The Histone Demethylase Jarid1b Ensures Faithful Mouse Development by Protecting Developmental Genes from Aberrant H3K4me3
Embryonic development is tightly regulated by transcription factors and chromatin-associated proteins. H3K4me3 is associated with active transcription and H3K27me3 with gene repression, while the combination of both keeps genes required for development in a plastic state. Here we show that deletion of the H3K4me2/3 histone demethylase Jarid1b (Kdm5b/Plu1) results in major neonatal lethality due to respiratory failure. Jarid1b knockout embryos have several neural defects including disorganized cranial nerves, defects in eye development, and increased incidences of exencephaly. Moreover, in line with an overlap of Jarid1b and Polycomb target genes, Jarid1b knockout embryos display homeotic skeletal transformations typical for Polycomb mutants, supporting a functional interplay between Polycomb proteins and Jarid1b. To understand how Jarid1b regulates mouse development, we performed a genome-wide analysis of histone modifications, which demonstrated that normally inactive genes encoding developmental regulators acquire aberrant H3K4me3 during early embryogenesis in Jarid1b knockout embryos. H3K4me3 accumulates as embryonic development proceeds, leading to increased expression of neural master regulators like Pax6 and Otx2 in Jarid1b knockout brains. Taken together, these results suggest that Jarid1b regulates mouse development by protecting developmental genes from inappropriate acquisition of active histone modifications.
Vyšlo v časopise:
The Histone Demethylase Jarid1b Ensures Faithful Mouse Development by Protecting Developmental Genes from Aberrant H3K4me3. PLoS Genet 9(4): e32767. doi:10.1371/journal.pgen.1003461
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1003461
Souhrn
Embryonic development is tightly regulated by transcription factors and chromatin-associated proteins. H3K4me3 is associated with active transcription and H3K27me3 with gene repression, while the combination of both keeps genes required for development in a plastic state. Here we show that deletion of the H3K4me2/3 histone demethylase Jarid1b (Kdm5b/Plu1) results in major neonatal lethality due to respiratory failure. Jarid1b knockout embryos have several neural defects including disorganized cranial nerves, defects in eye development, and increased incidences of exencephaly. Moreover, in line with an overlap of Jarid1b and Polycomb target genes, Jarid1b knockout embryos display homeotic skeletal transformations typical for Polycomb mutants, supporting a functional interplay between Polycomb proteins and Jarid1b. To understand how Jarid1b regulates mouse development, we performed a genome-wide analysis of histone modifications, which demonstrated that normally inactive genes encoding developmental regulators acquire aberrant H3K4me3 during early embryogenesis in Jarid1b knockout embryos. H3K4me3 accumulates as embryonic development proceeds, leading to increased expression of neural master regulators like Pax6 and Otx2 in Jarid1b knockout brains. Taken together, these results suggest that Jarid1b regulates mouse development by protecting developmental genes from inappropriate acquisition of active histone modifications.
Zdroje
1. BarskiA, CuddapahS, CuiK, RohT-Y, SchonesDE, et al. (2007) High-Resolution Profiling of Histone Methylations in the Human Genome. Cell 129: 823–837.
2. SchübelerD, MacAlpineDM, ScalzoD, WirbelauerC, KooperbergC, et al. (2004) The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes & Development 18: 1263–1271.
3. GuentherMG, LevineSS, BoyerLA, JaenischR, YoungRA (2007) A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130: 77–88.
4. HublitzP, AlbertM, PetersAHFM (2009) Mechanisms of transcriptional repression by histone lysine methylation. Int J Dev Biol 53: 335–354.
5. YuBD, HessJL, HorningSE, BrownGA, KorsmeyerSJ (1995) Altered Hox expression and segmental identity in Mll-mutant mice. Nature 378: 505–508.
6. GlaserS, SchaftJ, LubitzS, VinterstenK, van der HoevenF, et al. (2006) Multiple epigenetic maintenance factors implicated by the loss of Mll2 in mouse development. Development 133: 1423–1432.
7. YagiH, DeguchiK, AonoA, TaniY, KishimotoT, et al. (1998) Growth disturbance in fetal liver hematopoiesis of Mll-mutant mice. Blood 92: 108–117.
8. ErnstP, FisherJK, AveryW, WadeS, FoyD, et al. (2004) Definitive hematopoiesis requires the mixed-lineage leukemia gene. Developmental Cell 6: 437–443.
