KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism in neurons

. 2024 Jun 24 ; 52 (11) : 6201-6219.

Jazyk angličtina Země Velká Británie, Anglie Médium print

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid38597673

Grantová podpora
09150181910022 Dutch Research Council - Netherlands
F31 GM146347 NIGMS NIH HHS - United States
P50 HD105352 NICHD NIH HHS - United States
S10 OD023591 NIH HHS - United States
23-07810S Czech Science Foundation
American Federation for Aging Research
T32GM149364 NIH HHS - United States
1-S10-OD030286-01 NIH Office of the Director
IG-5310-2023 EMBO
S10 OD030286 NIH HHS - United States
Junior Investigator in Neuroscience Research Award
Dominick P. Purpura Department of Neuroscience
P60 DK020541 NIDDK NIH HHS - United States
P30 CA013330 NCI NIH HHS - United States
Irma T. Hirschl Trust
R01 GM112783 NIGMS NIH HHS - United States
APP1117394 National Health and Medical Research Council

Genes encoding the KDM5 family of transcriptional regulators are disrupted in individuals with intellectual disability (ID). To understand the link between KDM5 and ID, we characterized five Drosophila strains harboring missense alleles analogous to those observed in patients. These alleles disrupted neuroanatomical development, cognition and other behaviors, and displayed a transcriptional signature characterized by the downregulation of many ribosomal protein genes. A similar transcriptional profile was observed in KDM5C knockout iPSC-induced human glutamatergic neurons, suggesting an evolutionarily conserved role for KDM5 proteins in regulating this class of gene. In Drosophila, reducing KDM5 changed neuronal ribosome composition, lowered the translation efficiency of mRNAs required for mitochondrial function, and altered mitochondrial metabolism. These data highlight the cellular consequences of altered KDM5-regulated transcriptional programs that could contribute to cognitive and behavioral phenotypes. Moreover, they suggest that KDM5 may be part of a broader network of proteins that influence cognition by regulating protein synthesis.

Zobrazit více v PubMed

Pavlenko  E., Ruengeler  T., Engel  P., Poepsel  S.  Functions and interactions of mammalian KDM5 demethylases. Front. Genet.  2022; 13:906662. PubMed PMC

Garzón-Porras  A.M., Chory  E., Gryder  B.E.  Dynamic opposition of histone modifications. ACS Chem. Biol.  2023; 18:1027–1036. PubMed

Harrington  J., Wheway  G., Willaime-Morawek  S., Gibson  J., Walters  Z.S.  Pathogenic KDM5B variants in the context of developmental disorders. Biochim. Biophys Acta Gene Regul. Mech.  2022; 1865:194848. PubMed

Hatch  H.A.M., Secombe  J.  Molecular and cellular events linking variants in the histone demethylase KDM5C to the intellectual disability disorder Claes-Jensen syndrome. FEBS J.  2021; 289:7776–7787. PubMed PMC

Vallianatos  C.N., Iwase  S.  Disrupted intricacy of histone H3K4 methylation in neurodevelopmental disorders. Epigenomics. 2015; 7:503–519. PubMed PMC

Leonardi  E., Aspromonte  M.C., Drongitis  D., Bettella  E., Verrillo  L., Polli  R., McEntagart  M., Licchetta  L., Dilena  R., D’Arrigo  S.  et al. .  Expanding the genetics and phenotypic spectrum of lysine-specific demethylase 5C (KDM5C): A report of 13 novel variants. Eur. J. Hum. Genet.  2022; 31:202–215. PubMed PMC

Carmignac  V., Nambot  S., Lehalle  D., Callier  P., Moortgat  S., Benoit  V., Ghoumid  J., Delobel  B., Smol  T., Thuillier  C.  et al. .  Further delineation of the female phenotype with KDM5C disease causing variants: 19 new individuals and review of the literature. Clin. Genet.  2020; 98:43–55. PubMed

Iwase  S., Brookes  E., Agarwal  S., Badeaux  A.I., Ito  H., Vallianatos  C.N., Tomassy  G.S., Kasza  T., Lin  G., Thompson  A.  et al. .  A mouse model of X-linked intellectual disability associated with impaired removal of histone methylation. Cell Rep.  2016; 14:1000–1009. PubMed PMC

Scandaglia  M., Lopez-Atalaya  J.P., Medrano-Fernandez  A., Lopez-Cascales  M.T., Del Blanco  B., Lipinski  M., Benito  E., Olivares  R., Iwase  S., Shi  Y  et al. .  Loss of Kdm5c causes spurious transcription and prevents the fine-tuning of activity-regulated enhancers in neurons. Cell Rep.  2017; 21:47–59. PubMed PMC

