Enrichment of HP1a on Drosophila Chromosome 4 Genes Creates an Alternate Chromatin Structure Critical for Regulation in this Heterochromatic Domain
Chromatin environments differ greatly within a eukaryotic genome, depending on expression state, chromosomal location, and nuclear position. In genomic regions characterized by high repeat content and high gene density, chromatin structure must silence transposable elements but permit expression of embedded genes. We have investigated one such region, chromosome 4 of Drosophila melanogaster. Using chromatin-immunoprecipitation followed by microarray (ChIP–chip) analysis, we examined enrichment patterns of 20 histone modifications and 25 chromosomal proteins in S2 and BG3 cells, as well as the changes in several marks resulting from mutations in key proteins. Active genes on chromosome 4 are distinct from those in euchromatin or pericentric heterochromatin: while there is a depletion of silencing marks at the transcription start sites (TSSs), HP1a and H3K9me3, but not H3K9me2, are enriched strongly over gene bodies. Intriguingly, genes on chromosome 4 are less frequently associated with paused polymerase. However, when the chromatin is altered by depleting HP1a or POF, the RNA pol II enrichment patterns of many chromosome 4 genes shift, showing a significant decrease over gene bodies but not at TSSs, accompanied by lower expression of those genes. Chromosome 4 genes have a low incidence of TRL/GAGA factor binding sites and a low Tm downstream of the TSS, characteristics that could contribute to a low incidence of RNA polymerase pausing. Our data also indicate that EGG and POF jointly regulate H3K9 methylation and promote HP1a binding over gene bodies, while HP1a targeting and H3K9 methylation are maintained at the repeats by an independent mechanism. The HP1a-enriched, POF-associated chromatin structure over the gene bodies may represent one type of adaptation for genes embedded in repetitive DNA.
Vyšlo v časopise:
Enrichment of HP1a on Drosophila Chromosome 4 Genes Creates an Alternate Chromatin Structure Critical for Regulation in this Heterochromatic Domain. PLoS Genet 8(9): e32767. doi:10.1371/journal.pgen.1002954
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1002954
Souhrn
Chromatin environments differ greatly within a eukaryotic genome, depending on expression state, chromosomal location, and nuclear position. In genomic regions characterized by high repeat content and high gene density, chromatin structure must silence transposable elements but permit expression of embedded genes. We have investigated one such region, chromosome 4 of Drosophila melanogaster. Using chromatin-immunoprecipitation followed by microarray (ChIP–chip) analysis, we examined enrichment patterns of 20 histone modifications and 25 chromosomal proteins in S2 and BG3 cells, as well as the changes in several marks resulting from mutations in key proteins. Active genes on chromosome 4 are distinct from those in euchromatin or pericentric heterochromatin: while there is a depletion of silencing marks at the transcription start sites (TSSs), HP1a and H3K9me3, but not H3K9me2, are enriched strongly over gene bodies. Intriguingly, genes on chromosome 4 are less frequently associated with paused polymerase. However, when the chromatin is altered by depleting HP1a or POF, the RNA pol II enrichment patterns of many chromosome 4 genes shift, showing a significant decrease over gene bodies but not at TSSs, accompanied by lower expression of those genes. Chromosome 4 genes have a low incidence of TRL/GAGA factor binding sites and a low Tm downstream of the TSS, characteristics that could contribute to a low incidence of RNA polymerase pausing. Our data also indicate that EGG and POF jointly regulate H3K9 methylation and promote HP1a binding over gene bodies, while HP1a targeting and H3K9 methylation are maintained at the repeats by an independent mechanism. The HP1a-enriched, POF-associated chromatin structure over the gene bodies may represent one type of adaptation for genes embedded in repetitive DNA.
Zdroje
1. KornbergRD (1974) Chromatin structure: a repeating unit of histones and DNA. Science 184: 868–871.
2. LugerK, MaderAW, RichmondRK, SargentDF, RichmondTJ (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389: 251–260.
3. BannisterAJ, KouzaridesT (2011) Regulation of chromatin by histone modifications. Cell Res 21: 381–395.
4. LeungW, ShafferCD, CordonnierT, WongJ, ItanoMS, et al. (2010) Evolution of a distinct genomic domain in Drosophila: comparative analysis of the dot chromosome in Drosophila melanogaster and Drosophila virilis. Genetics 185: 1519–1534.
5. LockeJ, McDermidHE (1993) Analysis of Drosophila chromosome 4 using pulsed field gel electrophoresis. Chromosoma 102: 718–723.
