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  1. Article: ZEB2, the Mowat-Wilson Syndrome Transcription Factor: Confirmations, Novel Functions, and Continuing Surprises

    Birkhoff, Judith C. / Huylebroeck, Danny / Conidi, Andrea

    Genes. 2021 July 03, v. 12, no. 7

    2021  

    Abstract: After its publication in 1999 as a DNA-binding and SMAD-binding transcription factor (TF) that co-determines cell fate in amphibian embryos, ZEB2 was from 2003 studied by embryologists mainly by documenting the consequences of conditional, cell-type ... ...

    Abstract After its publication in 1999 as a DNA-binding and SMAD-binding transcription factor (TF) that co-determines cell fate in amphibian embryos, ZEB2 was from 2003 studied by embryologists mainly by documenting the consequences of conditional, cell-type specific Zeb2 knockout (cKO) in mice. In between, it was further identified as causal gene causing Mowat-Wilson Syndrome (MOWS) and novel regulator of epithelial–mesenchymal transition (EMT). ZEB2’s functions and action mechanisms in mouse embryos were first addressed in its main sites of expression, with focus on those that helped to explain neurodevelopmental and neural crest defects seen in MOWS patients. By doing so, ZEB2 was identified in the forebrain as the first TF that determined timing of neuro-/gliogenesis, and thereby also the extent of different layers of the cortex, in a cell non-autonomous fashion, i.e., by its cell-intrinsic control within neurons of neuron-to-progenitor paracrine signaling. Transcriptomics-based phenotyping of Zeb2 mutant mouse cells have identified large sets of intact-ZEB2 dependent genes, and the cKO approaches also moved to post-natal brain development and diverse other systems in adult mice, including hematopoiesis and various cell types of the immune system. These new studies start to highlight the important adult roles of ZEB2 in cell–cell communication, including after challenge, e.g., in the infarcted heart and fibrotic liver. Such studies may further evolve towards those documenting the roles of ZEB2 in cell-based repair of injured tissue and organs, downstream of actions of diverse growth factors, which recapitulate developmental signaling principles in the injured sites. Evident questions are about ZEB2’s direct target genes, its various partners, and ZEB2 as a candidate modifier gene, e.g., in other (neuro)developmental disorders, but also the accurate transcriptional and epigenetic regulation of its mRNA expression sites and levels. Other questions start to address ZEB2’s function as a niche-controlling regulatory TF of also other cell types, in part by its modulation of growth factor responses (e.g., TGFβ/BMP, Wnt, Notch). Furthermore, growing numbers of mapped missense as well as protein non-coding mutations in MOWS patients are becoming available and inspire the design of new animal model and pluripotent stem cell-based systems. This review attempts to summarize in detail, albeit without discussing ZEB2’s role in cancer, hematopoiesis, and its emerging roles in the immune system, how intense ZEB2 research has arrived at this exciting intersection.
    Keywords adults ; amphibians ; animal models ; brain ; cortex ; epigenetics ; gene expression ; heart ; hematopoiesis ; immune system ; liver cirrhosis ; mice ; modifiers (genes) ; mutants ; neural crest ; phenotype ; transcription (genetics) ; transcription factors ; transcriptomics
    Language English
    Dates of publication 2021-0703
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes12071037
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: ZEB2, the Mowat-Wilson Syndrome Transcription Factor: Confirmations, Novel Functions, and Continuing Surprises.

    Birkhoff, Judith C / Huylebroeck, Danny / Conidi, Andrea

    Genes

    2021  Volume 12, Issue 7

    Abstract: After its publication in 1999 as a DNA-binding and SMAD-binding transcription factor (TF) that co-determines cell fate in amphibian embryos, ZEB2 was from 2003 studied by embryologists mainly by documenting the consequences of conditional, cell-type ... ...

    Abstract After its publication in 1999 as a DNA-binding and SMAD-binding transcription factor (TF) that co-determines cell fate in amphibian embryos, ZEB2 was from 2003 studied by embryologists mainly by documenting the consequences of conditional, cell-type specific
    MeSH term(s) Animals ; Disease Models, Animal ; Epigenesis, Genetic ; Facies ; Genetic Predisposition to Disease/genetics ; Hirschsprung Disease/genetics ; Humans ; Intellectual Disability/genetics ; Mice ; Mice, Knockout ; Microcephaly/genetics ; Mutation ; Phenotype ; Pluripotent Stem Cells/metabolism ; Transcription Factors/chemistry ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Zinc Finger E-box Binding Homeobox 2/chemistry ; Zinc Finger E-box Binding Homeobox 2/genetics ; Zinc Finger E-box Binding Homeobox 2/metabolism
    Chemical Substances Transcription Factors ; ZEB2 protein, human ; ZEB2 protein, mouse ; Zinc Finger E-box Binding Homeobox 2
    Language English
    Publishing date 2021-07-03
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes12071037
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Zeb2 DNA-Binding Sites in Neuroprogenitor Cells Reveal Autoregulation and Affirm Neurodevelopmental Defects, Including in Mowat-Wilson Syndrome

