Recent CIG publications Archive

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Curr Biol.: auth.: group Vastenhouw

Curr Biol. 2023 Jan 9;33(1):164-173.e5. doi: 10.1016/j.cub.2022.11.015. Epub 2022 Dec 6.

Nanog organizes transcription bodies

Ksenia Kuznetsova 1Noémie M Chabot 2Martino Ugolini 2Edlyn Wu 2Manan Lalit 3Haruka Oda 4Yuko Sato 4Hiroshi Kimura 4Florian Jug 5Nadine L Vastenhouw 6

Abstract

The localization of transcriptional activity in specialized transcription bodies is a hallmark of gene expression in eukaryotic cells.13 How proteins of the transcriptional machinery come together to form such bodies, however, is unclear. Here, we take advantage of two large, isolated, and long-lived transcription bodies that reproducibly form during early zebrafish embryogenesis to characterize the dynamics of transcription body formation. Once formed, these transcription bodies are enriched for initiating and elongating RNA polymerase II, as well as the transcription factors Nanog and Sox19b. Analyzing the events leading up to transcription, we find that Nanog and Sox19b cluster prior to transcription. The clustering of transcription factors is sequential; Nanog clusters first, and this is required for the clustering of Sox19b and the initiation of transcription. Mutant analysis revealed that both the DNA-binding domain as well as one of the two intrinsically disordered regions of Nanog are required to organize the two bodies of transcriptional activity. Taken together, our data suggest that the clustering of transcription factors dictates the formation of transcription bodies.

Keywords: Nanog; RNA polymerase II; nuclear organization; transcription; transcription bodies; transcription factors; zebrafish.

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Sci Adv.: auth.: group Gatfield

Sci Adv. 2023 Jan 13;9(2):eade2828. doi: 10.1126/sciadv.ade2828. Epub 2023 Jan 13.

A conditional Smg6 mutant mouse model reveals circadian clock regulation through the nonsense-mediated mRNA decay pathway

Georgia Katsioudi 1René Dreos 1Enes S Arpa 1Sevasti Gaspari 1Angelica Liechti 1Miho Sato 2Christian H Gabriel 3Achim Kramer 3Steven A Brown 2David Gatfield 1

Abstract

Nonsense-mediated messenger RNA (mRNA) decay (NMD) has been intensively studied as a surveillance pathway that degrades erroneous transcripts arising from mutations or RNA processing errors. While additional roles in physiological control of mRNA stability have emerged, possible functions in mammalian physiology in vivo remain unclear. Here, we created a conditional mouse allele that allows converting the NMD effector nuclease SMG6 from wild-type to nuclease domain-mutant protein. We find that NMD down-regulation affects the function of the circadian clock, a system known to require rapid mRNA turnover. Specifically, we uncover strong lengthening of free-running circadian periods for liver and fibroblast clocks and direct NMD regulation of Cry2 mRNA, encoding a key transcriptional repressor within the rhythm-generating feedback loop. Transcriptome-wide changes in daily mRNA accumulation patterns in the entrained liver, as well as an altered response to food entrainment, expand the known scope of NMD regulation in mammalian gene expression and physiology.

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Alzheimers Res Ther.: co-auth.: M.Quadroni

Alzheimers Res Ther. 2023 Jan 9;15(1):8. doi: 10.1186/s13195-023-01162-4.

Molecular insights into sex-specific metabolic alterations in Alzheimer’s mouse brain using multi-omics approach

Abigail Strefeler 1Maxime Jan 2Manfredo Quadroni 3Tony Teav 1Nadia Rosenberg 4Jean-Yves Chatton 4Nicolas Guex 2Hector Gallart-Ayala 5Julijana Ivanisevic 6

Free PMC article

Abstract

Background: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder that is characterized by altered cellular metabolism in the brain. Several of these alterations have been found to be exacerbated in females, known to be disproportionately affected by AD. We aimed to unravel metabolic alterations in AD at the metabolic pathway level and evaluate whether they are sex-specific through integrative metabolomic, lipidomic, and proteomic analysis of mouse brain tissue.

Methods: We analyzed male and female triple-transgenic mouse whole brain tissue by untargeted mass spectrometry-based methods to obtain a molecular signature consisting of polar metabolite, complex lipid, and protein data. These data were analyzed using multi-omics factor analysis. Pathway-level alterations were identified through joint pathway enrichment analysis or by separately evaluating lipid ontology and known proteins related to lipid metabolism.

