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1. Additional file 5 of Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome

Author

Cousin, Margot A., Veale, Emma L., Dsouza, Nikita R., Tripathi, Swarnendu, Holden, Robyn G., Arelin, Maria, Beek, Geoffrey, Bekheirnia, Mir Reza, Beygo, Jasmin, Bhambhani, Vikas, Bialer, Martin, Bigoni, Stefania, Boelman, Cyrus, Carmichael, Jenny, Courtin, Thomas, Cogne, Benjamin, Dabaj, Ivana, Doummar, Diane, Fazilleau, Laura, Ferlini, Alessandra, Gavrilova, Ralitza H., Graham, John M., Haack, Tobias B., Juusola, Jane, Kant, Sarina G., Kayani, Saima, Keren, Boris, Ketteler, Petra, Klöckner, Chiara, Koopmann, Tamara T., Kruisselbrink, Teresa M., Kuechler, Alma, Lambert, Laëtitia, Latypova, Xénia, Lebel, Robert Roger, Leduc, Magalie S., Leonardi, Emanuela, Lewis, Andrea M., Liew, Wendy, Machol, Keren, Mardini, Samir, McWalter, Kirsty, Mignot, Cyril, McLaughlin, Julie, Murgia, Alessandra, Narayanan, Vinodh, Nava, Caroline, Neuser, Sonja, Nizon, Mathilde, Ognibene, Davide, Park, Joohyun, Platzer, Konrad, Poirsier, Céline, Radtke, Maximilian, Ramsey, Keri, Runke, Cassandra K., Guillen Sacoto, Maria J., Scaglia, Fernando, Shinawi, Marwan, Spranger, Stephanie, Tan, Ee Shien, Taylor, John, Trentesaux, Anne-Sophie, Vairo, Filippo, Willaert, Rebecca, Zadeh, Neda, Urrutia, Raul, Babovic-Vuksanovic, Dusica, Zimmermann, Michael T., Mathie, Alistair, and Klee, Eric W.

Abstract

Additional file 5: Table S2. Seizure and seizure-like episodes in affected individuals with at least one afebrile seizure.

Published
2022
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2. Additional file 6 of Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome

Author

Cousin, Margot A., Veale, Emma L., Dsouza, Nikita R., Tripathi, Swarnendu, Holden, Robyn G., Arelin, Maria, Beek, Geoffrey, Bekheirnia, Mir Reza, Beygo, Jasmin, Bhambhani, Vikas, Bialer, Martin, Bigoni, Stefania, Boelman, Cyrus, Carmichael, Jenny, Courtin, Thomas, Cogne, Benjamin, Dabaj, Ivana, Doummar, Diane, Fazilleau, Laura, Ferlini, Alessandra, Gavrilova, Ralitza H., Graham, John M., Haack, Tobias B., Juusola, Jane, Kant, Sarina G., Kayani, Saima, Keren, Boris, Ketteler, Petra, Klöckner, Chiara, Koopmann, Tamara T., Kruisselbrink, Teresa M., Kuechler, Alma, Lambert, Laëtitia, Latypova, Xénia, Lebel, Robert Roger, Leduc, Magalie S., Leonardi, Emanuela, Lewis, Andrea M., Liew, Wendy, Machol, Keren, Mardini, Samir, McWalter, Kirsty, Mignot, Cyril, McLaughlin, Julie, Murgia, Alessandra, Narayanan, Vinodh, Nava, Caroline, Neuser, Sonja, Nizon, Mathilde, Ognibene, Davide, Park, Joohyun, Platzer, Konrad, Poirsier, Céline, Radtke, Maximilian, Ramsey, Keri, Runke, Cassandra K., Guillen Sacoto, Maria J., Scaglia, Fernando, Shinawi, Marwan, Spranger, Stephanie, Tan, Ee Shien, Taylor, John, Trentesaux, Anne-Sophie, Vairo, Filippo, Willaert, Rebecca, Zadeh, Neda, Urrutia, Raul, Babovic-Vuksanovic, Dusica, Zimmermann, Michael T., Mathie, Alistair, and Klee, Eric W.