    Birkhoff, Judith C. / Korporaal, Anne L. / Brouwer, Rutger W. W. / Nowosad, Karol / Milazzo, Claudia / Mouratidou, Lidia / van den Hout, Mirjam C. G. N. / van IJcken, Wilfred F. J. / Huylebroeck, Danny / Conidi, Andrea

    Genes (Basel). 2023 Mar. 02, v. 14, no. 3

    2023  

    Abstract: Functional perturbation and action mechanism studies have shown that the transcription factor Zeb2 controls cell fate decisions, differentiation, and/or maturation in multiple cell lineages in embryos and after birth. In cultured embryonic stem cells ( ... ...

    Abstract Functional perturbation and action mechanism studies have shown that the transcription factor Zeb2 controls cell fate decisions, differentiation, and/or maturation in multiple cell lineages in embryos and after birth. In cultured embryonic stem cells (ESCs), Zeb2’s mRNA/protein upregulation is necessary for the exit from primed pluripotency and for entering general and neural differentiation. We edited mouse ESCs to produce Flag-V5 epitope-tagged Zeb2 protein from one endogenous allele. Using chromatin immunoprecipitation coupled with sequencing (ChIP-seq), we mapped 2432 DNA-binding sites for this tagged Zeb2 in ESC-derived neuroprogenitor cells (NPCs). A new, major binding site maps promoter-proximal to Zeb2 itself. The homozygous deletion of this site demonstrates that autoregulation of Zeb2 is necessary to elicit the appropriate Zeb2-dependent effects in ESC-to-NPC differentiation. We have also cross-referenced all the mapped Zeb2 binding sites with previously obtained transcriptome data from Zeb2 perturbations in ESC-derived NPCs, GABAergic interneurons from the ventral forebrain of mouse embryos, and stem/progenitor cells from the post-natal ventricular-subventricular zone (V-SVZ) in mouse forebrain, respectively. Despite the different characteristics of each of these neurogenic systems, we found interesting target gene overlaps. In addition, our study also contributes to explaining developmental disorders, including Mowat-Wilson syndrome caused by ZEB2 deficiency, and also other monogenic syndromes.
    Keywords alleles ; autoregulation ; brain ; chromatin immunoprecipitation ; homozygosity ; interneurons ; mice ; transcription factors ; transcriptome
    Language English
    Dates of publication 2023-0302
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14030629
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Zeb2 DNA-Binding Sites in Neuroprogenitor Cells Reveal Autoregulation and Affirm Neurodevelopmental Defects, Including in Mowat-Wilson Syndrome.

    Birkhoff, Judith C / Korporaal, Anne L / Brouwer, Rutger W W / Nowosad, Karol / Milazzo, Claudia / Mouratidou, Lidia / van den Hout, Mirjam C G N / van IJcken, Wilfred F J / Huylebroeck, Danny / Conidi, Andrea

    Genes

    2023  Volume 14, Issue 3

    Abstract: Functional perturbation and action mechanism studies have shown that the transcription factor Zeb2 controls cell fate decisions, differentiation, and/or maturation in multiple cell lineages in embryos and after birth. In cultured embryonic stem cells ( ... ...

    Abstract Functional perturbation and action mechanism studies have shown that the transcription factor Zeb2 controls cell fate decisions, differentiation, and/or maturation in multiple cell lineages in embryos and after birth. In cultured embryonic stem cells (ESCs), Zeb2's mRNA/protein upregulation is necessary for the exit from primed pluripotency and for entering general and neural differentiation. We edited mouse ESCs to produce Flag-V5 epitope-tagged Zeb2 protein from one endogenous allele. Using chromatin immunoprecipitation coupled with sequencing (ChIP-seq), we mapped 2432 DNA-binding sites for this tagged Zeb2 in ESC-derived neuroprogenitor cells (NPCs). A new, major binding site maps promoter-proximal to
    MeSH term(s) Animals ; Mice ; Binding Sites ; DNA/chemistry ; DNA/metabolism ; Homozygote ; Neurons/metabolism ; Neurons/pathology ; Sequence Deletion ; Zinc Finger E-box Binding Homeobox 2/genetics ; Zinc Finger E-box Binding Homeobox 2/metabolism ; Mouse Embryonic Stem Cells/metabolism
    Chemical Substances DNA (9007-49-2) ; ZEB2 protein, mouse ; Zinc Finger E-box Binding Homeobox 2
    Language English
    Publishing date 2023-03-02
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14030629
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Identification of SOX2 Interacting Proteins in the Developing Mouse Lung With Potential Implications for Congenital Diaphragmatic Hernia.

