Joke van Bemmel - Academia.edu (original) (raw)

Papers by Joke van Bemmel

bioRxiv (Cold Spring Harbor Laboratory), Jul 25, 2022

Cell, Oct 1, 2010

Chromatin is important for the regulation of transcription and other functions, yet the diversity... more Chromatin is important for the regulation of transcription and other functions, yet the diversity of chromatin composition and the distribution along chromosomes are still poorly characterized. By integrative analysis of genome-wide binding maps of 53 broadly selected chromatin components in Drosophila cells, we show that the genome is segmented into five principal chromatin types that are defined by unique yet overlapping combinations of proteins and form domains that can extend over > 100 kb. We identify a repressive chromatin type that covers about half of the genome and lacks classic heterochromatin markers. Furthermore, transcriptionally active euchromatin consists of two types that differ in molecular organization and H3K36 methylation and regulate distinct classes of genes. Finally, we provide evidence that the different chromatin types help to target DNA-binding factors to specific genomic regions. These results provide a global view of chromatin diversity and domain organization in a metazoan cell.

Current Biology, Oct 1, 2010

Background: Developmental abnormalities observed in Cornelia de Lange syndrome have been genetica... more Background: Developmental abnormalities observed in Cornelia de Lange syndrome have been genetically linked to mutations in the cohesin machinery. These and other recent experimental findings have led to the suggestion that cohesin, in addition to its canonical function of mediating sister chromatid cohesion, might also be involved in regulating gene expression. Results: We report that cleavage of cohesin's kleisin subunit in postmitotic Drosophila salivary glands induces major changes in the transcript levels of many genes. Kinetic analyses of changes in transcript levels upon cohesin cleavage reveal that a subset of genes responds to cohesin cleavage within a few hours. In addition, cohesin binds to most of these loci, suggesting that cohesin is directly regulating their expression. Among these genes are several that are regulated by the steroid hormone ecdysone. Cytological visualization of transcription at selected ecdysone-responsive genes reveals that puffing at Eip74EF ceases within an hour or two of cohesin cleavage, long before any decline in ecdysone receptor could be detected at this locus. Conclusion: We conclude that cohesin regulates expression of a distinct set of genes, including those mediating the ecdysone response.

Journal of Visualized Experiments, Oct 14, 2022

The spatial organization of the genome contributes to its function and regulation in many context... more The spatial organization of the genome contributes to its function and regulation in many contexts, including transcription, replication, recombination, and repair. Understanding the exact causality between genome topology and function is therefore crucial and increasingly the subject of intensive research. Chromosome conformation capture technologies (3C) allow inferring the 3D structure of chromatin by measuring the frequency of interactions between any region of the genome. Here we describe a fast and simple protocol to perform Capture Hi-C, a 3C-based target enrichment method that characterizes the allele-specific 3D organization of megabased-sized genomic targets at high-resolution. In Capture Hi-C, target regions are captured by an array of biotinylated probes before downstream high-throughput sequencing. Thus, higher resolution and allele-specificity are achieved while improving the timeeffectiveness and affordability of the technology. To demonstrate its strengths, the Capture Hi-C protocol was applied to the mouse X-inactivation center (Xic), the master regulatory locus of X-chromosome inactivation (XCI).