9. LimDA, HuangY-C, SwigutT, MirickAL, Garcia-VerdugoJM, et al. (2009) Chromatin remodelling factor Mll1 is essential for neurogenesis from postnatal neural stem cells. Nature 458: 529–533.
10. BernsteinBE, MikkelsenTS, XieX, KamalM, HuebertDJ, et al. (2006) A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells. Cell 125: 315–326.
11. PietersenAM, van LohuizenM (2008) Stem cell regulation by polycomb repressors: postponing commitment. Current Opinion in Cell Biology 20: 201–207.
12. MargueronR, ReinbergD (2011) The Polycomb complex PRC2 and its mark in life. Nature 469: 343–349.
13. CaoR, WangL, WangH, XiaL, Erdjument-BromageH, et al. (2002) Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298: 1039–1043.
14. CaoR, TsukadaY-I, ZhangY (2005) Role of Bmi-1 and Ring1A in H2A ubiquitylation and Hox gene silencing. Molecular Cell 20: 845–854.
15. WangL, BrownJL, CaoR, ZhangY, KassisJA, et al. (2004) Hierarchical recruitment of polycomb group silencing complexes. Molecular Cell 14: 637–646.
16. SchoeftnerS, SenguptaAK, KubicekS, MechtlerK, SpahnL, et al. (2006) Recruitment of PRC1 function at the initiation of X inactivation independent of PRC2 and silencing. The EMBO Journal 25: 3110–3122.
17. PuschendorfM, TerranovaR, BoutsmaE, MaoX, IsonoK-I, et al. (2008) PRC1 and Suv39h specify parental asymmetry at constitutive heterochromatin in early mouse embryos. Nat Genet 40: 411–420.
18. TavaresL, DimitrovaE, OxleyD, WebsterJ, PootR, et al. (2012) RYBP-PRC1 Complexes Mediate H2A Ubiquitylation at Polycomb Target Sites Independently of PRC2 and H3K27me3. Cell 148: 664–678.
19. ShiY, LanF, MatsonC, MulliganP, WhetstineJR, et al. (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119: 941–953.
20. KooistraSM, HelinK (2012) Molecular mechanisms and potential functions of histone demethylases. Nat Rev Mol Cell Biol 13: 297–311.
21. GildeaJJ, LopezR, ShearnA (2000) A screen for new trithorax group genes identified little imaginal discs, the Drosophila melanogaster homologue of human retinoblastoma binding protein 2. Genetics 156: 645–663.
22. GreerEL, MauresTJ, UcarD, HauswirthAG, ManciniE, et al. (2011) Transgenerational epigenetic inheritance of longevity in Caenorhabditis elegans. Nature 479: 365–371.
23. ChristensenJ, AggerK, CloosPAC, PasiniD, RoseS, et al. (2007) RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3. Cell 128: 1063–1076.
24. KloseRJ, YanQ, TothovaZ, YamaneK, Erdjument-BromageH, et al. (2007) The retinoblastoma binding protein RBP2 is an H3K4 demethylase. Cell 128: 889–900.
25. CatchpoleS, Spencer-DeneB, HallD, SantangeloS, RosewellI, et al. (2011) PLU-1/JARID1B/KDM5B is required for embryonic survival and contributes to cell proliferation in the mammary gland and in ER+ breast cancer cells. Int J Oncol 38: 1267–1277.
26. BlairLP, CaoJ, ZouMR, SayeghJ, YanQ (2011) Epigenetic Regulation by Lysine Demethylase 5 (KDM5) Enzymes in Cancer. Cancers 3: 1383–1404.
27. DeyBK, StalkerL, SchnerchA, BhatiaM, Taylor-PapidimitriouJ, et al. (2008) The Histone Demethylase KDM5b/JARID1b Plays a Role in Cell Fate Decisions by Blocking Terminal Differentiation. Molecular and Cellular Biology 28: 5312–5327.
28. SchmitzSU, AlbertM, MalatestaM, MoreyL, JohansenJV, et al. (2011) Jarid1b targets genes regulating development and is involved in neural differentiation. The EMBO Journal 30: 4586–4600.
29. MadsenB, TarsounasM, BurchellJM, HallD, PoulsomR, et al. (2003) PLU-1, a transcriptional repressor and putative testis-cancer antigen, has a specific expression and localisation pattern during meiosis. Chromosoma 112: 124–132.