6. BarigozziC, DolfiniS, FraccaroM, RaimondiGR, TiepoloL (1966) In vitro study of the DNA replication patterns of somatic chromosomes of Drosophila melanogaster. Exp Cell Res 43: 231–234.
7. ArguelloJR, ZhangY, KadoT, FanC, ZhaoR, et al. (2010) Recombination yet inefficient selection along the Drosophila melanogaster subgroup's fourth chromosome. Mol Biol Evol 27: 848–861.
8. BridgesCB (1935) The mutants and linkage data of chromosome four of Drosophila melanogaster. Biol Zh 4: 401–420.
9. RiddleNC, ElginSC (2008) A role for RNAi in heterochromatin formation in Drosophila. Curr Top Microbiol Immunol 320: 185–209.
10. SunFL, HaynesK, SimpsonCL, LeeSD, CollinsL, et al. (2004) cis-Acting determinants of heterochromatin formation on Drosophila melanogaster chromosome four. Mol Cell Biol 24: 8210–8220.
11. WallrathLL, ElginSC (1995) Position effect variegation in Drosophila is associated with an altered chromatin structure. Genes Dev 9: 1263–1277.
12. JamesTC, EissenbergJC, CraigC, DietrichV, HobsonA, et al. (1989) Distribution patterns of HP1, a heterochromatin-associated nonhistone chromosomal protein of Drosophila. Eur J Cell Biol 50: 170–180.
13. SchottaG, EbertA, KraussV, FischerA, HoffmannJ, et al. (2002) Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing. Embo J 21: 1121–1131.
14. KharchenkoPV, AlekseyenkoAA, SchwartzYB, MinodaA, RiddleNC, et al. (2011) Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471: 480–485.
15. RiddleNC, MinodaA, KharchenkoPV, AlekseyenkoAA, SchwartzYB, et al. (2011) Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res 21: 147–163.
16. LarssonJ, ChenJD, RashevaV, Rasmuson-LestanderA, PirrottaV (2001) Painting of fourth, a chromosome-specific protein in Drosophila. Proc Natl Acad Sci U S A 98: 6273–6278.
17. JohanssonAM, StenbergP, PetterssonF, LarssonJ (2007) POF and HP1 bind expressed exons, suggesting a balancing mechanism for gene regulation. PLoS Genet 3: e209 doi:10.1371/journal.pgen.0030209.
18. StenbergP, LundbergLE, JohanssonAM, RydenP, SvenssonMJ, et al. (2009) Buffering of segmental and chromosomal aneuploidies in Drosophila melanogaster. PLoS Genet 5: e1000465 doi:10.1371/journal.pgen.1000465.
19. JohanssonAM, StenbergP, AllgardssonA, LarssonJ (2012) POF Regulates the Expression of Genes on the Fourth Chromosome in Drosophila melanogaster by Binding to Nascent RNA. Mol Cell Biol 32: 2121–2134.
20. Brower-TolandB, RiddleNC, JiangH, HuisingaKL, ElginSC (2009) Multiple SET methyltransferases are required to maintain normal heterochromatin domains in the genome of Drosophila melanogaster. Genetics 181: 1303–1319.
21. SeumC, ReoE, PengH, RauscherFJ3rd, SpiererP, et al. (2007) Drosophila SETDB1 is required for chromosome 4 silencing. PLoS Genet 3: e76 doi:10.1371/journal.pgen.0030076.
22. TzengTY, LeeCH, ChanLW, ShenCK (2007) Epigenetic regulation of the Drosophila chromosome 4 by the histone H3K9 methyltransferase dSETDB1. Proc Natl Acad Sci U S A 104: 12691–12696.
23. RoyS, ErnstJ, KharchenkoPV, KheradpourP, NegreN, et al. (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330: 1787–1797.
24. RiddleNC, LeungW, HaynesKA, GranokH, WullerJ, et al. (2008) An investigation of heterochromatin domains on the fourth chromosome of Drosophila melanogaster. Genetics 178: 1177–1191.
25. SchwartzYB, KahnTG, StenbergP, OhnoK, BourgonR, et al. (2010) Alternative epigenetic chromatin states of polycomb target genes. PLoS Genet 6: e1000805 doi:10.1371/journal.pgen.1000805.
26. LarschanE, BishopEP, KharchenkoPV, CoreLJ, LisJT, et al. (2011) X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila. Nature 471: 115–118.
27. CoreLJ, WaterfallJJ, LisJT (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322: 1845–1848.
28. SlawsonEE, ShafferCD, MaloneCD, LeungW, KellmannE, et al. (2006) Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains. Genome Biol 7: R15.
