accordingly, coelectroporations of DLX3 or KDM4B encoding constructs, but not a catalytically dead mutant of KDM4B, rescue the ear invagination phenotype caused by KDM4B knockdown. Moreover, a loss of DLX3 phenocopies a loss of KDM4B. Collectively, our findings suggest that KDM4B play a critical role during inner ear invagination via modulating histone methylation of the direct target Dlx3.

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The Sound of Silence: Mouse Models for Hearing Loss

Genetics Research International ◽

10.4061/2011/416450 ◽

2011 ◽

Vol 2011 ◽

pp. 1-9 ◽

Cited By ~ 2

Author(s):

Sumantra Chatterjee ◽

Thomas Lufkin

Keyword(s):

Hearing Loss ◽

Inner Ear ◽

Hearing Impairment ◽

Economic Loss ◽

Signaling Cascades ◽

Otic Vesicle ◽

New Genes ◽

Personal Loss ◽

The Individual

Sensorineural hearing loss is one of the most common disabilities in humans. It is estimated that about 278 million people worldwide have slight to extreme hearing loss in both ears, which results in an economic loss for the country and personal loss for the individual. It is thus critical to have a deeper understanding of the causes for hearing loss to better manage and treat the affected individuals. The mouse serves as an excellent model to study and recapitulate some of these phenotypes, identify new genes which cause deafness, and to study their roles in vivo and in detail. Mutant mice have been instrumental in elucidating the function and mechanisms of the inner ear. The development and morphogenesis of the inner ear from an ectodermal layer into distinct auditory and vestibular components depends on well-coordinated gene expression and well-orchestrated signaling cascades within the otic vesicle and interactions with surrounding layers of tissues. Any disruption in these pathways can lead to hearing impairment. This review takes a look at some of the genes and their corresponding mice mutants that have shed light on the mechanism governing hearing impairment (HI) in humans.

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Ets-dependent Regulation of Target Gene Expression during Megakaryopoiesis

Journal of Biological Chemistry ◽

10.1074/jbc.m407489200 ◽

2004 ◽

Vol 279 (50) ◽

pp. 52183-52190 ◽

Cited By ~ 57

Author(s):

Pascale Jackers ◽

Gabor Szalai ◽

Omar Moussa ◽

Dennis K. Watson

Keyword(s):

Transcription Factors ◽

Rna Polymerase Ii ◽

Chromatin Immunoprecipitation ◽

Target Genes ◽

Hematopoietic Stem ◽

Exogenous Expression ◽

Direct Target ◽

Transcriptional Complex

Megakaryopoiesis is the process by which hematopoietic stem cells in the bone marrow differentiate into mature megakaryocytes. The expression of megakaryocytic genes during megakaryopoiesis is controlled by specific transcription factors. Fli-1 and GATA-1 transcription factors are required for development of megakaryocytes and promoter analysis has definedin vitrofunctional binding sites for these factors in several megakaryocytic genes, includingGPIIb,GPIX, andC-MPL. Herein, we utilize chromatin immunoprecipitation to examine the presence of Ets-1, Fli-1, and GATA-1 on these promotersin vivo. Fli-1 and Ets-1 occupy the promoters ofGPIIb,GPIX, andC-MPLgenes in both Meg-01 and CMK11-5 cells. WhereasGPIIbis expressed in both Meg-01 and CMK11-5 cells,GPIXandC-MPLare only expressed in the more differentiated CMK11–5 cells. Thus,in vivooccupancy by an Ets factor is not sufficient to promote transcription of some megakaryocytic genes. GATA-1 and Fli-1 are both expressed in CMK11-5 cells and co-occupy theGPIXandC-MPLpromoters. Transcription of all three megakaryocytic genes is correlated with the presence of acetylated histone H3 and phosphorylated RNA polymerase II on their promoters. We also show that exogenous expression of GATA-1 in Meg-01 cells leads to the expression of endogenous c-mpl and gpIX mRNA. WhereasGPIIb,GPIX, andC-MPLare direct target genes for Fli-1, both Fli-1 and GATA-1 are required for formation of an active transcriptional complex on theC-MPLandGPIXpromotersin vivo. In contrast,GPIIbexpression appears to be independent of GATA-1 in Meg-01 cells.

