Electron microscopy reveals toroidal shape of master neuronal cell differentiator REST - RE1-silencing transcription factor
Status PubMed-not-MEDLINE Jazyk angličtina Země Nizozemsko Médium electronic-ecollection
Typ dokumentu časopisecké články
PubMed
36698979
PubMed Central
PMC9860152
DOI
10.1016/j.csbj.2022.12.026
PII: S2001-0370(22)00582-7
Knihovny.cz E-zdroje
- Klíčová slova
- CD, circular dichroism, CoIP, coimmunoprecipitation, DLS, dynamic light scattering, Differentiation, EM, EM, electron microscopy, Electron microscopy, IDRs, intrinsically disordered regions, NRSE, neuron-restrictive silencer element, NRSF, NRSF, neuron-restrictive silencer factor, Neuron-restrictive silencer factor, Neuronal, PCNA, proliferating cell nuclear antigen, RD1/2, repressor domain 1/2, RE1, repressor element-1, RE1-silencing transcription factor, REST, REST, RE1-silencing transcription factor, REST-FL, full-length REST, REST-N62, REST-N62, splicing isoform of REST, also known as REST4 or REST4-S3, REST4, ZF, zinc finger, aa, amino acid(s), bp, base pair(s), kDa, kilodaltons,
- Publikační typ
- časopisecké články MeSH
The RE1-Silencing Transcription factor (REST) is essential for neuronal differentiation. Here, we report the first 18.5-angstrom electron microscopy structure of human REST. The refined electron map suggests that REST forms a torus that can accommodate DNA double-helix in the central hole. Additionally, we quantitatively described REST binding to the canonical DNA sequence of the neuron-restrictive silencer element. We developed protocols for the expression and purification of full-length REST and the shortened variant REST-N62 produced by alternative splicing. We tested the mutual interaction of full-length REST and the splicing variant REST-N62. Revealed structure-function relationships of master neuronal repressor REST will allow finding new biological ways of prevention and treatment of neurodegenerative disorders and diseases.
CEITEC Masaryk University Brno Czech Republic
LifeB FGP NCBR Faculty of Science Masaryk University Kamenice 753 5 Brno 625 00 Czech Republic
Zobrazit více v PubMed
Lambert S.A., et al. The human transcription factors. Cell. 2018;172(4):650–665. doi: 10.1016/j.cell.2018.01.029. PubMed DOI
Schoenherr C.J., Paquette A.J., Anderson D.J. Identification of potential target genes for the neuron-restrictive silencer factor. Proc Natl Acad Sci USA. 1996;93(18):9881–9886. doi: 10.1073/pnas.93.18.9881. PubMed DOI PMC
Chong J.H.A., et al. Rest - a mammalian silencer protein that restricts sodium-channel gene-expression to neurons. Cell. 1995;80(6):949–957. doi: 10.1016/0092867495902988. doi: PubMed DOI
Schoenherr C.J., Anderson D.J. The neuron-restrictive silencer factor (NRSF): a coordinate repressor of multiple neuron-specific genes. Science. 1995;267(5202):1360–1363. doi: 10.1126/science.7871435. PubMed DOI
Gao Z., et al. The master negative regulator REST/NRSF controls adult neurogenesis by restraining the neurogenic program in quiescent stem cells. JNeurosc. 2011;31(26):9772–9786. doi: 10.1523/jneurosci.1604-11.2011. PubMed DOI PMC
Hwang J.-Y., Zukin R.S. REST, a master transcriptional regulator in neurodegenerative disease. Curr Opin Neurobiol. 2018;48:193–200. doi: 10.1016/j.conb.2017.12.008. PubMed DOI PMC
Rodenas-Ruano A., Chávez A.E., Cossio M.J., Castillo P.E., Zukin R.S. REST-dependent epigenetic remodeling promotes the developmental switch in synaptic NMDA receptors. Nat Neurosc. 2012;15(10):1382–1390. doi: 10.1038/nn.3214. PubMed DOI PMC
Lu T., et al. REST and stress resistance in ageing and Alzheimer's disease. Nature. 2014;507(7493):448–454. doi: 10.1038/nature13163. PubMed DOI PMC