29. HendrixDA, HongJW, ZeitlingerJ, RokhsarDS, LevineMS (2008) Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proc Natl Acad Sci U S A 105: 7762–7767.
30. MuseGW, GilchristDA, NechaevS, ShahR, ParkerJS, et al. (2007) RNA polymerase is poised for activation across the genome. Nat Genet 39: 1507–1511.
31. ZeitlingerJ, StarkA, KellisM, HongJW, NechaevS, et al. (2007) RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet 39: 1512–1516.
32. ZhangY, MaloneJH, PowellSK, PeriwalV, SpanaE, et al. (2010) Expression in aneuploid Drosophila S2 cells. PLoS Biol 8: e1000320 doi:10.1371/journal.pbio.1000320.
33. NechaevS, FargoDC, dos SantosG, LiuL, GaoY, et al. (2010) Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science 327: 335–338.
34. WakimotoBT, HearnMG (1990) The effects of chromosome rearrangements on the expression of heterochromatic genes in chromosome 2L of Drosophila melanogaster. Genetics 125: 141–154.
35. PiacentiniL, FantiL, NegriR, Del VescovoV, FaticaA, et al. (2009) Heterochromatin protein 1 (HP1a) positively regulates euchromatic gene expression through RNA transcript association and interaction with hnRNPs in Drosophila. PLoS Genet 5: e1000670 doi:10.1371/journal.pgen.1000670.
36. JohanssonAM, StenbergP, BernhardssonC, LarssonJ (2007) Painting of fourth and chromosome-wide regulation of the 4th chromosome in Drosophila melanogaster. Embo J 26: 2307–2316.
37. PhalkeS, NickelO, WalluscheckD, HortigF, OnoratiMC, et al. (2009) Retrotransposon silencing and telomere integrity in somatic cells of Drosophila depends on the cytosine-5 methyltransferase DNMT2. Nat Genet 41: 696–702.
38. CrydermanDE, TangH, BellC, GilmourDS, WallrathLL (1999) Heterochromatic silencing of Drosophila heat shock genes acts at the level of promoter potentiation. Nucleic Acids Res 27: 3364–3370.
39. NechaevS, AdelmanK (2011) Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation. Biochim Biophys Acta 1809: 34–45.
40. MinIM, WaterfallJJ, CoreLJ, MunroeRJ, SchimentiJ, et al. (2011) Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells. Genes Dev 25: 742–754.
41. BaoX, DengH, JohansenJ, GirtonJ, JohansenKM (2007) Loss-of-function alleles of the JIL-1 histone H3S10 kinase enhance position-effect variegation at pericentric sites in Drosophila heterochromatin. Genetics 176: 1355–1358.
42. EbertA, SchottaG, LeinS, KubicekS, KraussV, et al. (2004) Su(var) genes regulate the balance between euchromatin and heterochromatin in Drosophila. Genes Dev 18: 2973–2983.
43. LerachS, ZhangW, BaoX, DengH, GirtonJ, et al. (2006) Loss-of-function alleles of the JIL-1 kinase are strong suppressors of position effect variegation of the wm4 allele in Drosophila. Genetics 173: 2403–2406.
44. ZhangW, DengH, BaoX, LerachS, GirtonJ, et al. (2006) The JIL-1 histone H3S10 kinase regulates dimethyl H3K9 modifications and heterochromatic spreading in Drosophila. Development 133: 229–235.
45. RegnardC, StraubT, MitterwegerA, DahlsveenIK, FabianV, et al. (2011) Global analysis of the relationship between JIL-1 kinase and transcription. PLoS Genet 7: e1001327 doi:10.1371/journal.pgen.1001327.
46. DengH, BaoX, ZhangW, GirtonJ, JohansenJ, et al. (2007) Reduced levels of Su(var)3-9 but not Su(var)2-5 (HP1) counteract the effects on chromatin structure and viability in loss-of-function mutants of the JIL-1 histone H3S10 kinase. Genetics 177: 79–87.
47. CrydermanDE, GradeSK, LiY, FantiL, PimpinelliS, et al. (2005) Role of Drosophila HP1 in euchromatic gene expression. Dev Dyn 232: 767–774.
48. de WitE, GreilF, van SteenselB (2007) High-resolution mapping reveals links of HP1 with active and inactive chromatin components. PLoS Genet 3: e38 doi:10.1371/journal.pgen.0030038.
49. LiuLP, NiJQ, ShiYD, OakeleyEJ, SunFL (2005) Sex-specific role of Drosophila melanogaster HP1 in regulating chromatin structure and gene transcription. Nat Genet 37: 1361–1366.