    Schilders, Kim A A / Edel, Gabriëla G / Eenjes, Evelien / Oresta, Bianca / Birkhoff, Judith / Boerema-de Munck, Anne / Buscop-van Kempen, Marjon / Liakopoulos, Panagiotis / Kolovos, Petros / Demmers, Jeroen A A / Poot, Raymond / Wijnen, Rene M H / Tibboel, Dick / Rottier, Robbert J

    Frontiers in pediatrics

    2022  Volume 10, Page(s) 881287

    Abstract: Congenital diaphragmatic hernia is a structural birth defect of the diaphragm, with lung hypoplasia and persistent pulmonary hypertension. Aside from vascular defects, the lungs show a disturbed balance of differentiated airway epithelial cells. The Sry ... ...

    Abstract Congenital diaphragmatic hernia is a structural birth defect of the diaphragm, with lung hypoplasia and persistent pulmonary hypertension. Aside from vascular defects, the lungs show a disturbed balance of differentiated airway epithelial cells. The Sry related HMG box protein SOX2 is an important transcription factor for proper differentiation of the lung epithelium. The transcriptional activity of SOX2 depends on interaction with other proteins and the identification of SOX2-associating factors may reveal important complexes involved in the disturbed differentiation in CDH. To identify SOX2-associating proteins, we purified SOX2 complexes from embryonic mouse lungs at 18.5 days of gestation. Mass spectrometry analysis of SOX2-associated proteins identified several potential candidates, among which were the Chromodomain Helicase DNA binding protein 4 (CHD4), Cut-Like Homeobox1 (CUX1), and the Forkhead box proteins FOXP2 and FOXP4. We analyzed the expression patterns of FOXP2, FOXP4, CHD4, and CUX1 in lung during development and showed co-localization with SOX2. Co-immunoprecipitations validated the interactions of these four transcription factors with SOX2, and large-scale chromatin immunoprecipitation (ChIP) data indicated that SOX2 and CHD4 bound to unique sites in the genome, but also co-occupied identical regions, suggesting that these complexes could be involved in co-regulation of genes involved in the respiratory system.
    Language English
    Publishing date 2022-05-09
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2711999-3
    ISSN 2296-2360
    ISSN 2296-2360
    DOI 10.3389/fped.2022.881287
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Integrative and perturbation-based analysis of the transcriptional dynamics of TGFβ/BMP system components in transition from embryonic stem cells to neural progenitors.

    Dries, Ruben / Stryjewska, Agata / Coddens, Kathleen / Okawa, Satoshi / Notelaers, Tineke / Birkhoff, Judith / Dekker, Mike / Verfaillie, Catherine M / Del Sol, Antonio / Mulugeta, Eskeatnaf / Conidi, Andrea / Grosveld, Frank G / Huylebroeck, Danny

    Stem cells (Dayton, Ohio)

    2019  Volume 38, Issue 2, Page(s) 202–217

    Abstract: Cooperative actions of extrinsic signals and cell-intrinsic transcription factors alter gene regulatory networks enabling cells to respond appropriately to environmental cues. Signaling by transforming growth factor type β (TGFβ) family ligands (eg, bone ...