Vallianatos  C.N., Raines  B., Porter  R.S., Bonefas  K.M., Wu  M.C., Garay  P.M., Collette  K.M., Seo  Y.A., Dou  Y., Keegan  C.E.  et al. .  Mutually suppressive roles of KMT2A and KDM5C in behaviour, neuronal structure, and histone H3K4 methylation. Commun. Biol.  2020; 3:278. PubMed PMC

El Hayek  L., Tuncay  I.O., Nijem  N., Russell  J., Ludwig  S., Kaur  K., Li  X., Anderton  P., Tang  M., Gerard  A.  et al. .  KDM5A mutations identified in autism spectrum disorder using forward genetics. eLife. 2020; 9:e56883. PubMed PMC

Belalcazar  H.M., Hendricks  E.L., Zamurrad  S., Liebl  F.L.W., Secombe  J.  The histone demethylase KDM5 is required for synaptic structure and function at the Drosophila neuromuscular junction. Cell Rep.  2021; 34:108753. PubMed PMC

Zamurrad  S., Hatch  H.A.M., Drelon  C., Belalcazar  H.M., Secombe  J.  A Drosophila model of intellectual disability caused by mutations in the histone demethylase KDM5. Cell Rep.  2018; 22:2359–2369. PubMed PMC

Ford  T.J.L., Jeon  B.T., Lee  H., Kim  W.Y.  Dendritic spine and synapse pathology in chromatin modifier-associated autism spectrum disorders and intellectual disability. Front. Mol. Neurosci.  2022; 15:1048713. PubMed PMC

Exposito-Alonso  D., Rico  B.  Mechanisms underlying circuit dysfunction in neurodevelopmental disorders. Annu. Rev. Genet.  2022; 56:391–422. PubMed

Iwase  S., Lan  F., Bayliss  P., De La Torre-Ubieta  L., Huarte  M., Qi  H.H., Whetstine  R., Johnathan  Bonni, A., Roberts  T.M., Shi  Y  The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell. 2007; 128:1077–1088. PubMed

Lussi  Y.C., Mariani  L., Friis  C., Peltonen  J., Myers  T.R., Krag  C., Wong  G., Salcini  A.E.  Impaired removal of H3K4 methylation affects cell fate determination and gene transcription. Development. 2016; 143:3751–3762. PubMed

Mariani  L., Lussi  Y.C., Vandamme  J., Riveiro  A., Salcini  A.E.  The H3K4me3/2 histone demethylase RBR-2 controls axon guidance by repressing the actin-remodeling gene wsp-1. Development. 2016; 143:851–863. PubMed

Hatch  H.A.M., Belalcazar  H.M., Marshall  O.J., Secombe  J.  A KDM5-Prospero transcriptional axis functions during early neurodevelopment to regulate mushroom body formation. eLife. 2021; 10:e63886. PubMed PMC

Holt  C.E., Martin  K.C., Schuman  E.M.  Local translation in neurons: visualization and function. Nat. Struct. Mol. Biol.  2019; 26:557–566. PubMed

Mila  M., Alvarez-Mora  M.I., Madrigal  I., Rodriguez-Revenga  L.  Fragile X syndrome: An overview and update of the FMR1 gene. Clin. Genet.  2018; 93:197–205. PubMed

Dockendorff  T.C., Labrador  M.  The fragile X protein and genome function. Mol. Neurobiol.  2018; 56:711–721. PubMed

Drelon  C., Belalcazar  H.M., Secombe  J.  The histone demethylase KDM5 is essential for larval growth in Drosophila. Genetics. 2018; 209:773–787. PubMed PMC

Navarro-Costa  P., McCarthy  A., Prudencio  P., Greer  C., Guilgur  L.G., Becker  J.D., Secombe  J., Rangan  P., Martinho  R.G.  Early programming of the oocyte epigenome temporally controls late prophase I transcription and chromatin remodelling. Nat. Commun.  2016; 7:12331. PubMed PMC

Bischof  J., Maeda  R.K., Hediger  M., Karch  F., Basler  K.  An optimized transgenesis system for Drosophila using germ-line-specific phiC31 integrases. Proc. Natl. Acad. Sci. U.S.A.  2007; 104:3312–3317. PubMed PMC