Results: Our analysis revealed significant AD-associated and in part sex-specific alterations across the molecular signature. Sex-dependent alterations were identified in GABA synthesis, arginine biosynthesis, and in alanine, aspartate, and glutamate metabolism. AD-associated alterations involving lipids were also found in the fatty acid elongation pathway and lysophospholipid metabolism, with a significant sex-specific effect for the latter.

Conclusions: Through multi-omics analysis, we report AD-associated and sex-specific metabolic alterations in the AD brain involving lysophospholipid and amino acid metabolism. These findings contribute to the characterization of the AD phenotype at the molecular level while considering the effect of sex, an overlooked yet determinant metabolic variable.

Keywords: 3xTg AD mouse; Alzheimer’s disease; Amino acids; Lipidomics; Lysophospholipids; Metabolomics; Multi-omics; Proteomics; Sex differences.

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Plant Physiol.: auth.: C. Fankhauser

Plant Physiol. 2023 Jan 9;kiad004. doi: 10.1093/plphys/kiad004. 

Shade avoidance in the context of climate change

Jorge J Casal 1 2Christian Fankhauser 3

Abstract

When exposed to changes in the light environment caused by neighbouring vegetation, shade-avoiding plants modify their growth and/or developmental patterns to access more sunlight. In Arabidopsis (Arabidopsis thaliana), neighbour cues reduce the activity of the photo-sensory receptors phytochrome B (phyB) and cryptochrome 1 (cry1), releasing photoreceptor repression imposed on PHYTOCHROME INTERACTING FACTORs (PIFs) and leading to transcriptional reprogramming. The phyB-PIF hub is at the core of all shade-avoidance responses, whilst other photo-sensory receptors and transcription factors contribute in a context-specific manner. CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) is a master regulator of this hub, indirectly stabilising PIFs and targeting negative regulators of shade avoidance for degradation. Warm temperatures reduce the activity of phyB, which operates as a temperature sensor, and further increases the activities of PIF4 and PIF7 by independent temperature sensing mechanisms. The signalling network controlling shade avoidance is not buffered against climate change; rather, it integrates information about shade, temperature, salinity, drought, and likely flooding. We therefore predict that climate change will exacerbate shade-induced growth responses in some regions of the planet while limiting the growth potential in others.

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J Mol Biol.: auth.: PAF

J Mol Biol. 2022 Dec 26;167933. doi: 10.1016/j.jmb.2022.167933. Online ahead of print.

A database of accurate electrophoretic migration patterns for human proteins

Roman Mylonas 1Alexandra Potts 1Patrice Waridel 1Jachen Barblan 1Maria Del Carmen Conde Rubio 2Christian Widmann 2Manfredo Quadroni 3

Abstract

Native molecular weight (MW) is one of the defining features of proteins. Denaturing gel electrophoresis (SDS-PAGE) is a very popular technique for separating proteins and determining their MW. Coupled with antibody-based detection, SDS-PAGE is widely applied for protein identification and quantitation. Yet, electrophoresis is poorly reproducible and the MWs obtained are often inaccurate. This hampers antibody validation and negatively impacts the reliability of western blot data, resulting worldwide in a considerable waste of reagents and labour. We argue that, to alleviate these problems there is a need to establish a database of reference MWs measured by SDS-PAGE. Using mass spectrometry as an orthogonal detection method, we acquired electrophoretic migration patterns for approximately 10’000 human proteins in five commonly used cell lines. We applied a robust internal calibration of migration to determine accurate and reproducible molecular weights. This in turn allows merging replicates to increase accuracy, but also enables comparing different cell lines. Mining of the data obtained highlights structural factors that affect migration of distinct classes of proteins. When combined with peptide coverage, the data produced recapitulates known post-translational modifications and differential splicing and can be used to formulate hypotheses on new or poorly known processing events. The full information is freely accessible as a web resource through a user friendly graphical interface (https://pumba.dcsr.unil.ch/). We anticipate that this database will be useful to investigators worldwide for troubleshooting western blot experiments, but could also contribute to the characterization of human proteoforms.

Keywords: SDS-PAGE; differential splicing; electrophoresis; internal calibration; mass spectrometry; molecular weight; post-translational modifications; proteins; proteoforms.