Abstract

Additional file 6: Figure S1. TASK3 conformational changes define PC motions and channel gating. Figure S2. Detailed view of the TASK3 selectivity filter and surrounding residues. Figure S3. Distributions of K+ ions for selected positions along the transport process, and across variants. Figure S4. Genomic variants lead to changes in K+ concentration at the selectivity filter. Figure S5. Cellular localization of labelled TASK3 variants. Figure S6. Comparison of whole cell current density for Tyr205Cys in the presence of various cysteine-modifying agents.

Published
2022
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3. Additional file 1 of Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome

Author

Cousin, Margot A., Veale, Emma L., Dsouza, Nikita R., Tripathi, Swarnendu, Holden, Robyn G., Arelin, Maria, Beek, Geoffrey, Bekheirnia, Mir Reza, Beygo, Jasmin, Bhambhani, Vikas, Bialer, Martin, Bigoni, Stefania, Boelman, Cyrus, Carmichael, Jenny, Courtin, Thomas, Cogne, Benjamin, Dabaj, Ivana, Doummar, Diane, Fazilleau, Laura, Ferlini, Alessandra, Gavrilova, Ralitza H., Graham, John M., Haack, Tobias B., Juusola, Jane, Kant, Sarina G., Kayani, Saima, Keren, Boris, Ketteler, Petra, Klöckner, Chiara, Koopmann, Tamara T., Kruisselbrink, Teresa M., Kuechler, Alma, Lambert, Laëtitia, Latypova, Xénia, Lebel, Robert Roger, Leduc, Magalie S., Leonardi, Emanuela, Lewis, Andrea M., Liew, Wendy, Machol, Keren, Mardini, Samir, McWalter, Kirsty, Mignot, Cyril, McLaughlin, Julie, Murgia, Alessandra, Narayanan, Vinodh, Nava, Caroline, Neuser, Sonja, Nizon, Mathilde, Ognibene, Davide, Park, Joohyun, Platzer, Konrad, Poirsier, Céline, Radtke, Maximilian, Ramsey, Keri, Runke, Cassandra K., Guillen Sacoto, Maria J., Scaglia, Fernando, Shinawi, Marwan, Spranger, Stephanie, Tan, Ee Shien, Taylor, John, Trentesaux, Anne-Sophie, Vairo, Filippo, Willaert, Rebecca, Zadeh, Neda, Urrutia, Raul, Babovic-Vuksanovic, Dusica, Zimmermann, Michael T., Mathie, Alistair, and Klee, Eric W.

Abstract

Additional file 1: Supplementary Note. Clinical Histories. Written clinical histories including genetic testing for each novel family in this study. Molecular Modeling Reveals Mutation-Specific Effects on Channel Mechanics. Molecular Dynamics Simulations Show Changes in Potassium Ion Distribution.

Published
2022
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4. Additional file 9 of Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome

Author

Cousin, Margot A., Veale, Emma L., Dsouza, Nikita R., Tripathi, Swarnendu, Holden, Robyn G., Arelin, Maria, Beek, Geoffrey, Bekheirnia, Mir Reza, Beygo, Jasmin, Bhambhani, Vikas, Bialer, Martin, Bigoni, Stefania, Boelman, Cyrus, Carmichael, Jenny, Courtin, Thomas, Cogne, Benjamin, Dabaj, Ivana, Doummar, Diane, Fazilleau, Laura, Ferlini, Alessandra, Gavrilova, Ralitza H., Graham, John M., Haack, Tobias B., Juusola, Jane, Kant, Sarina G., Kayani, Saima, Keren, Boris, Ketteler, Petra, Klöckner, Chiara, Koopmann, Tamara T., Kruisselbrink, Teresa M., Kuechler, Alma, Lambert, Laëtitia, Latypova, Xénia, Lebel, Robert Roger, Leduc, Magalie S., Leonardi, Emanuela, Lewis, Andrea M., Liew, Wendy, Machol, Keren, Mardini, Samir, McWalter, Kirsty, Mignot, Cyril, McLaughlin, Julie, Murgia, Alessandra, Narayanan, Vinodh, Nava, Caroline, Neuser, Sonja, Nizon, Mathilde, Ognibene, Davide, Park, Joohyun, Platzer, Konrad, Poirsier, Céline, Radtke, Maximilian, Ramsey, Keri, Runke, Cassandra K., Guillen Sacoto, Maria J., Scaglia, Fernando, Shinawi, Marwan, Spranger, Stephanie, Tan, Ee Shien, Taylor, John, Trentesaux, Anne-Sophie, Vairo, Filippo, Willaert, Rebecca, Zadeh, Neda, Urrutia, Raul, Babovic-Vuksanovic, Dusica, Zimmermann, Michael T., Mathie, Alistair, and Klee, Eric W.