30. TurgeonB, MelocheS (2009) Interpreting Neonatal Lethal Phenotypes in Mouse Mutants: Insights Into Gene Function and Human Diseases. Physiological Reviews 89: 1–26.
31. MoseleyAE, LieskeSP, WetzelRK, JamesPF, HeS, et al. (2003) The Na,K-ATPase alpha 2 isoform is expressed in neurons, and its absence disrupts neuronal activity in newborn mice. J Biol Chem 278: 5317–5324.
32. WhitsettJA, WeaverTE (2002) Hydrophobic surfactant proteins in lung function and disease. N Engl J Med 347: 2141–2148.
33. KlingerS, TurgeonB, LévesqueK, WoodGA, Aagaard-TilleryKM, et al. (2009) Loss of Erk3 function in mice leads to intrauterine growth restriction, pulmonary immaturity, and neonatal lethality. Proc Natl Acad Sci USA 106: 16710–16715.
34. BordayC, ChatonnetF, Thoby-BrissonM, ChampagnatJ, FortinG (2005) Neural tube patterning by Krox20 and emergence of a respiratory control. Respiratory Physiology & Neurobiology 149: 63–72.
35. GomezaJ, HülsmannS, OhnoK, EulenburgV, SzökeK, et al. (2003) Inactivation of the glycine transporter 1 gene discloses vital role of glial glycine uptake in glycinergic inhibition. Neuron 40: 785–796.
36. GuthrieS (2007) Patterning and axon guidance of cranial motor neurons. Nat Rev Neurosci 8: 859–871.
37. CordesSP (2001) Molecular genetics of cranial nerve development in mouse. Nat Rev Neurosci 2: 611–623.
38. MadsenB, Spencer-DeneB, PoulsomR, HallD, LuPJ, et al. (2002) Characterisation and developmental expression of mouse Plu-1, a homologue of a human nuclear protein (PLU-1) which is specifically up-regulated in breast cancer. Mech Dev 119 (Suppl 1) S239–S246.
39. AkasakaT, KannoM, BallingR, MiezaMA, TaniguchiM, et al. (1996) A role for mel-18, a Polycomb group-related vertebrate gene, during theanteroposterior specification of the axial skeleton. Development 122: 1513–1522.
40. del Mar LorenteM, Marcos-GutiérrezC, PérezC, SchoorlemmerJ, RamírezA, et al. (2000) Loss- and gain-of-function mutations show a polycomb group function for Ring1A in mice. Development 127: 5093–5100.
41. ChowRL, LangRA (2001) Early eye development in vertebrates. Annu Rev Cell Dev Biol 17: 255–296.
42. AlexanderT, NolteC, KrumlaufR (2009) HoxGenes and Segmentation of the Hindbrain and Axial Skeleton. Annu Rev Cell Dev Biol 25: 431–456.
43. YamaneK, TateishiK, KloseRJ, FangJ, FabrizioLA, et al. (2007) PLU-1 Is an H3K4 Demethylase Involved in Transcriptional Repression and Breast Cancer Cell Proliferation. Molecular Cell 25: 801–812.
44. SansomSN, GriffithsDS, FaedoA, KleinjanD-J, RuanY, et al. (2009) The level of the transcription factor Pax6 is essential for controlling the balance between neural stem cell self-renewal and neurogenesis. PLoS Genet 5: e1000511 doi:10.1371/journal.pgen.1000511.
45. HaoH, KimDS, KlockeB, JohnsonKR, CuiK, et al. (2012) Transcriptional regulation of rod photoreceptor homeostasis revealed by in vivo NRL targetome analysis. PLoS Genet 8: e1002649 doi:10.1371/journal.pgen.1002649.
46. JensenLR, AmendeM, GurokU, MoserB, GimmelV, et al. (2005) Mutations in the JARID1C Gene, Which Is Involved in Transcriptional Regulation and Chromatin Remodeling, Cause X-Linked Mental Retardation. The American Journal of Human Genetics 76: 227–236.
47. CoxBJ, VollmerM, TamplinO, LuM, BiecheleS, et al. (2010) Phenotypic annotation of the mouse X chromosome. Genome Res 20: 1154–1164.
48. JiangH, ShuklaA, WangX, ChenW-Y, BernsteinBE, et al. (2011) Role for Dpy-30 in ES cell-fate specification by regulation of H3K4 methylation within bivalent domains. Cell 144: 513–525.