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The Saccharomyces cerevisiae Histone Demethylase Jhd1 Fine-Tunes the Distribution of H3K36me2

Molecular and Cellular Biology ◽

10.1128/mcb.00127-07 ◽

2007 ◽

Vol 27 (13) ◽

pp. 5055-5065 ◽

Cited By ~ 26

Author(s):

Jia Fang ◽

Gregory J. Hogan ◽

Gaoyang Liang ◽

Jason D. Lieb ◽

Yi Zhang

Keyword(s):

Saccharomyces Cerevisiae ◽

Histone Methylation ◽

Histone Demethylase ◽

Lysine Methylation ◽

Chromatin Dynamics ◽

Histone Lysine Methylation ◽

Jmjc Domain ◽

Steady State Levels ◽

Microarray Studies

ABSTRACT Histone methylation plays important roles in the regulation of chromatin dynamics and transcription. Steady-state levels of histone lysine methylation are regulated by a balance between enzymes that catalyze either the addition or removal of methyl groups. Using an activity-based biochemical approach, we recently uncovered the JmjC domain as an evolutionarily conserved signature motif for histone demethylases. Furthermore, we demonstrated that Jhd1, a JmjC domain-containing protein in Saccharomyces cerevisiae, is an H3K36-specific demethylase. Here we report further characterization of Jhd1. Similar to its mammalian homolog, Jhd1-catalyzed histone demethylation requires iron and α-ketoglutarate as cofactors. Mutation and deletion studies indicate that the JmjC domain and adjacent sequences are critical for Jhd1 enzymatic activity, while the N-terminal PHD domain is dispensable. Overexpression of JHD1 results in a global reduction of H3K36 methylation in vivo. Finally, chromatin immunoprecipitation-coupled microarray studies reveal subtle changes in the distribution of H3K36me2 upon overexpression or deletion of JHD1. Our studies establish Jhd1 as a histone demethylase in budding yeast and suggest that Jhd1 functions to maintain the fidelity of histone methylation patterns along transcription units.

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Prenatal electroporation-mediated gene transfer restores Slc26a4 knock-out mouse hearing and vestibular function

Scientific Reports ◽

10.1038/s41598-019-54262-3 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Hiroki Takeda ◽

Toru Miwa ◽

Min Young Kim ◽

Byung Yoon Choi ◽

Yorihisa Orita ◽

...

Keyword(s):

Survival Rate ◽

Gene Transfer ◽

Inner Ear ◽

Morphological Changes ◽

Treatment Strategies ◽

Vestibular Function ◽

Knock Out ◽

Genetic Hearing Loss ◽

Mouse Hearing

AbstractThe otocyst, an anlage of the inner ear, presents an attractive target to study treatment strategies for genetic hearing loss and inner ear development. We have previously reported that electroporation-mediated transuterine gene transfer of Connexin30, utilizing a monophasic pulse into Connexin30−/− mouse otocysts at embryonic day 11.5, is able to prevent putative hearing deterioration. However, it is not clear whether supplementary gene transfer can rescue significant morphological changes, caused by genetic deficits. In addition, with the transuterine gene transfer technique utilized in our previous report, the survival rate of embryos and their mothers after treatment was low, which became a serious obstacle for effective in vivo experiments. Here, we set out to elucidate the feasibility of supplementation therapy in Slc26a4 deficient mice, utilizing biphasic pulses, optimized by modifying pulse conditions. Modification of the biphasic pulse conditions during electroporation increased the survival rate. In addition, supplementation of the target gene cDNA into the otocysts of homozygous Slc24a4 knockout mice significantly prevented enlargement of the endolymphatic space in the inner ear areas; moreover, it rescued hearing and vestibular function of mice in vivo.