50. LuBY, EmtagePC, DuyfBJ, HillikerAJ, EissenbergJC (2000) Heterochromatin protein 1 is required for the normal expression of two heterochromatin genes in Drosophila. Genetics 155: 699–708.
51. YasuharaJC, WakimotoBT (2008) Molecular landscape of modified histones in Drosophila heterochromatic genes and euchromatin-heterochromatin transition zones. PLoS Genet 4: e16 doi:10.1371/journal.pgen.0040016.
52. CrydermanDE, VitaliniMW, WallrathLL (2011) Heterochromatin protein 1a is required for an open chromatin structure. Transcription 2: 95–99.
53. LinCH, LiB, SwansonS, ZhangY, FlorensL, et al. (2008) Heterochromatin protein 1a stimulates histone H3 lysine 36 demethylation by the Drosophila KDM4A demethylase. Mol Cell 32: 696–706.
54. KimT, BuratowskiS (2007) Two Saccharomyces cerevisiae JmjC domain proteins demethylate histone H3 Lys36 in transcribed regions to promote elongation. J Biol Chem 282: 20827–20835.
55. LarssonJ, SvenssonMJ, StenbergP, MakitaloM (2004) Painting of fourth in genus Drosophila suggests autosome-specific gene regulation. Proc Natl Acad Sci U S A 101: 9728–9733.
56. GreilF, van der KraanI, DelrowJ, SmothersJF, de WitE, et al. (2003) Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17: 2825–2838.
57. SchottaG, ReuterG (2000) Controlled expression of tagged proteins in Drosophila using a new modular P-element vector system. Mol Gen Genet 262: 916–920.
58. FritschL, RobinP, MathieuJR, SouidiM, HinauxH, et al. (2010) A subset of the histone H3 lysine 9 methyltransferases Suv39h1, G9a, GLP, and SETDB1 participate in a multimeric complex. Mol Cell 37: 46–56.
59. WangSH, ElginSC (2011) Drosophila Piwi functions downstream of piRNA production mediating a chromatin-based transposon silencing mechanism in female germ line. Proc Natl Acad Sci U S A
60. ZampariniAL, DavisMY, MaloneCD, VieiraE, ZavadilJ, et al. (2011) Vreteno, a gonad-specific protein, is essential for germline development and primary piRNA biogenesis in Drosophila. Development 138: 4039–4050.
61. ShafferCD, WullerJM, ElginSC (1994) Raising large quantities of Drosophila for biochemical experiments. Methods Cell Biol 44: 99–108.
62. EissenbergJC, MorrisGD, ReuterG, HartnettT (1992) The heterochromatin-associated protein HP-1 is an essential protein in Drosophila with dosage-dependent effects on position-effect variegation. Genetics 131: 345–352.
63. EgelhoferTA, MinodaA, KlugmanS, LeeK, Kolasinska-ZwierzP, et al. (2011) An assessment of histone-modification antibody quality. Nat Struct Mol Biol 18: 91–93.
64. CherbasL, WillinghamA, ZhangD, YangL, ZouY, et al. (2011) The transcriptional diversity of 25 Drosophila cell lines. Genome Res 21: 301–314.
65. MartinD, BrunC, RemyE, MourenP, ThieffryD, et al. (2004) GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol 5: R101.
66. JiH, JiangH, MaW, JohnsonDS, MyersRM, et al. (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 26: 1293–1300.
67. TrapnellC, WilliamsBA, PerteaG, MortazaviA, KwanG, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511–515.
68. HardcastleTJ, KellyKA (2010) baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 11: 422.
69. RobinsonMD, McCarthyDJ, SmythGK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139–140.
70. AndersS, HuberW (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106.
71. PengS, AlekseyenkoAA, LarschanE, KurodaMI, ParkPJ (2007) Normalization and experimental design for ChIP-chip data. BMC Bioinformatics 8: 219.
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2012 Číslo 9
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
Najčítanejšie v tomto čísle
- Enrichment of HP1a on Drosophila Chromosome 4 Genes Creates an Alternate Chromatin Structure Critical for Regulation in this Heterochromatic Domain
- Normal DNA Methylation Dynamics in DICER1-Deficient Mouse Embryonic Stem Cells
- The NDR Kinase Scaffold HYM1/MO25 Is Essential for MAK2 MAP Kinase Signaling in
- Functional Variants in and Involved in Activation of the NF-κB Pathway Are Associated with Rheumatoid Arthritis in Japanese