cGAS-mediated induction of type I interferon due to inborn errors of histone pre-mRNA processing.
Autoimmune Diseases of the Nervous System
/ genetics
Cell Line
Chromatin
/ metabolism
DNA
/ immunology
Gene Expression Regulation
/ genetics
HCT116 Cells
HEK293 Cells
Hereditary Autoinflammatory Diseases
/ genetics
Histones
/ metabolism
Humans
Interferon Type I
/ biosynthesis
Membrane Proteins
/ metabolism
Nervous System Malformations
/ genetics
Nucleotides, Cyclic
/ biosynthesis
Nucleotidyltransferases
/ metabolism
RNA Precursors
/ metabolism
RNA-Binding Proteins
/ genetics
Ribonucleoprotein, U7 Small Nuclear
/ genetics
Journal
Nature genetics
ISSN: 1546-1718
Titre abrégé: Nat Genet
Pays: United States
ID NLM: 9216904
Informations de publication
Date de publication:
12 2020
12 2020
Historique:
received:
03
07
2020
accepted:
09
10
2020
pubmed:
25
11
2020
medline:
26
1
2021
entrez:
24
11
2020
Statut:
ppublish
Résumé
Inappropriate stimulation or defective negative regulation of the type I interferon response can lead to autoinflammation. In genetically uncharacterized cases of the type I interferonopathy Aicardi-Goutières syndrome, we identified biallelic mutations in LSM11 and RNU7-1, which encode components of the replication-dependent histone pre-mRNA-processing complex. Mutations were associated with the misprocessing of canonical histone transcripts and a disturbance of linker histone stoichiometry. Additionally, we observed an altered distribution of nuclear cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS) and enhanced interferon signaling mediated by the cGAS-stimulator of interferon genes (STING) pathway in patient-derived fibroblasts. Finally, we established that chromatin without linker histone stimulates cyclic guanosine monophosphate-adenosine monophosphate (cGAMP) production in vitro more efficiently. We conclude that nuclear histones, as key constituents of chromatin, are essential in suppressing the immunogenicity of self-DNA.
Identifiants
pubmed: 33230297
doi: 10.1038/s41588-020-00737-3
pii: 10.1038/s41588-020-00737-3
doi:
Substances chimiques
Chromatin
0
Histones
0
Interferon Type I
0
Lsm11 protein, human
0
Membrane Proteins
0
Nucleotides, Cyclic
0
RNA Precursors
0
RNA-Binding Proteins
0
Ribonucleoprotein, U7 Small Nuclear
0
STING1 protein, human
0
cyclic guanosine monophosphate-adenosine monophosphate
0
DNA
9007-49-2
Nucleotidyltransferases
EC 2.7.7.-
cGAS protein, human
EC 2.7.7.-
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1364-1372Subventions
Organisme : Wellcome Trust
ID : 208345/Z/17/Z
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/P028071/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : U127580972
Pays : United Kingdom
Organisme : Department of Health
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_UU_00007/13
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_UU_00007/5
Pays : United Kingdom
Organisme : Cancer Research UK
ID : C47648/A20837
Pays : United Kingdom
Commentaires et corrections
Type : CommentIn
Références
Roers, A., Hiller, B. & Hornung, V. Recognition of endogenous nucleic acids by the innate immune system. Immunity 44, 739–754 (2016).
pubmed: 27096317
doi: 10.1016/j.immuni.2016.04.002
Uggenti, C., Lepelley, A. & Crow, Y. J. Self-awareness: nucleic acid-driven inflammation and the type I interferonopathies. Annu. Rev. Immunol. 37, 247–267 (2019).
pubmed: 30633609
doi: 10.1146/annurev-immunol-042718-041257
Bartsch, K. et al. Absence of RNase H2 triggers generation of immunogenic micronuclei removed by autophagy. Hum. Mol. Genet. 26, 3960–3972 (2017).
pubmed: 29016854
doi: 10.1093/hmg/ddx283
Harding, S. M. et al. Mitotic progression following DNA damage enables pattern recognition within micronuclei. Nature 548, 466–470 (2017).
pubmed: 28759889
pmcid: 5857357
Mackenzie, K. J. et al. cGAS surveillance of micronuclei links genome instability to innate immunity. Nature 548, 461–465 (2017).
pubmed: 28738408
pmcid: 5870830
doi: 10.1038/nature23449
Gentili, M. et al. The N-terminal domain of cGAS determines preferential association with centromeric DNA and innate immune activation in the nucleus. Cell Rep. 26, 3798 (2019).
pubmed: 30917330
pmcid: 6444014
doi: 10.1016/j.celrep.2019.03.049
Yang, H., Wang, H., Ren, J., Chen, Q. & Chen, Z. J. cGAS is essential for cellular senescence. Proc. Natl Acad. Sci. USA 114, E4612–E4620 (2017).
pubmed: 28533362
pmcid: 5468617
Zierhut, C. et al. The cytoplasmic DNA sensor cGAS promotes mitotic cell death. Cell 178, 302–315.e23 (2019).