49. El-SamadH, MadhaniHD (2011) Can a Systems Perspective Help Us Appreciate the Biological Meaning of Small Effects? Developmental Cell 21: 11–13.
50. HeverAM, WilliamsonKA, van HeyningenV (2006) Developmental malformations of the eye: the role of PAX6, SOX2 and OTX2. Clin Genet 69: 459–470.
51. OsumiN, ShinoharaH, Numayama-TsurutaK, MaekawaM (2008) Concise review: Pax6 transcription factor contributes to both embryonic and adult neurogenesis as a multifunctional regulator. Stem Cells 26: 1663–1672.
52. SchedlA, RossA, LeeM, EngelkampD, RashbassP, et al. (1996) Influence of PAX6 gene dosage on development: overexpression causes severe eye abnormalities. Cell 86: 71–82.
53. WorthamM, JinG, SunJL, BignerDD, HeY, et al. (2012) Aberrant Otx2 expression enhances migration and induces ectopic proliferation of hindbrain neuronal progenitor cells. PLoS ONE 7: e36211 doi:10.1371/journal.pone.0036211.
54. Lloret-Llinares M, Pérez-Lluch S, Rossell D, Morán T, Ponsa-Cobas J, et al.. (2012) dKDM5/LID regulates H3K4me3 dynamics at the transcription-start site (TSS) of actively transcribed developmental genes. Nucleic Acids Res.
55. FukudaT, TokunagaA, SakamotoR, YoshidaN (2011) Fbxl10/Kdm2b deficiency accelerates neural progenitor cell death and leads to exencephaly. Molecular and Cellular Neuroscience 46: 614–624.
56. HarrisMJ, JuriloffDM (2010) An update to the list of mouse mutants with neural tube closure defects and advances toward a complete genetic perspective of neural tube closure. Birth Defects Research Part A: Clinical and Molecular Teratology 88: 653–669.
57. BurgaA, CasanuevaMO, LehnerB (2011) Predicting mutation outcome from early stochastic variation in genetic interaction partners. Nature 480: 250–253.
58. RajA, RifkinSA, AndersenE, van OudenaardenA (2010) Variability in gene expression underlies incomplete penetrance. Nature 463: 913–918.
59. AngelA, SongJ, DeanC, HowardM (2011) A Polycomb-based switch underlying quantitative epigenetic memory. Nature 476: 105–108.
60. SimpsonAJG, CaballeroOL, JungbluthA, ChenY-T, OldLJ (2005) Cancer/testis antigens, gametogenesis and cancer. Nat Rev Cancer 5: 615–625.
61. SchwenkF, BaronU, RajewskyK (1995) A cre-transgenic mouse strain for the ubiquitous deletion of loxP-flanked gene segments including deletion in germ cells. Nucleic Acids Res 23: 5080–5081.
62. VitobelloA, FerrettiE, LampeX, VilainN, DucretS, et al. (2011) Hox and Pbx Factors Control Retinoic Acid Synthesis during Hindbrain Segmentation. Developmental Cell 20: 469–482.
63. PanchisionDM, ChenH-L, PistollatoF, PapiniD, NiH-T, et al. (2007) Optimized flow cytometric analysis of central nervous system tissue reveals novel functional relationships among cells expressing CD133, CD15, and CD24. Stem Cells 25: 1560–1570.
64. ZhangY, LiuT, MeyerCA, EeckhouteJ, JohnsonDS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137.
65. LangmeadB, TrapnellC, PopM, SalzbergSL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
66. LiH, HandsakerB, WysokerA, FennellT, RuanJ, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078–2079.
67. QuinlanAR, HallIM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841–842.
68. GellertP, TeranishiM, JennichesK, De GaspariP, JohnD, et al. (2012) Gene Array Analyzer: alternative usage of gene arrays to study alternative splicing events. Nucleic Acids Res 40: 2414–2425.
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2013 Číslo 4
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
Najčítanejšie v tomto čísle
- The G4 Genome
- Neutral Genomic Microevolution of a Recently Emerged Pathogen, Serovar Agona
- The Histone Demethylase Jarid1b Ensures Faithful Mouse Development by Protecting Developmental Genes from Aberrant H3K4me3
- The Tissue-Specific RNA Binding Protein T-STAR Controls Regional Splicing Patterns of Pre-mRNAs in the Brain