Polyglutamine-expanded ATXN7 alters a specific epigenetic signature underlying photoreceptor identity gene expression in SCA7 mouse retinopathy

Martin JJ, Van Regemorter N, Krols L, Brucher JM, de Barsy T, Szliwowski H, et al. On an autosomal dominant form of retinal-cerebellar degeneration: an autopsy study of five patients in one family. Acta Neuropathol (Berl). 1994;88(4):277–86.

Article  CAS  Google Scholar 

Trottier Y, Lutz Y, Stevanin G, Imbert G, Devys D, Cancel G, et al. Polyglutamine expansion as a pathological epitope in Huntington’s disease and four dominant cerebellar ataxias. Nature. 1995;378(6555):403–6.

Article  CAS  Google Scholar 

David G, Abbas N, Stevanin G, Durr A, Yvert G, Cancel G, et al. Cloning of the SCA7 gene reveals a highly unstable CAG repeat expansion. Nat Genet. 1997;17(1):65–70.

Article  CAS  Google Scholar 

Helmlinger D, Tora L. Sharing the SAGA. Trends Biochem Sci. 2017;42(11):850–61.

Article  CAS  Google Scholar 

Karmodiya K, Krebs AR, Oulad-Abdelghani M, Kimura H, Tora L. H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells. BMC Genomics. 2012;13:424.

Article  CAS  Google Scholar 

Wang L, Dent SY. Functions of SAGA in development and disease. Epigenomics. 2014;6(3):329–39.

Article  CAS  Google Scholar 

La Spada AR, Fu YH, Sopher BL, Libby RT, Wang X, Li LY, et al. Polyglutamine-expanded ataxin-7 antagonizes CRX function and induces cone-rod dystrophy in a mouse model of SCA7. Neuron. 2001;31(6):913–27.

Article  Google Scholar 

Yoo SY, Pennesi ME, Weeber EJ, Xu B, Atkinson R, Chen S, et al. SCA7 knockin mice model human SCA7 and reveal gradual accumulation of mutant ataxin-7 in neurons and abnormalities in short-term plasticity. Neuron. 2003;37(3):383–401.

Article  CAS  Google Scholar 

Helmlinger D, Abou-Sleymane G, Yvert G, Rousseau S, Weber C, Trottier Y, et al. Disease progression despite early loss of polyglutamine protein expression in SCA7 mouse model. J Neurosci. 2004;24(8):1881–7.

Article  CAS  Google Scholar 

Abou-Sleymane G, Chalmel F, Helmlinger D, Lardenois A, Thibault C, Weber C, et al. Polyglutamine expansion causes neurodegeneration by altering the neuronal differentiation program. Hum Mol Genet. 2006;15(5):691–703.

Article  CAS  Google Scholar 

Niewiadomska-Cimicka A, Doussau F, Perot JB, Roux MJ, Keime C, Hache A, et al. SCA7 mouse cerebellar pathology reveals preferential downregulation of key purkinje cell-identity genes and shared disease signature with SCA1 and SCA2. J Neurosci. 2021;41(22):4910–36.

Article  CAS  Google Scholar 

Goldberg AF, Moritz OL, Williams DS. Molecular basis for photoreceptor outer segment architecture. Prog Retin Eye Res. 2016;55:52–81.

Article  CAS  Google Scholar 

Yanicostas C, Barbieri E, Hibi M, Brice A, Stevanin G, Soussi-Yanicostas N. Requirement for zebrafish ataxin-7 in differentiation of photoreceptors and cerebellar neurons. PLoS ONE. 2012;7(11): e50705.

Article  CAS  Google Scholar 

Carrillo-Rosas S, Weber C, Fievet L, Messaddeq N, Karam A, Trottier Y. Loss of zebrafish Ataxin-7, a SAGA subunit responsible for SCA7 retinopathy, causes ocular coloboma and malformation of photoreceptors. Hum Mol Genet. 2018;28:912.

Article  Google Scholar 

Swaroop A, Kim D, Forrest D. Transcriptional regulation of photoreceptor development and homeostasis in the mammalian retina. Nat Rev Neurosci. 2010;11(8):563–76.

Article  CAS  Google Scholar 

Brzezinski JA, Reh TA. Photoreceptor cell fate specification in vertebrates. Development. 2015;142(19):3263–73.

Article  CAS  Google Scholar 

Chen S, Peng GH, Wang X, Smith AC, Grote SK, Sopher BL, et al. Interference of Crx-dependent transcription by ataxin-7 involves interaction between the glutamine regions and requires the ataxin-7 carboxy-terminal region for nuclear localization. Hum Mol Genet. 2004;13(1):53–67.

Article  CAS  Google Scholar 

Helmlinger D, Hardy S, Abou-Sleymane G, Eberlin A, Bowman AB, Gansmuller A, et al. Glutamine-expanded ataxin-7 alters TFTC/STAGA recruitment and chromatin structure leading to photoreceptor dysfunction. PLoS Biol. 2006;4(3): e67.