pubmed: 31299200
pmcid: 6693521
doi: 10.1016/j.cell.2019.05.035
Denais, C. M. et al. Nuclear envelope rupture and repair during cancer cell migration. Science 352, 353–358 (2016).
pubmed: 27013428
pmcid: 4833568
doi: 10.1126/science.aad7297
Raab, M. et al. ESCRT III repairs nuclear envelope ruptures during cell migration to limit DNA damage and cell death. Science 352, 359–362 (2016).
pubmed: 27013426
doi: 10.1126/science.aad7611
Jiang, H. et al. Chromatin-bound cGAS is an inhibitor of DNA repair and hence accelerates genome destabilization and cell death. EMBO J. 38, e102718 (2019).
pubmed: 31544964
pmcid: 6826206
doi: 10.15252/embj.2019102718
Lahaye, X. et al. NONO detects the nuclear HIV capsid to promote cGAS-mediated innate immune activation. Cell 175, 488–501.e22 (2018).
pubmed: 30270045
doi: 10.1016/j.cell.2018.08.062
Liu, H. et al. Nuclear cGAS suppresses DNA repair and promotes tumorigenesis. Nature 563, 131–136 (2018).
pubmed: 30356214
doi: 10.1038/s41586-018-0629-6
Volkman, H. E., Cambier, S., Gray, E. E. & Stetson, D. B. Tight nuclear tethering of cGAS is essential for preventing autoreactivity. eLife 8, e47491 (2019).
pubmed: 31808743
pmcid: 6927687
doi: 10.7554/eLife.47491
Crow, Y. J. et al. Mutations in the gene encoding the 3′-5′ DNA exonuclease TREX1 cause Aicardi–Goutières syndrome at the AGS1 locus. Nat. Genet. 38, 917–920 (2006).
pubmed: 16845398
doi: 10.1038/ng1845
Crow, Y. J. et al. Mutations in genes encoding ribonuclease H2 subunits cause Aicardi–Goutières syndrome and mimic congenital viral brain infection. Nat. Genet. 38, 910–916 (2006).
pubmed: 16845400
doi: 10.1038/ng1842
Rice, G. I. et al. Mutations involved in Aicardi–Goutières syndrome implicate SAMHD1 as regulator of the innate immune response. Nat. Genet. 41, 829–832 (2009).
pubmed: 19525956
pmcid: 4154505
doi: 10.1038/ng.373
Rice, G. I. et al. Mutations in ADAR1 cause Aicardi–Goutières syndrome associated with a type I interferon signature. Nat. Genet. 44, 1243–1248 (2012).
pubmed: 23001123
pmcid: 4154508
doi: 10.1038/ng.2414
Rice, G. I. et al. Gain-of-function mutations in IFIH1 cause a spectrum of human disease phenotypes associated with upregulated type I interferon signaling. Nat. Genet. 46, 503–509 (2014).
pubmed: 24686847
pmcid: 4004585
doi: 10.1038/ng.2933
Crow, Y. J. & Manel, N. Aicardi–Goutières syndrome and the type I interferonopathies. Nat. Rev. Immunol. 15, 429–440 (2015).
doi: 10.1038/nri3850
pubmed: 26052098
Pillai, R. S. et al. Unique Sm core structure of U7 snRNPs: assembly by a specialized SMN complex and the role of a new component, Lsm11, in histone RNA processing. Genes Dev. 17, 2321–2333 (2003).
pubmed: 12975319
pmcid: 196468
doi: 10.1101/gad.274403
Kolev, N. G. & Steitz, J. A. In vivo assembly of functional U7 snRNP requires RNA backbone flexibility within the Sm-binding site. Nat. Struct. Mol. Biol. 13, 347–353 (2006).
pubmed: 16547514
doi: 10.1038/nsmb1075
Badrock, A. P. et al. Analysis of U8 snoRNA variants in zebrafish reveals how bi-allelic variants cause leukoencephalopathy with calcifications and cysts. Am. J. Hum. Genet. 106, 694–706 (2020).
pubmed: 32359472
pmcid: 7212298
doi: 10.1016/j.ajhg.2020.04.003
Marzluff, W. F., Wagner, E. J. & Duronio, R. J. Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail. Nat. Rev. Genet. 9, 843–854 (2008).
pubmed: 18927579
pmcid: 2715827
doi: 10.1038/nrg2438
Müller, B. & Schümperli, D. The U7 snRNP and the hairpin binding protein: key players in histone mRNA metabolism. Semin. Cell Dev. Biol. 8, 567–576 (1997).
pubmed: 9642171
doi: 10.1006/scdb.1997.0182
Dominski, Z. & Marzluff, W. F. Formation of the 3′ end of histone mRNA: getting closer to the end. Gene 396, 373–390 (2007).
pubmed: 17531405
pmcid: 2888136
doi: 10.1016/j.gene.2007.04.021
Wang, Z. F., Whitfield, M. L., Ingledue, T. I.3rd, Dominski, Z. & Marzluff, W. F. The protein which binds the 3′ end of histone mRNA: a novel RNA- binding protein required for histone pre-mRNA processing. Genes Dev. 10, 3028–3040 (1996).