Abstract

Additional file 9: Table S5. A comparison of GPCRs regulation between TASK3 clinical variants and WT controls.

Published
2022
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5. Additional file 7 of Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome

Author

Cousin, Margot A., Veale, Emma L., Dsouza, Nikita R., Tripathi, Swarnendu, Holden, Robyn G., Arelin, Maria, Beek, Geoffrey, Bekheirnia, Mir Reza, Beygo, Jasmin, Bhambhani, Vikas, Bialer, Martin, Bigoni, Stefania, Boelman, Cyrus, Carmichael, Jenny, Courtin, Thomas, Cogne, Benjamin, Dabaj, Ivana, Doummar, Diane, Fazilleau, Laura, Ferlini, Alessandra, Gavrilova, Ralitza H., Graham, John M., Haack, Tobias B., Juusola, Jane, Kant, Sarina G., Kayani, Saima, Keren, Boris, Ketteler, Petra, Klöckner, Chiara, Koopmann, Tamara T., Kruisselbrink, Teresa M., Kuechler, Alma, Lambert, Laëtitia, Latypova, Xénia, Lebel, Robert Roger, Leduc, Magalie S., Leonardi, Emanuela, Lewis, Andrea M., Liew, Wendy, Machol, Keren, Mardini, Samir, McWalter, Kirsty, Mignot, Cyril, McLaughlin, Julie, Murgia, Alessandra, Narayanan, Vinodh, Nava, Caroline, Neuser, Sonja, Nizon, Mathilde, Ognibene, Davide, Park, Joohyun, Platzer, Konrad, Poirsier, Céline, Radtke, Maximilian, Ramsey, Keri, Runke, Cassandra K., Guillen Sacoto, Maria J., Scaglia, Fernando, Shinawi, Marwan, Spranger, Stephanie, Tan, Ee Shien, Taylor, John, Trentesaux, Anne-Sophie, Vairo, Filippo, Willaert, Rebecca, Zadeh, Neda, Urrutia, Raul, Babovic-Vuksanovic, Dusica, Zimmermann, Michael T., Mathie, Alistair, and Klee, Eric W.

Abstract

Additional file 7: Table S3. A comparison of whole cell current density and reversal potentials between TASK3 clinical variants and matched WT controls.

Published
2022
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6. Additional file 8 of Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome

Author

Cousin, Margot A., Veale, Emma L., Dsouza, Nikita R., Tripathi, Swarnendu, Holden, Robyn G., Arelin, Maria, Beek, Geoffrey, Bekheirnia, Mir Reza, Beygo, Jasmin, Bhambhani, Vikas, Bialer, Martin, Bigoni, Stefania, Boelman, Cyrus, Carmichael, Jenny, Courtin, Thomas, Cogne, Benjamin, Dabaj, Ivana, Doummar, Diane, Fazilleau, Laura, Ferlini, Alessandra, Gavrilova, Ralitza H., Graham, John M., Haack, Tobias B., Juusola, Jane, Kant, Sarina G., Kayani, Saima, Keren, Boris, Ketteler, Petra, Klöckner, Chiara, Koopmann, Tamara T., Kruisselbrink, Teresa M., Kuechler, Alma, Lambert, Laëtitia, Latypova, Xénia, Lebel, Robert Roger, Leduc, Magalie S., Leonardi, Emanuela, Lewis, Andrea M., Liew, Wendy, Machol, Keren, Mardini, Samir, McWalter, Kirsty, Mignot, Cyril, McLaughlin, Julie, Murgia, Alessandra, Narayanan, Vinodh, Nava, Caroline, Neuser, Sonja, Nizon, Mathilde, Ognibene, Davide, Park, Joohyun, Platzer, Konrad, Poirsier, Céline, Radtke, Maximilian, Ramsey, Keri, Runke, Cassandra K., Guillen Sacoto, Maria J., Scaglia, Fernando, Shinawi, Marwan, Spranger, Stephanie, Tan, Ee Shien, Taylor, John, Trentesaux, Anne-Sophie, Vairo, Filippo, Willaert, Rebecca, Zadeh, Neda, Urrutia, Raul, Babovic-Vuksanovic, Dusica, Zimmermann, Michael T., Mathie, Alistair, and Klee, Eric W.