Barnes  J., Salas  F., Mokhtari  R., Dolstra  H., Pedrosa  E., Lachman  H.M.  Modeling the neuropsychiatric manifestations of Lowe syndrome using induced pluripotent stem cells: defective F-actin polymerization and WAVE-1 expression in neuronal cells. Mol. Autism. 2018; 9:44. PubMed PMC

Zhang  Y., Pak  C., Han  Y., Ahlenius  H., Zhang  Z., Chanda  S., Marro  S., Patzke  C., Acuna  C., Covy  J.  et al. .  Rapid single-step induction of functional neurons from human pluripotent stem cells. Neuron. 2013; 78:785–798. PubMed PMC

Ji  Z., Kiparaki  M., Folgado  V., Kumar  A., Blanco  J., Rimesso  G., Chuen  J., Liu  Y., Zheng  D., Baker  N.E.  Drosophila RpS12 controls translation, growth, and cell competition through Xrp1. PLoS Genet.  2019; 15:e1008513. PubMed PMC

Schneider  C.A., Rasband  W.S., Eliceiri  K.W.  NIH Image to ImageJ: 25 years of image analysis. Nat. Methods. 2012; 9:671–675. PubMed PMC

Trannoy  S., Redt-Clouet  C., Dura  J.M., Preat  T.  Parallel processing of appetitive short- and long-term memories in Drosophila. Curr. Biol.  2011; 21:1647–1653. PubMed

Fenckova  M., Blok  L.E.R., Asztalos  L., Goodman  D.P., Cizek  P., Singgih  E.L., Glennon  J.C., IntHout  J., Zweier  C., Eichler  E.E.  et al. .  Habituation learning is a widely affected mechanism in Drosophila models of intellectual disability and autism spectrum disorders. Biol. Psychiatry. 2019; 86:294–305. PubMed PMC

Mituzaite  J., Petersen  R., Claridge-Chang  A., Baines  R.A.  Characterization of seizure induction methods inDrosophila. Eneuro. 2021; 8:ENEURO.0079-0021. PubMed PMC

Fischer  F.P., Karge  R.A., Weber  Y.G., Koch  H., Wolking  S., Voigt  A.  Drosophila melanogaster as a versatile model organism to study genetic epilepsies: an overview. Front Mol. Neurosci.  2023; 16:1116000. PubMed PMC

Mi  K., Li  Y., Yang  Y., Secombe  J., Liu  X.  DVT: a high-throughput analysis pipeline for locomotion and social behavior in adult Drosophila melanogaster. Cell Biosci.  2023; 13:187. PubMed PMC

Yamanaka  O., Takeuchi  R.  UMATracker: an intuitive image-based tracking platform. J. Exp. Biol.  2018; 16:221. PubMed

Love  M.I., Huber  W., Anders  S.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol.  2014; 15:550. PubMed PMC

Dobin  A., Davis  C.A., Schlesinger  F., Drenkow  J., Zaleski  C., Jha  S., Batut  P., Chaisson  M., Gingeras  T.R.  STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013; 29:15–21. PubMed PMC

Harrow  J., Frankish  A., Gonzalez  J.M., Tapanari  E., Diekhans  M., Kokocinski  F., Aken  B.L., Barrell  D., Zadissa  A., Searle  S.  et al. .  GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res.  2012; 22:1760–1774. PubMed PMC

Li  B., Dewey  C.N.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinf.  2011; 12:323. PubMed PMC

Chen  X., Dickman  D  Tissue-specific ribosome profiling in Drosophila. Methods Mol. Biol.  2021; 2252:175–188. PubMed

Tjeldnes  H., Labun  K., Torres Cleuren  Y., Chyzynska  K., Swirski  M., Valen  E.  ORFik: a comprehensive R toolkit for the analysis of translation. BMC Bioinf.  2021; 22:336. PubMed PMC

Aguilan  J.T., Kulej  K., Sidoli  S.  Guide for protein fold change and p-value calculation for non-experts in proteomics. Mol. Omics. 2020; 16:573–582. PubMed

Pang  Z., Zhou  G., Ewald  J., Chang  L., Hacariz  O., Basu  N., Xia  J.  Using MetaboAnalyst 5.0 for LC-HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data. Nat. Protoc.  2022; 17:1735–1761. PubMed

Jensen  L.R., Amende  M., Gurok  U., Moser  B., Gimmel  V., Tzschach  A., Janecke  A.R., Tariverdian  G., Chelly  J., Fryns  J.P.  et al. .  Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation. Am. J. Hum. Genet.  2005; 76:227–236. PubMed PMC