    Abstract Cooperative actions of extrinsic signals and cell-intrinsic transcription factors alter gene regulatory networks enabling cells to respond appropriately to environmental cues. Signaling by transforming growth factor type β (TGFβ) family ligands (eg, bone morphogenetic proteins [BMPs] and Activin/Nodal) exerts cell-type specific and context-dependent transcriptional changes, thereby steering cellular transitions throughout embryogenesis. Little is known about coordinated regulation and transcriptional interplay of the TGFβ system. To understand intrafamily transcriptional regulation as part of this system's actions during development, we selected 95 of its components and investigated their mRNA-expression dynamics, gene-gene interactions, and single-cell expression heterogeneity in mouse embryonic stem cells transiting to neural progenitors. Interrogation at 24 hour intervals identified four types of temporal gene transcription profiles that capture all stages, that is, pluripotency, epiblast formation, and neural commitment. Then, between each stage we performed esiRNA-based perturbation of each individual component and documented the effect on steady-state mRNA levels of the remaining 94 components. This exposed an intricate system of multilevel regulation whereby the majority of gene-gene interactions display a marked cell-stage specific behavior. Furthermore, single-cell RNA-profiling at individual stages demonstrated the presence of detailed co-expression modules and subpopulations showing stable co-expression modules such as that of the core pluripotency genes at all stages. Our combinatorial experimental approach demonstrates how intrinsically complex transcriptional regulation within a given pathway is during cell fate/state transitions.
    MeSH term(s) Bone Morphogenetic Proteins/metabolism ; Cell Differentiation ; Embryonic Stem Cells/metabolism ; Humans ; Transforming Growth Factor beta/metabolism
    Chemical Substances Bone Morphogenetic Proteins ; Transforming Growth Factor beta
    Language English
    Publishing date 2019-12-13
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1143556-2
    ISSN 1549-4918 ; 1066-5099
    ISSN (online) 1549-4918
    ISSN 1066-5099
    DOI 10.1002/stem.3111
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Targeted chromatin conformation analysis identifies novel distal neural enhancers of ZEB2 in pluripotent stem cell differentiation.

    Birkhoff, Judith C / Brouwer, Rutger W W / Kolovos, Petros / Korporaal, Anne L / Bermejo-Santos, Ana / Boltsis, Ilias / Nowosad, Karol / van den Hout, Mirjam C G N / Grosveld, Frank G / van IJcken, Wilfred F J / Huylebroeck, Danny / Conidi, Andrea

    Human molecular genetics

    2020  Volume 29, Issue 15, Page(s) 2535–2550

    Abstract: The transcription factor zinc finger E-box binding protein 2 (ZEB2) controls embryonic and adult cell fate decisions and cellular maturation in many stem/progenitor cell types. Defects in these processes in specific cell types underlie several aspects of ...

    Abstract The transcription factor zinc finger E-box binding protein 2 (ZEB2) controls embryonic and adult cell fate decisions and cellular maturation in many stem/progenitor cell types. Defects in these processes in specific cell types underlie several aspects of Mowat-Wilson syndrome (MOWS), which is caused by ZEB2 haplo-insufficiency. Human ZEB2, like mouse Zeb2, is located on chromosome 2 downstream of a ±3.5 Mb-long gene-desert, lacking any protein-coding gene. Using temporal targeted chromatin capture (T2C), we show major chromatin structural changes based on mapping in-cis proximities between the ZEB2 promoter and this gene desert during neural differentiation of human-induced pluripotent stem cells, including at early neuroprogenitor cell (NPC)/rosette state, where ZEB2 mRNA levels increase significantly. Combining T2C with histone-3 acetylation mapping, we identified three novel candidate enhancers about 500 kb upstream of the ZEB2 transcription start site. Functional luciferase-based assays in heterologous cells and NPCs reveal co-operation between these three enhancers. This study is the first to document in-cis Regulatory Elements located in ZEB2's gene desert. The results further show the usability of T2C for future studies of ZEB2 REs in differentiation and maturation of multiple cell types and the molecular characterization of newly identified MOWS patients that lack mutations in ZEB2 protein-coding exons.
    MeSH term(s) Animals ; Cell Differentiation/genetics ; Cell Lineage/genetics ; Chromatin/genetics ; Chromatin/ultrastructure ; Enhancer Elements, Genetic/genetics ; Facies ; Gene Expression Regulation/genetics ; Hirschsprung Disease/genetics ; Hirschsprung Disease/pathology ; Homeodomain Proteins/genetics ; Humans ; Intellectual Disability/genetics ; Intellectual Disability/pathology ; Mice ; Microcephaly/genetics ; Microcephaly/pathology ; Neural Stem Cells/metabolism ; Neural Stem Cells/pathology ; Pluripotent Stem Cells/metabolism ; Pluripotent Stem Cells/ultrastructure ; Regulatory Sequences, Nucleic Acid ; Zinc Finger E-box Binding Homeobox 2/genetics
    Chemical Substances Chromatin ; Homeodomain Proteins ; ZEB2 protein, human ; Zinc Finger E-box Binding Homeobox 2
    Language English
    Publishing date 2020-07-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1108742-0
    ISSN 1460-2083 ; 0964-6906
    ISSN (online) 1460-2083
    ISSN 0964-6906
    DOI 10.1093/hmg/ddaa141
    Database MEDical Literature Analysis and Retrieval System OnLINE

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