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Fra-1 Induces Morphological Transformation and Increases In Vitro Invasiveness and Motility of Epithelioid Adenocarcinoma Cells

Molecular and Cellular Biology ◽

10.1128/mcb.18.12.7095 ◽

1998 ◽

Vol 18 (12) ◽

pp. 7095-7105 ◽

Cited By ~ 132

Author(s):

Olga Kustikova ◽

Dmitrii Kramerov ◽

Mariam Grigorian ◽

Vladimir Berezin ◽

Elisabeth Bock ◽

...

Keyword(s):

Tumor Progression ◽

Cell Lines ◽

Transcriptional Activation ◽

Morphological Changes ◽

Critical Role ◽

Morphological Transformation ◽

Morphological Alterations ◽

Nuclear Extracts

ABSTRACT Two cell lines originating from a common ancestral tumor, CSML0 and CSML100, were used as a model to study AP-1 transcription factors at different steps of tumor progression. CSML0 cells have an epithelial morphology; they express epithelial but not mesenchymal markers and are invasive neither in vitro nor in vivo. CSML100 possesses all characteristics of a highly progressive carcinoma. These cells do not form tight contacts, are highly invasive in vitro, and are metastatic in vivo. AP-1 activity was considerably higher in CSML100 cells than in CSML0 cells. There was a common predominant Jun component, namely, JunD, detected in both cell lines. We found that the enhanced level of AP-1 in CSML100 cells was due to high expression of Fra-1 and Fra-2 proteins, which were undetectable in CSML0 nuclear extracts. Analysis of the transcription of different AP-1 members in various cell lines derived from tumors of epithelial origin revealed a correlation of fra-1 expression with mesenchymal characteristics of carcinoma cells. Moreover, we show here for the first time that the expression of exogenous Fra-1 in epithelioid cells results in morphological changes that resemble fibroblastoid conversion. Cells acquire an elongated shape and become more motile and invasive in vitro. Morphological alterations were accompanied by transcriptional activation of certain genes whose expression is often induced at late stages of tumor progression. These data suggest a critical role of the Fra-1 protein in the development of epithelial tumors.

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Nanomedicine for Inner Ear Diseases: A Review of Recent In Vivo Studies

BioMed Research International ◽

10.1155/2017/3098230 ◽

2017 ◽

Vol 2017 ◽

pp. 1-6 ◽

Cited By ~ 6

Author(s):

Dong-Kee Kim

Keyword(s):

Inner Ear ◽

Animal Studies ◽

Morphological Changes ◽

In Vivo Studies ◽

Ear Diseases ◽

Age Related ◽

Effective Delivery ◽

Inner Ear Disease ◽

Or Genes

Nanoparticles are promising therapeutic options for inner ear disease. In this report, we review in vivo animal studies in the otologic field using nanoparticles over the past 5 years. Many studies have used nanoparticles to deliver drugs, genes, and growth factors, and functional and morphological changes have been observed. The constituents of nanoparticles are also diversifying into various biocompatible materials, including poly(lactic-co-glycolic acid) (PLGA). The safe and effective delivery of drugs or genes in the inner ear will be a breakthrough for the treatment of inner ear diseases, including age-related hearing loss.

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In Vivo Study of Trichoderma-Pathogen-Plant Interactions, Using Constitutive and Inducible Green Fluorescent Protein Reporter Systems

Applied and Environmental Microbiology ◽

10.1128/aem.70.5.3073-3081.2004 ◽

2004 ◽

Vol 70 (5) ◽

pp. 3073-3081 ◽

Cited By ~ 97

Author(s):

Zexun Lu ◽

Riccardo Tombolini ◽

Sheridan Woo ◽

Susanne Zeilinger ◽

Matteo Lorito ◽

...