Abstract

Additional file 8: Table S4. A comparison of inhibition by extracellular acidification (pH 6.4) between TASK3 clinical variants and WT controls.

Published
2022
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7. The spliceosome-associated protein Nrl1 suppresses homologous recombination-dependent R-loop formation in fission yeast

Author

Aronica, Lucia, Kasparek, Torben, Ruchman, David, Marquez, Yamile, Cipak, Lubos, Cipakova, Ingrid, Anrather, Dorothea, Mikolaskova, Barbora, Radtke, Maximilian, Sarkar, Sovan, Pai, Chen-Chun, Blaikley, Elizabeth, Walker, Carol, Shen, Kuo-Fang, Schroeder, Renee, Barta, Andrea, Forsburg, Susan L., and Humphrey, Timothy C.

Subjects
Alternative Splicing, DNA Repair, Schizosaccharomyces, RNA Precursors, Spliceosomes, RNA, DNA, Rad51 Recombinase, Schizosaccharomyces pombe Proteins, Genome Integrity, Repair and Replication, Homologous Recombination, Genomic Instability, Rad52 DNA Repair and Recombination Protein
Abstract

The formation of RNA-DNA hybrids, referred to as R-loops, can promote genome instability and cancer development. Yet the mechanisms by which R-loops compromise genome instability are poorly understood. Here, we establish roles for the evolutionarily conserved Nrl1 protein in pre-mRNA splicing regulation, R-loop suppression and in maintaining genome stability. nrl1Δ mutants exhibit endogenous DNA damage, are sensitive to exogenous DNA damage, and have defects in homologous recombination (HR) repair. Concomitantly, nrl1Δ cells display significant changes in gene expression, similar to those induced by DNA damage in wild-type cells. Further, we find that nrl1Δ cells accumulate high levels of R-loops, which co-localize with HR repair factors and require Rad51 and Rad52 for their formation. Together, our findings support a model in which R-loop accumulation and subsequent DNA damage sequesters HR factors, thereby compromising HR repair at endogenously or exogenously induced DNA damage sites, leading to genome instability.

Published
2015

8. Exploring intra-splicing and its regulatory potential

Author

Radtke, Maximilian

Abstract

Die Diversität des menschlichen Proteoms ist das Ergebnis einer Kaskade regulativer Interaktionen, die genetisch kodierte Informationen nutzen und diesen durch einen transformativen Prozess führen. Dies erlaubt eine Maximierung der Diversität. Einer dieser Prozesse, und möglicherweise der mit dem größten Diversifikationspotential ist Transkription und die daran gekoppelten RNA Prozessierung. Viele regulative Ebenen dieser Prozesse, von Transkription bis Prozessierung, wurden bereits entdeckt und untersucht. Die führt zu einem bereits heute komplexen Gesamtbild, dieser zellulären Vorgänge. Diese Entdeckungen beinhalten molekulare Interaktionen und Interaktoren, kombinatorische Events, die das Transkriptom effektiv, als Antwort auf externe Stimuli, interne Anforderungen oder zelluläre Diversifikation formen. In der vorliegenden Arbeit präsentiere ich eine weitere regulative Ebene, welche durch den bereits intensiv erforschten Splicingmechanismus agiert. Intra-splicing, ursprünglich ein hypothetischer Mechanismus des langen-Intron-splicings wurde inzwischen experimentell verifiziert. Diesem wurde in jüngeren Studien eine weitere regulative Funktion zugeschrieben: recursive Exons. Diese erlauben eine flexible Einbindung zusätzlicher genetischer Information in langen Introns und ermöglichen außerdem, höchstwahrscheinlich, das Spleißen dieser langen Introns. Aufbauend auf diesem Ansatz habe ich weitere Intra-splicing Events genomweit identifiziert. Dies führte einerseits zu einer neuen Perspektive der RNA-Prozessierung und andererseits zu der Identifikation einiger Intra-splicing spezifischer regulativer Mechanismen. Die im Detail studierten Fälle beeinflussten Genexpression quantitativ und qualitativ. Teilweise Intronretention, beziehungsweise erhöhte RNA-Prozessierungseffizienz regulierten die Abundanz spezifischer Transkripte, während potentielle rekursive splicing Events in einer Art positioniert sind, die alternatives Splicing ermöglichen und, möglicherweise, forcieren. Die vorliegende Arbeit bildet das theoretische Grundgerüst der während des Doktorats durchgeführten praktischen Arbeiten und den daraus resultierten Publikationen., The diversity of the human proteome is the consequence of a cascade of regulatory network interactions that use the rather limited pool of direct genetically encoded information and push it through extensive transformative processes, allowing for maximum, or rather required, diversity. One of these processes, and arguably the one with the biggest diversification potential is transcription and its coupled RNA processing steps. Many regulatory layers in these processes, touching all aspects of transcription and RNA processing, have already been uncovered, drawing a complex interactive network. This includes the continuous discovery of molecular interactions and interactors and combinatorial events that allow for efficient shaping of the transcriptome in response to external stimuli, internal requirements or cellular diversification attempts. In this thesis, I want to present yet another layer of regulation via the extensively studied splicing process. Intra-splicing, previously hypothesized and later experimentally validated as a mechanism of long intron splicing, recently was accredited with a novel impact on gene expression: recursive exons. These allow for a flexible inclusion of additional genetic information in long introns and presumably facilitate long intron removal. Extending on this approach, I identified intrasplicing events on a genome-wide scale which allows for a more processing-focused approach to gene expression and additionally lead to the discovery of a number of regulatory splicing events that, in the cases studied in detail, lead to gene expression and isoform regulation. Down-regulation is achieved via partial intron retention, and increased gene expression via more efficient intron removal. The impact on isoform selection is hypothesized based on a novel intersection between recursive splicing and exon selection. This thesis provides the theoretical basis for the work performed in this doctorate and the resulting manuscripts attached.

