Recent CIG publications Archive

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

Abstract

The localization of transcriptional activity in specialized transcription bodies is a hallmark of gene expression in eukaryotic cells.^1–3 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.

• PMID: 36476751
• DOI: 10.1016/j.cub.2022.11.015

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

• PMID: 36638184
• DOI: 10.1126/sciadv.ade2828

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 ¹, Maxime Jan ², Manfredo Quadroni ³, Tony Teav ¹, Nadia Rosenberg ⁴, Jean-Yves Chatton ⁴, Nicolas Guex ², Hector Gallart-Ayala ⁵, Julijana 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.

• PMID: 36624525
• PMCID: PMC9827669
• DOI: 10.1186/s13195-023-01162-4

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

Shade avoidance in the context of climate change

Jorge J Casal ^1 2, Christian 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.

• PMID: 36617439
• DOI: 10.1093/plphys/kiad004

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 ¹, Alexandra Potts ¹, Patrice Waridel ¹, Jachen Barblan ¹, Maria Del Carmen Conde Rubio ², Christian Widmann ², Manfredo 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.

• PMID: 36581244
• DOI: 10.1016/j.jmb.2022.167933

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

• PMID: 36586412
• DOI: 10.1016/j.ajhg.2022.12.007