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Am J Hum Genet.: co-auth.: group Reymond

Am J Hum Genet. 2022 Dec 21;S0002-9297(22)00541-9. doi: 10.1016/j.ajhg.2022.12.007. Online ahead of print.

Deleterious, protein-altering variants in the transcriptional coregulator ZMYM3 in 27 individuals with a neurodevelopmental delay phenotype

Susan M Hiatt 1Slavica Trajkova 2Matteo Rossi Sebastiano 3E Christopher Partridge 4Fatima E Abidi 5Ashlyn Anderson 4Muhammad Ansar 6Stylianos E Antonarakis 7Azadeh Azadi 8Ruxandra Bachmann-Gagescu 9Andrea Bartuli 10Caroline Benech 11Jennifer L Berkowitz 12Michael J Betti 13Alfredo Brusco 2Ashley Cannon 14Giulia Caron 3Yanmin Chen 12Meagan E Cochran 4Tanner F Coleman 4Molly M Crenshaw 15Laurence Cuisset 16Cynthia J Curry 17Hossein Darvish 18Serwet Demirdas 19Maria Descartes 14Jessica Douglas 20David A Dyment 21Houda Zghal Elloumi 12Giuseppe Ermondi 3Marie Faoucher 22Emily G Farrow 23Stephanie A Felker 4Heather Fisher 24Anna C E Hurst 14Pascal Joset 25Melissa A Kelly 26Stanislav Kmoch 27Benjamin R Leadem 12Michael J Lyons 5Marina Macchiaiolo 10Martin Magner 28Giorgia Mandrile 29Francesca Mattioli 30Megan McEown 4Sarah K Meadows 4Livija Medne 31Naomi J L Meeks 32Sarah Montgomery 33Melanie P Napier 12Marvin Natowicz 34Kimberly M Newberry 4Marcello Niceta 10Lenka Noskova 27Catherine B Nowak 20Amanda G Noyes 12Matthew Osmond 21Eloise J Prijoles 5Jada Pugh 4Verdiana Pullano 2Chloé Quélin 35Simin Rahimi-Aliabadi 36Anita Rauch 37Sylvia Redon 38Alexandre Reymond 30Caitlin R Schwager 39Elizabeth A Sellars 40Angela E Scheuerle 41Elena Shukarova-Angelovska 42Cara Skraban 31Elliot Stolerman 5Bonnie R Sullivan 39Marco Tartaglia 10Isabelle Thiffault 23Kevin Uguen 38Luis A Umaña 41Yolande van Bever 19Saskia N van der Crabben 43Marjon A van Slegtenhorst 19Quinten Waisfisz 44Camerun Washington 5Lance H Rodan 45Richard M Myers 4Gregory M Cooper 46Affiliations expand

Abstract

Neurodevelopmental disorders (NDDs) result from highly penetrant variation in hundreds of different genes, some of which have not yet been identified. Using the MatchMaker Exchange, we assembled a cohort of 27 individuals with rare, protein-altering variation in the transcriptional coregulator ZMYM3, located on the X chromosome. Most (n = 24) individuals were males, 17 of which have a maternally inherited variant; six individuals (4 male, 2 female) harbor de novo variants. Overlapping features included developmental delay, intellectual disability, behavioral abnormalities, and a specific facial gestalt in a subset of males. Variants in almost all individuals (n = 26) are missense, including six that recurrently affect two residues. Four unrelated probands were identified with inherited variation affecting Arg441, a site at which variation has been previously seen in NDD-affected siblings, and two individuals have de novo variation resulting in p.Arg1294Cys (c.3880C>T). All variants affect evolutionarily conserved sites, and most are predicted to damage protein structure or function. ZMYM3 is relatively intolerant to variation in the general population, is widely expressed across human tissues, and encodes a component of the KDM1A-RCOR1 chromatin-modifying complex. ChIP-seq experiments on one variant, p.Arg1274Trp, indicate dramatically reduced genomic occupancy, supporting a hypomorphic effect. While we are unable to perform statistical evaluations to definitively support a causative role for variation in ZMYM3, the totality of the evidence, including 27 affected individuals, recurrent variation at two codons, overlapping phenotypic features, protein-modeling data, evolutionary constraint, and experimentally confirmed functional effects strongly support ZMYM3 as an NDD-associated gene.

Keywords: X-linked intellectual disability; ZMYM3; chromatin modifiers; neurodevelopmental disorder; transcriptional coregulators.