Genome Research, Dec 9, 2009

Joke Gerarda van Bemmel 1. De identificatie van eiwitten die interacties van het genoom met de nu... more Joke Gerarda van Bemmel 1. De identificatie van eiwitten die interacties van het genoom met de nucleaire lamina beïnvloeden bevestigt dat inactief chromatine niet louter aan de rand zit doordat actief chromatine zich in het centrum van de celkern bevindt. 2. Het beschouwen van insulator eiwitten als hoofdrolspelers in genoom-organizatie is eerder een hoopvolle gedachte dan op bewijs gebaseerd. 3. Het bestuderen van de rol van cohesin in genregulatie in mens en vlieg is appels met peren vergelijken. 4. De identificatie van 5 verschillende soorten chromatine bewijst dat de algemeen gebruikte verdeling in eu-en heterochromatine achterhaald is. 5. Een onbevooroordeelde benadering in plaats van hypothese gedreven onderzoek geeft de mogelijkheid tot nieuwe ontdekkingen en paradigma verschuivingen. 6. In de wetenschap heeft men geen gebrek aan tijd maar wel aan prioriteit 7. De impact van een wetenschappelijke presentatie is niet afhankelijk van de tijd die nodig was om de gegevens te genereren, maar van de tijd die besteed is aan het voorbereiden van de presentatie. 8. Promoveren is net als wonen in Amsterdam-Noord, je moet het voortdurend aan iedereen uitleggen. (Suzanne Pietersma) 9. Niet het onderwerp maar juist de methode van onderzoek bepaalt of iets wetenschap is. 10. Gebrek aan carrièredrang leidt tot meer openheid in wetenschappelijke publicaties. 11. "Je bent wat je schudt" brought to you by CORE View metadata, citation and similar papers at core.ac.uk provided by Erasmus University Digital Repository Propositions accompanying the dissertation Chromatin Flavors: Chromatin composition and domain organization in Drosophila melanogaster Joke Gerarda van Bemmel 1. The identification of proteins modulating genome-nuclear lamina interactions confirms that the localization of inactive chromatin at the periphery is not merely the consequence of active chromatin being in the interior of the nucleus. 2. Viewing insulator proteins as master regulators of genome-organization is wish-full thinking rather then evidence based. 3. Studying the role of cohesin in gene-regulation in humans and flies, is like comparing apples and oranges. 4. The identification of 5 distinct chromatin types proves the commonly used separation into euand heterochromatin to be outdated. 5. An unbiased approach instead of hypothesis driven research provides the opportunity for new discoveries and paradigm shifts. 6. In science, there is no lack of time but rather a lack of priorities. 7. The impact of a scientific talk does not depend on the time spent to generate the data but on the time spent to prepare the presentation. 8. Pursuing a PhD is like living in Amsterdam-North, both prompt for explanation. (Adapted from Suzanne Pietersma) 9. Not the subject of study but rather the method determines if something is science. 10. Lack of career ambitions results in increased transparency in scientific publications.

Circulation, Sep 6, 2022

BACKGROUND: GATA4 (GATA-binding protein 4), a zinc finger-containing, DNA-binding transcription f... more BACKGROUND: GATA4 (GATA-binding protein 4), a zinc finger-containing, DNA-binding transcription factor, is essential for normal cardiac development and homeostasis in mice and humans, and mutations in this gene have been reported in human heart defects. Defects in alternative splicing are associated with many heart diseases, yet relatively little is known about how cell type-or cell state-specific alternative splicing is achieved in the heart. Here, we show that GATA4 regulates cell typespecific splicing through direct interaction with RNA and the spliceosome in human induced pluripotent stem cell-derived cardiac progenitors. METHODS: We leveraged a combination of unbiased approaches including affinity purification of GATA4 and mass spectrometry, enhanced cross-linking with immunoprecipitation, electrophoretic mobility shift assays, in vitro splicing assays, and unbiased transcriptomic analysis to uncover GATA4's novel function as a splicing regulator in human induced pluripotent stem cellderived cardiac progenitors. RESULTS: We found that GATA4 interacts with many members of the spliceosome complex in human induced pluripotent stem cell-derived cardiac progenitors. Enhanced cross-linking with immunoprecipitation demonstrated that GATA4 also directly binds to a large number of mRNAs through defined RNA motifs in a sequence-specific manner. In vitro splicing assays indicated that GATA4 regulates alternative splicing through direct RNA binding, resulting in functionally distinct protein products. Correspondingly, knockdown of GATA4 in human induced pluripotent stem cell-derived cardiac progenitors resulted in differential alternative splicing of genes involved in cytoskeleton organization and calcium ion import, with functional consequences associated with the protein isoforms. CONCLUSIONS: This study shows that in addition to its well described transcriptional function, GATA4 interacts with members of the spliceosome complex and regulates cell type-specific alternative splicing via sequence-specific interactions with RNA. Several genes that have splicing regulated by GATA4 have functional consequences and many are associated with dilated cardiomyopathy, suggesting a novel role for GATA4 in achieving the necessary cardiac proteome in normal and stressresponsive conditions.

Journal of Visualized Experiments

Circulation

Background: GATA4 (GATA-binding protein 4), a zinc finger–containing, DNA-binding transcription f... more Background: GATA4 (GATA-binding protein 4), a zinc finger–containing, DNA-binding transcription factor, is essential for normal cardiac development and homeostasis in mice and humans, and mutations in this gene have been reported in human heart defects. Defects in alternative splicing are associated with many heart diseases, yet relatively little is known about how cell type– or cell state–specific alternative splicing is achieved in the heart. Here, we show that GATA4 regulates cell type–specific splicing through direct interaction with RNA and the spliceosome in human induced pluripotent stem cell–derived cardiac progenitors. Methods: We leveraged a combination of unbiased approaches including affinity purification of GATA4 and mass spectrometry, enhanced cross-linking with immunoprecipitation, electrophoretic mobility shift assays, in vitro splicing assays, and unbiased transcriptomic analysis to uncover GATA4’s novel function as a splicing regulator in human induced pluripotent ...