Keyword(s):

Green Fluorescent Protein ◽

Plant Pathogens ◽

Fluorescent Protein ◽

Morphological Changes ◽

Critical Role ◽

Pythium Ultimum ◽

Confocal Scanning Laser Microscopy ◽

Green Fluorescent

ABSTRACT Plant tissue colonization by Trichoderma atroviride plays a critical role in the reduction of diseases caused by phytopathogenic fungi, but this process has not been thoroughly studied in situ. We monitored in situ interactions between gfp-tagged biocontrol strains of T. atroviride and soilborne plant pathogens that were grown in cocultures and on cucumber seeds by confocal scanning laser microscopy and fluorescence stereomicroscopy. Spores of T. atroviride adhered to Pythium ultimum mycelia in coculture experiments. In mycoparasitic interactions of T. atroviride with P. ultimum or Rhizoctonia solani, the mycoparasitic hyphae grew alongside the pathogen mycelia, and this was followed by coiling and formation of specialized structures similar to hooks, appressoria, and papillae. The morphological changes observed depended on the pathogen tested. Branching of T. atroviride mycelium appeared to be an active response to the presence of the pathogenic host. Mycoparasitism of P. ultimum by T. atroviride occurred on cucumber seed surfaces while the seeds were germinating. The interaction of these fungi on the cucumber seeds was similar to the interaction observed in coculture experiments. Green fluorescent protein expression under the control of host-inducible promoters was also studied. The induction of specific Trichoderma genes was monitored visually in cocultures, on plant surfaces, and in soil in the presence of colloidal chitin or Rhizoctonia by confocal microscopy and fluorescence stereomicroscopy. These tools allowed initiation of the mycoparasitic gene expression cascade to be monitored in vivo.

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Comparison of Herpes Simplex Virus Reactivation in Ganglia In Vivo and in Explants Demonstrates Quantitative and Qualitative Differences

Journal of Virology ◽

10.1128/jvi.78.14.7784-7794.2004 ◽

2004 ◽

Vol 78 (14) ◽

pp. 7784-7794 ◽

Cited By ~ 43

Author(s):

N. M. Sawtell ◽

R. L. Thompson

Keyword(s):

Herpes Simplex Virus ◽

Herpes Simplex ◽

Neuronal Degeneration ◽

Morphological Changes ◽

Critical Role ◽

Primary Concern ◽

Reactivation Process ◽

Latently Infected ◽

Simplex Virus

ABSTRACT The in vivo ganglionic environment directs the latent herpes simplex virus transcriptional program. Since stress-driven perturbations in sensory neurons are thought to play a critical role in the transition from latency to reactivation, a primary concern in the selection of a valid model of the molecular interactions leading to reactivation is the faithful recapitulation of these environments. In this study reactivation of latently infected ganglia excised and cultured in vitro (explanted) is compared to reactivation occurring in latently infected ganglia in vivo following hyperthermic stress. Three notable points emerged. (i) Neurons in explanted ganglia exhibited marked morphological changes within 2 to 3 h postexplant. DNA fragmentation in neuronal nuclei was detected at 3 h, and atypical expression of cell cycle- and stress-regulated proteins such as geminin, cdk2, cdk4, and cytochrome c became apparent at 2 to 48 h. These changes were associated with axotomy and explant and not with the initiation or progression of reactivation and were not observed in ganglia following in vivo hyperthermic stress. (ii) Despite these differences, during the first 22 h primary reactivation events were restricted to a very small number of neurons in vivo and in explanted ganglia. This suggests that at any given time only a few latently infected neurons are competent to reactivate or that the probability of reactivation occurring in any particular neuron is very low. Importantly, the marked changes detected in explanted ganglia were not correlated with increased reactivation, demonstrating that these changes were not associated with the reactivation process per se. (iii) Secondary spread of virus was evident in explanted ganglia within 36 h, an event not observed in vivo. We conclude that explant reactivation may provide an ancillary system for selected studies of the early events in reactivation. However, clear signs of neuronal degeneration within 2 to 3 h postexplant indicate that these ganglia are undergoing major physiological changes not associated with the reactivation process. This ongoing neurodegeneration could alter even the early virus-host interactions in reactivation, and thus caution in the extrapolation of results obtained in explants to the in vivo interactions initiating reactivation is warranted.