Garcia-Manteiga J.M., D'Alessandro R., Meldolesi J. News about the role of the transcription factor REST in neurons: from physiology to pathology. Int J Mol Sci. 2019;21(1) doi: 10.3390/ijms21010235. PubMed DOI PMC
Calderone A., et al. Ischemic insults derepress the gene silencer REST in neurons destined to die. J Neurosci. 2003;23(6):2112–2121. doi: 10.1523/jneurosci.23-06-02112.2003. PubMed DOI PMC
McClelland S., et al. Neuron-restrictive silencer factor-mediated hyperpolarization-activated cyclic nucleotide gated channelopathy in experimental temporal lobe epilepsy. Ann Neurol. 2011;70(3):454–465. doi: 10.1002/ana.22479. PubMed DOI PMC
Zuccato C., et al. Huntingtin interacts with REST/NRSF to modulate the transcription of NRSE-controlled neuronal genes. Nat Genet. 2003;35(1):76–83. doi: 10.1038/ng1219. PubMed DOI
Bruce A.W., et al. Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes. Proc Natl Acad Sci USA. 2004;101(28):10458–10463. doi: 10.1073/pnas.0401827101. PubMed DOI PMC
Tang Y., Jia Z., Xu H., Da L.-T., Wu Q. Mechanism of REST/NRSF regulation of clustered protocadherin α genes. Nucleic Acids Res. 2021;49(8):4506–4521. doi: 10.1093/nar/gkab248. PubMed DOI PMC
Thiel G., Ekici M., Rössler O.G. RE-1 silencing transcription factor (REST): a regulator of neuronal development and neuronal/endocrine function. Cell and Tissue Res. 2015;359(1):99–109. doi: 10.1007/s00441-014-1963-0. PubMed DOI
Roopra A., Qazi R., Schoenike B., Daley T.J., Morrison J.F. Localized domains of G9a-mediated histone methylation are required for silencing of neuronal genes. Mol Cell. 2004;14(6):727–738. doi: 10.1016/j.molcel.2004.05.026. PubMed DOI
Ooi L., Belyaev N.D., Miyake K., Wood I.C., Buckley N.J. BRG1 chromatin remodeling activity is required for efficient chromatin binding by repressor element 1-silencing Transcription Factor (REST) and facilitates REST-mediated Repression. J Biol Chem. 2006;281(51):38974–38980. doi: 10.1074/jbc.M605370200. PubMed DOI PMC
Palm K., Metsis M., Timmusk T. Neuron-specific splicing of zinc finger transcription factor REST/NRSF/XBR is frequent in neuroblastomas and conserved in human, mouse and rat. Mol Brain Res. 1999;72(1):30–39. doi: 10.1016/S0169-328X(99)00196-5. PubMed DOI
Shimojo M., Paquette A.J., Anderson D.J., Hersh L.B. Protein kinase A regulates cholinergic gene expression in PC12 cells: REST4 silences the silencing activity of neuron-restrictive silencer factor/REST. Mol Cell Biol. 1999;19(10):6788–6795. doi: 10.1128/mcb.19.10.6788. PubMed DOI PMC
Raj B., et al. Cross-regulation between an alternative splicing activator and a transcription repressor controls neurogenesis. Mol Cell. 2011;43(5):843–850. doi: 10.1016/j.molcel.2011.08.014. PubMed DOI
Li C.L., Wang Z.F., Tang X.Y., Zeng L., Fan X.T., Li Z. Molecular mechanisms and potential prognostic effects of REST and REST4 in glioma (Review) Mol Med Rep. 2017;16(4):3707–3712. doi: 10.3892/mmr.2017.7071. PubMed DOI
Varadi M., et al. AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res. 2021;50(D1):D439–D444. doi: 10.1093/nar/gkab1061. PubMed DOI PMC
Jumper J., et al. Highly accurate protein structure prediction with AlphaFold. Nature. 2021;596(7873):583–589. doi: 10.1038/s41586-021-03819-2. PubMed DOI PMC
Westbrook T.F., et al. SCFβ-TRCP controls oncogenic transformation and neural differentiation through REST degradation. Nature. 2008;452:370. doi: 10.1038/nature06780. PubMed DOI PMC
Janovic T., Stojaspal M., Veverka P., Horakova D., Hofr C. Human telomere repeat binding factor TRF1 Replaces TRF2 bound to shelterin core hub TIN2 when TPP1 is absent. J Mol Biology. 2019;431(17):3289–3301. doi: 10.1016/j.jmb.2019.05.038. PubMed DOI
Veverka P., Janovic T., Hofr C. Quantitative biology of human shelterin and telomerase: searching for the weakest point. Int J Mol Sci Rev. 2019;20(13):13. doi: 10.3390/ijms20133186. Art no. 3186. PubMed DOI PMC