Abidi  F.E., Holloway  L., Moore  C.A., Weaver  D.D., Simensen  R.J., Stevenson  R.E., Rogers  R.C., Schwartz  C.E.  Mutations in JARID1C are associated with X-linked mental retardation, short stature and hyperreflexia. J. Med. Genet.  2008; 45:787–793. PubMed PMC

Tzschach  A., Lenzner  S., Moser  B., Reinhardt  R., Chelly  J., Fryns  J.P., Kleefstra  T., Raynaud  M., Turner  G., Ropers  H.H.  et al. .  Novel JARID1C/SMCX mutations in patients with X-linked mental retardation. Hum. Mutat.  2006; 27:389. PubMed

Li  L., Greer  C., Eisenman  R.N., Secombe  J.  Essential functions of the histone demethylase lid. PLoS Genet.  2010; 6:e1001221. PubMed PMC

Blok  L.E.R., Boon  M., van Reijmersdal  B., Hoffler  K.D., Fenckova  M., Schenck  A.  Genetics, molecular control and clinical relevance of habituation learning. Neurosci. Biobehav. Rev.  2022; 143:104883. PubMed

Vivanti  G., Hocking  D.R., Fanning  P.A.J., Uljarevic  M., Postorino  V., Mazzone  L., Dissanayake  C.  Attention to novelty versus repetition: contrasting habituation profiles in Autism and Williams syndrome. Dev. Cogn. Neurosci.  2018; 29:54–60. PubMed PMC

Ethridge  L.E., White  S.P., Mosconi  M.W., Wang  J., Byerly  M.J., Sweeney  J.A.  Reduced habituation of auditory evoked potentials indicate cortical hyper-excitability in fragile X syndrome. Translational Psychiatry. 2016; 6:e787. PubMed PMC

Liu  X., Secombe  J.  The histone demethylase KDM5 activates gene expression by recognizing chromatin context through its PHD reader motif. Cell Rep.  2015; 13:2219–2231. PubMed PMC

Chen  X., Dickman  D  Development of a tissue-specific ribosome profiling approach in Drosophila enables genome-wide evaluation of translational adaptations. PLoS Genet.  2017; 13:e1007117. PubMed PMC

Eissenberg  J.C., Lee  M.G., Schneider  J., Ilvarsonn  A., Shiekhattar  R., Shilatifard  A.  The trithorax-group gene in Drosophila little imaginal discs encodes a trimethylated histone H3 Lys4 demethylase. Nat. Struct. Mol. Biol.  2007; 14:344–346. PubMed

Sidhaye  J., Trepte  P., Sepke  N., Novatchkova  M., Schutzbier  M., Dürnberger  G., Mechtler  K., Knoblich  J.A.  Integrated transcriptome and proteome analysis reveals posttranscriptional regulation of ribosomal genes in human brain organoids. eLife. 2023; 12:e85135. PubMed PMC

Anger  A.M., Armache  J.-P., Berninghausen  O., Habeck  M., Subklewe  M., Wilson  D.N., Beckmann  R.  Structures of the human and Drosophila 80S ribosome. Nature. 2013; 497:80–85. PubMed

Wahl  M.C., Möller  W.  Structure and function of the acidic ribosomal stalk proteins. Curr Protein Pept Sci.  2002; 3:93–106. PubMed

Kanehisa  M., Goto  S.  KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res.  2000; 28:27–30. PubMed PMC

Barrington  C.L., Koch  A.L., Galindo  G., Larkin-Gero  E., Morrison  E.J., Tisa  S., Stasevich  T.J., Rissland  O.S.  Synonymous codon usage regulates translation initiation. Cell Rep.  2023; 42:113413. PubMed PMC

Rubio  A., Ghosh  S., Mülleder  M., Ralser  M., Mata  J.  Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast. Nucleic Acids Res.  2021; 49:383–399. PubMed PMC

Vicario  S., Moriyama  E.N., Powell  J.R.  Codon usage in twelve species of Drosophila. BMC Evol. Biol.  2007; 7:226. PubMed PMC

Xia  J., Psychogios  N., Young  N., Wishart  D.S.  MetaboAnalyst: a web server for metabolomic data analysis and interpretation. Nucleic Acids Res.  2009; 37:W652–W660. PubMed PMC

Drelon  C., Belalcazar  H.M., Secombe  J.  The histone demethylase KDM5 is essential for larval growth in drosophila. Genetics. 2018; 209:773–787. PubMed PMC

Kidder  B.L., Hu  G., Zhao  K.  KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation. Genome Biol.  2014; 15:R32. PubMed PMC