Article  Google Scholar 

Palhan VB, Chen S, Peng GH, Tjernberg A, Gamper AM, Fan Y, et al. Polyglutamine-expanded ataxin-7 inhibits STAGA histone acetyltransferase activity to produce retinal degeneration. Proc Natl Acad Sci USA. 2005;102(24):8472–7.

Article  CAS  Google Scholar 

McMahon SJ, Pray-Grant MG, Schieltz D, Yates JR 3rd, Grant PA. Polyglutamine-expanded spinocerebellar ataxia-7 protein disrupts normal SAGA and SLIK histone acetyltransferase activity. Proc Natl Acad Sci USA. 2005;102(24):8478–82.

Article  CAS  Google Scholar 

Alcala-Vida R, Awada A, Boutillier AL, Merienne K. Epigenetic mechanisms underlying enhancer modulation of neuronal identity, neuronal activity and neurodegeneration. Neurobiol Dis. 2021;147: 105155.

Article  CAS  Google Scholar 

Achour M, Le Gras S, Keime C, Parmentier F, Lejeune FX, Boutillier AL, et al. Neuronal identity genes regulated by super-enhancers are preferentially down-regulated in the striatum of Huntington’s disease mice. Hum Mol Genet. 2015;24(12):3481–96.

Article  CAS  Google Scholar 

Gjoneska E, Pfenning AR, Mathys H, Quon G, Kundaje A, Tsai LH, et al. Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease. Nature. 2015;518(7539):365–9.

Article  CAS  Google Scholar 

Marzi SJ, Leung SK, Ribarska T, Hannon E, Smith AR, Pishva E, et al. A histone acetylome-wide association study of Alzheimer’s disease identifies disease-associated H3K27ac differences in the entorhinal cortex. Nat Neurosci. 2018;21(11):1618–27.

Article  CAS  Google Scholar 

Plank JL, Dean A. Enhancer function: mechanistic and genome-wide insights come together. Mol Cell. 2014;55(1):5–14.

Article  CAS  Google Scholar 

Arnold PR, Wells AD, Li XC. Diversity and emerging roles of enhancer RNA in regulation of gene expression and cell fate. Front Cell Dev Biol. 2019;7:377.

Article  Google Scholar 

Raisner R, Kharbanda S, Jin L, Jeng E, Chan E, Merchant M, et al. Enhancer activity requires CBP/P300 bromodomain-dependent histone H3K27 acetylation. Cell Rep. 2018;24(7):1722–9.

Article  CAS  Google Scholar 

Heinz S, Romanoski CE, Benner C, Glass CK. The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol. 2015;16(3):144–54.

Article  CAS  Google Scholar 

Lipinski M, Munoz-Viana R, Del Blanco B, Marquez-Galera A, Medrano-Relinque J, Carames JM, et al. KAT3-dependent acetylation of cell type-specific genes maintains neuronal identity in the adult mouse brain. Nat Commun. 2020;11(1):2588.

Article  CAS  Google Scholar 

Niewiadomska-Cimicka A, Hache A, Trottier Y. Gene deregulation and underlying mechanisms in spinocerebellar ataxias with polyglutamine expansion. Front Neurosci. 2020;14:571.

Article  Google Scholar 

Krebs AR, Karmodiya K, Lindahl-Allen M, Struhl K, Tora L. SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers. Mol Cell. 2011;44(3):410–23.

Article  CAS  Google Scholar 

Clerin E, Yang Y, Forster V, Fontaine V, Sahel JA, Leveillard T. Vibratome sectioning mouse retina to prepare photoreceptor cultures. J Vis Exp. 2014(94).

Craggs JK, Ball JK, Thomson BJ, Irving WL, Grabowska AM. Development of a strand-specific RT-PCR based assay to detect the replicative form of hepatitis C virus RNA. J Virol Methods. 2001;94(1–2):111–20.

Article  CAS  Google Scholar 

Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25.

Article  Google Scholar 

Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36.

Article  Google Scholar 

Anders S, Pyl PT, Huber W. HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31(2):166–9.

Article  CAS  Google Scholar 

Benjamini Y, Hochberg Y. Controlling the false discovery rate—a practical and powerful approach to multiple testing. J R Stat Soc B. 1995;57(1):289–300.

Google Scholar 

Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11(10):R106.

Article  CAS  Google Scholar 

Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics. 2009;25(15):1952–8.

Article  CAS  Google Scholar 

Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38(4):576–89.

Article  CAS  Google Scholar 

Ye T, Krebs AR, Choukrallah MA, Keime C, Plewniak F, Davidson I, et al. seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res. 2011;39(6): e35.

Article  CAS  Google Scholar 

Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29(1):24–6.

Article  CAS  Google Scholar 

Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell. 2013;153(2):307–19.

Article  CAS  Google Scholar 

Loven J, Hoke HA, Lin CY, Lau A, Orlando DA, Vakoc CR, et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell. 2013;153(2):320–34.

Article  CAS 

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