Published
2017
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9. ZMYND11 variants are a novel cause of centrotemporal and generalised epilepsies with neurodevelopmental disorder

Author

Oates, Stephanie, Absoud, Michael, Goyal, Sushma, Bayley, Sophie, Baulcomb, Jennifer, Sims, Annemarie, Riddett, Amy, Allis, Katrina, Brasch-Andersen, Charlotte, Balasubramanian, Meena, Bai, Renkui, Callewaert, Bert, H��ffmeier, Ulrike, Le Duc, Diana, Radtke, Maximilian, Korff, Christian, Kennedy, Joanna, Low, Karen, M��ller, Rikke S, Nielsen, Jens Erik Klint, Popp, Bernt, Quteineh, Lina, R��nde, Gitte, Sch��newolf-Greulich, Bitten, Shillington, Amelle, Taylor, Matthew Rg, Todd, Emily, Torring, Pernille M, T��mer, Zeynep, Vasileiou, Georgia, Yates, T Michael, Zweier, Christiane, Rosch, Richard, Basson, M Albert, and Pal, Deb K

Subjects
610 Medicine & health, 3. Good health
Abstract

ZMYND11 is the critical gene in chromosome 10p15.3 microdeletion syndrome, a syndromic cause of intellectual disability. The phenotype of ZMYND11 variants has recently been extended to autism and seizures. We expand on the epilepsy phenotype of 20 individuals with pathogenic variants in ZMYND11. We obtained clinical descriptions of 16 new and nine published individuals, plus detailed case history of two children. New individuals were identified through GeneMatcher, ClinVar and the European Network for Therapies in Rare Epilepsy (NETRE). Genetic evaluation was performed using gene panels or exome sequencing; variants were classified using American College of Medical Genetics (ACMG) criteria. Individuals with ZMYND11 associated epilepsy fell into three groups: (i) atypical benign partial epilepsy or idiopathic focal epilepsy (n��=��8); (ii) generalised epilepsies/infantile epileptic encephalopathy (n��=��4); (iii) unclassified (n��=��8). Seizure prognosis ranged from spontaneous remission to drug resistant. Neurodevelopmental deficits were invariable. Dysmorphic features were variable. Variants were distributed across the gene and mostly de novo with no precise genotype-phenotype correlation. ZMYND11 is one of a small group of chromatin reader genes associated in the pathogenesis of epilepsy, and specifically ABPE. More detailed epilepsy descriptions of larger cohorts and functional studies might reveal genotype-phenotype correlation. The epileptogenic mechanism may be linked to interaction with histone H3.3.

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