Kirtana  R., Manna  S., Patra  S.K.  KDM5A noncanonically binds antagonists MLL1/2 to mediate gene regulation and promotes epithelial to mesenchymal transition. Biochim. Biophys. Acta Gene Regul. Mech.  2023; 1866:194986. PubMed

Varaljai  R., Islam  A.B., Beshiri  M.L., Rehman  J., Lopez-Bigas  N., Benevolenskaya  E.V.  Increased mitochondrial function downstream from KDM5A histone demethylase rescues differentiation in pRB-deficient cells. Genes Dev.  2015; 29:1817–1834. PubMed PMC

Liu  H., Zhai  L., Liu  Y., Lu  D., Vander Ark  A., Yang  T., Krawczyk  C.M.  The histone demethylase KDM5C controls female bone mass by promoting energy metabolism in osteoclasts. Sci. Adv.  2023; 9:eadg0731. PubMed PMC

Costa-Mattioli  M., Sossin  W.S., Klann  E., Sonenberg  N.  Translational control of long-lasting synaptic plasticity and memory. Neuron. 2009; 61:10–26. PubMed PMC

Gal-Ben-Ari  S., Kenney  J.W., Ounalla-Saad  H., Taha  E., David  O., Levitan  D., Gildish  I., Panja  D., Pai  B., Wibrand  K.  et al. .  Consolidation and translation regulation. Learn Mem.  2012; 19:410–422. PubMed PMC

Huber  K.M., Kayser  M.S., Bear  M.F.  Role for rapid dendritic protein synthesis in hippocampal mGluR-dependent long-term depression. 2000; 288:1254–1257. PubMed

Luan  Y., Tang  N., Yang  J., Liu  S., Cheng  C., Wang  Y., Chen  C., Guo  Y.-N., Wang  H., Zhao  W.  et al. .  Deficiency of ribosomal proteins reshapes the transcriptional and translational landscape in human cells. Nucleic Acids Res.  2022; 50:6601–6617. PubMed PMC

Milenkovic  I., Santos Vieira  H.G., Lucas  M.C., Ruiz-Orera  J., Patone  G., Kesteven  S., Wu  J., Feneley  M., Espadas  G., Sabidó  E.  et al. .  Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart. Nucleic Acids Res.  2023; 51:5301–5324. PubMed PMC

Shi  Z., Fujii  K., Kovary  K.M., Genuth  N.R., Röst  H.L., Teruel  M.N., Barna  M.  Heterogeneous ribosomes preferentially translate distinct subpools of mRNAs genome-wide. Mol. Cell. 2017; 67:71–83. PubMed PMC

Fusco  C.M., Desch  K., Dörrbaum  A.R., Wang  M., Staab  A., Chan  I.C.W., Vail  E., Villeri  V., Langer  J.D., Schuman  E.M.  Neuronal ribosomes exhibit dynamic and context-dependent exchange of ribosomal proteins. Nat. Commun.  2021; 12:6127. PubMed PMC

Brooks  S.S., Wall  A.L., Golzio  C., Reid  D.W., Kondyles  A., Willer  J.R., Botti  C., Nicchitta  C.V., Katsanis  N., Davis  E.E.  A novel ribosomopathy caused by dysfunction of RPL10 disrupts neurodevelopment and causes X-linked microcephaly in humans. Genetics. 2014; 198:723–733. PubMed PMC

Perucho  L., Artero-Castro  A., Guerrero  S., Ramón Y Cajal  S., Lleonart  M.E., Wang  Z.-Q.  RPLP1, a crucial ribosomal protein for embryonic development of the nervous system. PLoS One. 2014; 9:e99956. PubMed PMC

Valenti  D., de Bari  L., De Filippis  B., Henrion-Caude  A., Vacca  R.A.  Mitochondrial dysfunction as a central actor in intellectual disability-related diseases: an overview of Down syndrome, autism, Fragile X and Rett syndrome. Neurosci. Biobehav. Rev.  2014; 202–217.46. PubMed

Rogers  M.F., Marshall  O.J., Secombe  J.  KDM5-mediated activation of genes required for mitochondrial biology is necessary for viability in Drosophila. Development. 2023; 150:dev202024. PubMed PMC

Cui  H., Kong  Y., Zhang  H.  Oxidative stress, mitochondrial dysfunction, and aging. J Signal Transduct. 2012; 2012:646354. PubMed PMC

Kataria  A., Tyagi  S.  Domain architecture and protein-protein interactions regulate KDM5A recruitment to the chromatin. Epigenetics. 2023; 18:2268813. PubMed PMC

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...