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Histone Demethylase PHF8 Is Required for the Development of the Zebrafish Inner Ear and Posterior Lateral Line

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2020.566504 ◽

2020 ◽

Vol 8 ◽

Author(s):

Jing He ◽

Zhiwei Zheng ◽

Xianyang Luo ◽

Yongjun Hong ◽

Wenling Su ◽

...

Keyword(s):

Cell Migration ◽

Inner Ear ◽

Lateral Line ◽

Target Genes ◽

Histone Demethylase ◽

Otic Vesicle ◽

Lateral Line System ◽

Potential Candidate ◽

Line System ◽

Posterior Lateral Line

Histone demethylase PHF8 is crucial for multiple developmental processes, and hence, the awareness of its function in developing auditory organs needs to be increased. Using in situ hybridization (ISH) labeling, the mRNA expression of PHF8 in the zebrafish lateral line system and otic vesicle was monitored. The knockdown of PHF8 by morpholino significantly disrupted the development of the posterior lateral line system, which impacted cell migration and decreased the number of lateral line neuromasts. The knockdown of PHF8 also resulted in severe malformation of the semicircular canal and otoliths in terms of size, quantity, and position during the inner ear development. The loss of function of PHF8 also induced a defective differentiation in sensory hair cells in both lateral line neuromasts and the inner ear. ISH analysis of embryos that lacked PHF8 showed alterations in the expression of many target genes of several signaling pathways concerning cell migration and deposition, including the Wnt and FGF pathways. In summary, the current findings established PHF8 as a novel epigenetic element in developing auditory organs, rendering it a potential candidate for hearing loss therapy.

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Histone demethylase KDM6B regulates human podocyte differentiation in vitro

Biochemical Journal ◽

10.1042/bcj20180968 ◽

2019 ◽

Vol 476 (12) ◽

pp. 1741-1751

Author(s):

Yanyan Guo ◽

Zuying Xiong ◽

Xiaoqiang Guo

Keyword(s):

Histone Methylation ◽

Chromatin Immunoprecipitation ◽

Kidney Development ◽

Histone Demethylase ◽

Differentiation Markers ◽

Chromatin Immunoprecipitation Assay ◽

H3k27 Methylation ◽

Filtration Barrier ◽

Histone H3k27

Abstract Podocytes are terminally differentiated and highly specialized glomerular cells, which have an essential role as a filtration barrier against proteinuria. Histone methylation has been shown to influence cell development, but its role in podocyte differentiation is less understood. In this study, we first examined the expression pattern of histone demethylase KDM6B at different times of cultured human podocytes in vitro. We found that the expression of KDM6B and podocyte differentiation markers WT1 and Nephrin are increased in the podocyte differentiation process. In cultured podocytes, KDM6B knockdown with siRNA impaired podocyte differentiation and led to expression down-regulation of WT1 and Nephrin. The treatment of podocytes with GSK-J4, a specific KDM6B inhibitor, can also obtain similar results. Overexpression of WT1 can rescue differentiated phenotype impaired by disruption of KDM6B. ChIP (chromatin immunoprecipitation) assay further indicated that KDM6B can bind the promoter region of WT1 and reduce the histone H3K27 methylation. Podocytes in glomeruli from nephrotic patients exhibited increased KDM6B contents and reduced H3K27me3 levels. These data suggest a role for KDM6B as a regulator of podocyte differentiation, which is important for the understanding of podocyte function in kidney development and related diseases.

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