pubmed: 8957003
doi: 10.1101/gad.10.23.3028
Martin, F., Schaller, A., Eglite, S., Schümperli, D. & Müller, B. The gene for histone RNA hairpin binding protein is located on human chromosome 4 and encodes a novel type of RNA binding protein. EMBO J. 16, 769–778 (1997).
pubmed: 9049306
pmcid: 1169678
doi: 10.1093/emboj/16.4.769
Sabath, I. et al. 3′-End processing of histone pre-mRNAs in Drosophila: U7 snRNP is associated with FLASH and polyadenylation factors. RNA 19, 1726–1744 (2013).
pubmed: 24145821
pmcid: 3884669
doi: 10.1261/rna.040360.113
Sullivan, E. et al. Drosophila stem loop binding protein coordinates accumulation of mature histone mRNA with cell cycle progression. Genes Dev. 15, 173–187 (2001).
pubmed: 11157774
pmcid: 312608
doi: 10.1101/gad.862801
Marzluff, W. F., Gongidi, P., Woods, K. R., Jin, J. & Maltais, L. J. The human and mouse replication-dependent histone genes. Genomics 80, 487–498 (2002).
pubmed: 12408966
doi: 10.1006/geno.2002.6850
Rice, G. I. et al. Assessment of interferon-related biomarkers in Aicardi–Goutières syndrome associated with mutations in TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, and ADAR: a case-control study. Lancet Neurol. 12, 1159–1169 (2013).
pubmed: 24183309
pmcid: 4349523
doi: 10.1016/S1474-4422(13)70258-8
Chen, Q., Sun, L. & Chen, Z. J. Regulation and function of the cGAS–STING pathway of cytosolic DNA sensing. Nat. Immunol. 17, 1142–1149 (2016).
doi: 10.1038/ni.3558
pubmed: 27648547
Streicher, F. & Jouvenet, N. Stimulation of innate immunity by host and viral RNAs. Trends Immunol. 40, 1134–1148 (2019).
pubmed: 31735513
doi: 10.1016/j.it.2019.10.009
Izquierdo-Bouldstridge, A. et al. Histone H1 depletion triggers an interferon response in cancer cells via activation of heterochromatic repeats. Nucleic Acids Res. 45, 11622–11642 (2017).
pubmed: 28977426
pmcid: 5714221
doi: 10.1093/nar/gkx746
Lepelley, A. et al. Mutations in COPA lead to abnormal trafficking of STING to the Golgi and interferon signaling. J. Exp. Med. 217, e20200600 (2020).
pubmed: 32725128
doi: 10.1084/jem.20200600
pmcid: 7596811
Gilbert, N. et al. Formation of facultative heterochromatin in the absence of HP1. EMBO J. 22, 5540–5550 (2003).
pubmed: 14532126
pmcid: 213774
doi: 10.1093/emboj/cdg520
Gilbert, N. et al. DNA methylation affects nuclear organization, histone modifications, and linker histone binding but not chromatin compaction. J. Cell Biol. 177, 401–411 (2007).
pubmed: 17485486
pmcid: 2064831
doi: 10.1083/jcb.200607133
Cook, A. J., Gurard-Levin, Z. A., Vassias, I. & Almouzni, G. A specific function for the histone chaperone NASP to fine-tune a reservoir of soluble H3-H4 in the histone supply chain. Mol. Cell 44, 918–927 (2011).
pubmed: 22195965
doi: 10.1016/j.molcel.2011.11.021
Peterson, C. L. & Hansen, J. C. Chicken erythrocyte histone octamer preparation. CSH Protoc. 2008, pdb.prot5112 (2008).
pubmed: 21356757
Allan, J., Staynov, D. Z. & Gould, H. Reversible dissociation of linker histone from chromatin with preservation of internucleosomal repeat. Proc. Natl Acad. Sci. USA 77, 885–889 (1980).
pubmed: 6928686
doi: 10.1073/pnas.77.2.885
pmcid: 348386
Yang, L., Duff, M. O., Graveley, B. R., Carmichael, G. G. & Chen, L.-L. Genomewide characterization of non-polyadenylated RNAs. Genome Biol. 12, R16 (2011).
pubmed: 21324177
pmcid: 3188798
doi: 10.1186/gb-2011-12-2-r16
Flicek, P. et al. Ensembl 2014. Nucleic Acids Res. 42, D749–D755 (2014).
pubmed: 24316576
doi: 10.1093/nar/gkt1196
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).
pubmed: 25751142
pmcid: 4655817
doi: 10.1038/nmeth.3317
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
pubmed: 19505943
pmcid: 2723002
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
pubmed: 20110278
pmcid: 2832824
doi: 10.1093/bioinformatics/btq033
Kent, W. J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002).
pubmed: 12045153
pmcid: 186604
doi: 10.1101/gr.229102
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
pubmed: 25516281
pmcid: 4302049
doi: 10.1186/s13059-014-0550-8