Fernandez Garcia M., et al. Structural features of transcription factors associating with nucleosome binding. Mol Cell. 2019;75(5):921–932.e6. doi: 10.1016/j.molcel.2019.06.009. PubMed DOI PMC
Hingorani M.M., O'Donnell M. A tale of toroids in DNA metabolism. Nat Rev Mol Cell Biol. 2000;1(1):22–30. doi: 10.1038/35036044. PubMed DOI
Li H., Doruker P., Hu G., Bahar I. Modulation of toroidal proteins dynamics in favor of functional mechanisms upon ligand binding. Biophys J. 2020;118(7):1782–1794. doi: 10.1016/j.bpj.2020.01.046. PubMed DOI PMC
Lee N., et al. Interactomic analysis of REST/NRSF and implications of its functional links with the transcription suppressor TRIM28 during neuronal differentiation. Sci Rep. 2016;6(1):39049. doi: 10.1038/srep39049. PubMed DOI PMC
Grimes J.A., et al. The Co-repressor mSin3A is a functional component of the REST-CoREST repressor complex. J Biol Chem. 2000;275(13):9461–9467. doi: 10.1074/jbc.275.13.9461. PubMed DOI
Barrios Á.P., et al. Differential properties of transcriptional complexes formed by the CoREST family. Mol Cell Biol. 2014;34(14):2760–2770. doi: 10.1128/MCB.00083-14. PubMed DOI PMC
Yang M., et al. Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase. Mol Cell. 2006;23(3):377–387. doi: 10.1016/j.molcel.2006.07.012. PubMed DOI
Shimizu K., Toh H. Interaction between intrinsically disordered proteins frequently occurs in a human protein–protein interaction network. J Mol Biol. 2009;392(5):1253–1265. doi: 10.1016/j.jmb.2009.07.088. PubMed DOI
Nomura M., Uda-Tochio H., Murai K., Mori N., Nishimura Y. The neural repressor NRSF/REST Binds the PAH1 domain of the Sin3 corepressor by using its distinct short hydrophobic helix. J Mol Biol. 2005;354(4):903–915. doi: 10.1016/j.jmb.2005.10.008. PubMed DOI
Paonessa F., et al. Regulation of neural gene transcription by optogenetic inhibition of the RE1-silencing transcription factor. Proc Natl Acad Sci USA. 2016;113(1):E91–E100. doi: 10.1073/pnas.1507355112. PubMed DOI PMC
Abrajano J.J., et al. Corepressor for element-1–silencing transcription factor preferentially mediates gene networks underlying neural stem cell fate decisions. Proc Natl Acad Sci USA. 2010;107(38):16685–16690. doi: 10.1073/pnas.0906917107. PubMed DOI PMC
Moumné L., Betuing S., Caboche J. Multiple aspects of gene dysregulation in huntington's disease. Front Neurol. 2013;4:127. doi: 10.3389/fneur.2013.00127. PubMed DOI PMC
Kaneko N., Hwang J.-Y., Gertner M., Pontarelli F., Zukin R.S. Casein Kinase 1 suppresses activation of REST in insulted hippocampal neurons and halts ischemia-induced neuronal death. J Neurosci. 2014;34(17):6030–6039. doi: 10.1523/jneurosci.4045-13.2014. PubMed DOI PMC
Zhang P., Lathia J.D., Flavahan W.A., Rich J.N., Mattson M.P. Squelching glioblastoma stem cells by targeting REST for proteasomal degradation. Trends Neurosci. 2009;32(11):559–565. doi: 10.1016/j.tins.2009.07.005. PubMed DOI PMC
Rieffel S., et al. Insect cell culture in reagent bottles. MethodsX. 2014;1:155–161. doi: 10.1016/j.mex.2014.08.006. PubMed DOI PMC
Jeong H.J., Abhiraman G.C., Story C.M., Ingram J.R., Dougan S.K. Generation of Ca2+-independent sortase A mutants with enhanced activity for protein and cell surface labeling. PLoS One. 2017;12(12) doi: 10.1371/journal.pone.0189068. PubMed DOI PMC
Goodrich J.A., Kugel J.F. Binding and kinetics for molecular biologists. Cold Spring Harbor Laboratory Press; 2006. ISBN 978-1-621820-79-6.
Mastronarde D.N. Automated electron microscope tomography using robust prediction of specimen movements. J Struct Biol. 2005;152(1):36–51. doi: 10.1016/j.jsb.2005.07.007. PubMed DOI
Punjani A., Rubinstein J.L., Fleet D.J., Brubaker M.A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat Methods. 2017;14(3):290–296. doi: 10.1038/nmeth.4169. PubMed DOI