Birth defects occur in ∼6% of all live births and can be caused by combinations of genetic and en... more Birth defects occur in ∼6% of all live births and can be caused by combinations of genetic and environmental influences1. Large-scale DNA sequencing efforts are revealing genetic influences2,3, but investigations into the contributions of environmental factors have largely been limited to association studies with limited mechanistic insight. Hyperglycemia present in pre-gestational diabetic mothers is among the most frequent environmental contributor to congenital defects and results in an increased incidence of congenital heart defects and craniofacial anomalies4. However, the cell types involved and underlying mechanisms by which maternal hyperglycemia affects these regions are unknown. Here, we utilized multi-modal single cell analyses to reveal that maternal diabetes affects the epigenomic and transcriptomic state of specific subsets of cardiac and craniofacial progenitors during embryogenesis. A previously unrecognized subpopulation of anterior heart field progenitors expressin...

The interplay between the topological organization of the genome and the regulation of gene expre... more The interplay between the topological organization of the genome and the regulation of gene expression remains unclear. Depletion of molecular factors underlying genome topology, such as CTCF and cohesin, leads to modest alterations in gene expression, while genomic rearrangements involving boundaries of topologically associating domains (TADs) disrupt normal gene expression and can lead to pathological phenotypes. Here we inverted an almost entire TAD (245kb out of 300kb) within the X-inactivation centre (Xic), leaving its boundaries intact. This led to a significant rearrangement of topological contacts within the TAD, mostly in accordance to the orientation of underlying CTCF binding sites but suggesting heterogeneity in the “contact” potential of different CTCF sites. The inversion also led to increased contact insulation with the neighbouring TAD. Expression of most genes within the inverted TAD remained unaffected in mouse embryonic stem cells and during differentiation. Inter...

Molecular Cell, 2019

Highlights d The Tsix-TAD regulates not only Tsix but also Xist, in part via LinxP d LinxP influe... more Highlights d The Tsix-TAD regulates not only Tsix but also Xist, in part via LinxP d LinxP influences choice making during random XCI by regulating Xist expression in cis d Linx transcription affects local topology but is not necessary for Xist regulation d LinxP is conserved in sequence and synteny across placental mammals

Molecular Cell, 2018

Highlights d Ftx is required for Xist accumulation and XCI during mouse ESC differentiation d Ftx... more Highlights d Ftx is required for Xist accumulation and XCI during mouse ESC differentiation d Ftx acts in cis to promote Xist transcriptional activation d Ftx transcription, but not Ftx noncoding transcripts, is required for Xist regulation

Chromosoma, 2015

Female mammalian cells compensate dosage of Xlinked gene expression through the inactivation of o... more Female mammalian cells compensate dosage of Xlinked gene expression through the inactivation of one of their two X chromosomes. X chromosome inactivation (XCI) in eutherians is dependent on the non-coding RNA Xist that is up-regulated from the future inactive X chromosome, coating it and recruiting factors involved in silencing and altering its chromatin state. Xist lies within the X-inactivation center (Xic), a region on the X that is required for XCI, and is regulated in cis by elements on the X chromosome and in trans by diffusible factors. In this review, we summarize the latest results in cis-and trans-regulation of the Xic. We discuss how the organization of the Xic in topologically associating domains is important for XCI (cis-regulation) and how proteins in the pluripotent state and upon development or differentiation of embryonic stem cells control proper inactivation of one X chromosome (trans-regulation).

Molecular Cell, 2013

Chromatin governs gene regulation and genome maintenance, yet a substantial fraction of the chrom... more Chromatin governs gene regulation and genome maintenance, yet a substantial fraction of the chromatin proteome is still unexplored. Moreover, a global model of the chromatin protein network is lacking. By screening >100 candidates we identify 42 Drosophila proteins that were not previously associated with chromatin, which all display specific genomic binding patterns. Bayesian network modeling of the binding profiles of these and 70 known chromatin components yields a detailed blueprint of the in vivo chromatin protein network. We demonstrate functional compartmentalization of this network, and predict functions for most of the previously unknown chromatin proteins, including roles in DNA replication and repair, and gene activation and repression.

Chromatin was originally identified by W. Flemming in 1882 as not much more than the stainable su... more Chromatin was originally identified by W. Flemming in 1882 as not much more than the stainable substance of the cell nucleus. Flemming named this substance according to the Greek word “chroma”, meaning color. In 1911 chromatin was characterized as proteins, named histones, that were attached to nucleic acid (DNA). In the following years it became clear that chromatin formed the structural basis of genetic information. Not until more than 30 years later the DNA, and not the histone proteins as was widely expected, was identified as the carrier of the genetic information. In 1952 the role of DNA in inheritance was confirmed and not much later Watson and Crick discovered the double-helical structure of DNA based on the DNA crystal analyses of Franklin, Gosling and Wilkins.