Chromosoma

, Volume 126, Issue 6, pp 753–768 | Cite as

Unique sequence organization and small RNA expression of a “selfish” B chromosome

  • Yue Li
  • Xueyuan A. Jing
  • John C. Aldrich
  • C. Clifford
  • Jian Chen
  • Omar S. Akbari
  • Patrick M. Ferree
Original Article

Abstract

B chromosomes are found in numerous plants and animals. These nonessential, supernumerary chromosomes are often composed primarily of noncoding DNA repeats similar to those found within transcriptionally “silenced” heterochromatin. In order to persist within their resident genomes, many B chromosomes exhibit exceptional cellular behaviors, including asymmetric segregation into gametes and induction of genome elimination during early development. An important goal in understanding these behaviors is to identify unique B chromosome sequences and characterize their transcriptional contributions. We investigated these properties by examining a paternally transmitted B chromosome known as paternal sex ratio (PSR), which is present in natural populations of the jewel wasp Nasonia vitripennis. To facilitate its own transmission, PSR severely biases the sex ratio by disrupting early chromatin remodeling processes. Through cytological mapping and other approaches, we identified multiple DNA repeats unique to PSR, as well as those found on the A chromosomes, suggesting that PSR arose through a merger of sequences from both within and outside the N. vitripennis genome. The majority of PSR-specific repeats are interspersed among each other across PSR’s long arm, in contrast with the distinct “blocks” observed in other organisms’ heterochromatin. Through transcriptional profiling, we identified a subset of repeat-associated, small RNAs expressed by PSR, most of which map to a single PSR-specific repeat. These RNAs are expressed at much higher levels than those arising from A chromosome-linked repeats, suggesting that in addition to its sequence organization, PSR’s transcriptional properties differ substantially from the pericentromeric regions of the normal chromosomes.

Keywords

B chromosomes Small RNAs Noncoding DNA repeats Satellite DNA Nasonia vitripennis Testis Spermatogenesis 

Supplementary material

412_2017_641_Fig6_ESM.gif (86 kb)
Fig. S1

The PSR chromosome contains abundant copies of repeats that are also present on the A chromosomes. DNA FISH shows that NV79 and NV126 (both in red) are present on a single A chromosome that uniquely contains PSR104 (green). (GIF 85 kb)

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High Resolution Image (TIFF 591 kb)
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Fig. S2

DNA FISH shows that PSR harbors repeats (PSR4656 and PSR8495) that generate polyadenylated transcripts. These repeats co-localize across PSR’s long arm, and are not detectable on the A chromosomes using this method. (GIF 65 kb)

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High Resolution Image (TIFF 497 kb)
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Fig. S3

PSR-specific repeats generate small RNAs at levels much higher than those expressed by repeats in the PSR(−) genome. Levels of small RNAs from A chromosome repeats and PSR-specific repeats are shown in grey and red, respectively. The Y axis portrays the total amount of small RNA traces per repeat in the testis. (GIF 15 kb)

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High Resolution Image (TIFF 219 kb)
412_2017_641_Fig9_ESM.gif (356 kb)
Fig. S4

Depiction of small RNAs deriving from PSR105. (A) Alignment of small RNAs corresponding to PSR105 (red text). (B) The canonical PSR105 repeat is shown, with the sequence of the corresponding small RNAs (highlighted in red text). The two highly conserved palindromic regions of this repeat are underlined. (C) A long RNA precursor for the PSR105-matching small RNAs is shown, with the region generating the small RNAs highlighted in red, and the complementary region shown in black underline. This RNA is predicted to form an imperfect hairpin (below arrow). The region matching to the small RNAs is marked by a red line. (GIF 356 kb)

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High Resolution Image (TIFF 2202 kb)
412_2017_641_Fig10_ESM.gif (299 kb)
Fig. S5

Depiction of small RNAs deriving from PSR2. (A) Alignment of small RNAs corresponding to PSR2 (red text). These RNAs form two distinct ‘clusters.’ (B) The canonical PSR2 repeat is shown, with the sequences of the corresponding small RNAs (highlighted in green text and underlined in blue). The two highly conserved palindromic regions of this repeat are underlined). (C) Two long RNA precursors for the PSR2-matching small RNAs are shown, with the region generating each cluster of small RNAs heighted in green and blue, respectively. Each of these RNAs is predicted to form hairpin structures (shown below each arrow). The regions matching to the small RNAs are marked by either a green or a blue line. (GIF 299 kb)

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High Resolution Image (TIFF 1511 kb)
412_2017_641_Fig11_ESM.gif (434 kb)
Fig. S6

Control conditions for RNA FISH of the 4317 transcript. Top row depicts PSR4317 probe hybridization to PSR(−) testes, resulting in no signal. Similarly, no signal results from hybridization of this same probe to PSR(+) testes pre-treated with RNase A (bottom row). Only the PSR(+) untreated testes show punctate hybridization signals with this probe. (GIF 434 kb)

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High Resolution Image (TIFF 3490 kb)
412_2017_641_Fig12_ESM.gif (90 kb)
Fig. S7

Large nuclei in the N. vitripennis testis are polyploid. (A) The large nuclei show multiple, distinct foci of PSR22, in addition to rDNA located at a single locus on an A chromosome. Nuclei of cyst cells following S-phase (B) and mature sperm (C) have exactly two foci and one focus, respectively, of PSR22 and rDNA. (GIF 89 kb)

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High Resolution Image (TIFF 649 kb)
412_2017_641_MOESM8_ESM.xlsx (11 kb)
Table S1Identification of a new PSR-specific transcript from unfiltered total RNA (XLSX 11 kb)
412_2017_641_MOESM9_ESM.xlsx (104 kb)
Table S2miRNAs, siRNAs, and rasi−/putative piRNAs identified from N. vitripennis testis and carcass (somatic tissues) of PSR(−) and PSR(+) males. Each of these small RNA classes is shown in a separate tab. (XLSX 103 kb)
412_2017_641_MOESM10_ESM.xlsx (159 kb)
Table S3Additional information for N. vitripennis miRNAs and piRNAs. (XLSX 159 kb)
412_2017_641_MOESM11_ESM.xlsx (73 kb)
Table S4Small RNAs that are exclusive to the PSR(+) genotype. (XLSX 72 kb)
412_2017_641_MOESM12_ESM.xlsx (47 kb)
Table S5Putative precursor RNAs for small RNAs derived from PSR repeats PSR2, PSR22, and PSR105. (XLSX 47 kb)
412_2017_641_MOESM13_ESM.xlsx (89 kb)
Table S6Oligonucleotides used for DNA FISH (XLSX 89 kb)
412_2017_641_MOESM14_ESM.xlsx (113 kb)
Table S7Oligonucleotides used for PCR (XLSX 112 kb)

References

  1. Akbari OS, Antoshechkin I, Hay BA, Ferree PM (2013) Transcriptome profiling of Nasonia vitripennis testis reveals novel transcripts expressed from the selfish B chromosome, paternal sex ratio. G3 (Bethesda) 3:1597–1605CrossRefGoogle Scholar
  2. Aldrich JC, Leibholz A, Cheema MS, Ausio J, Ferree PM (2017) A ‘selfish’ B chromosome induces genome elimination by disrupting the histone code in the jewel wasp Nasonia vitripennis. Sci Rep-Uk. 7Google Scholar
  3. Beukeboom LW, Werren JH (1993) Deletion analysis of the selfish B-chromosome, paternal sex-ratio (Psr), in the parasitic wasp Nasonia-vitripennis. Genetics 133:637–648PubMedPubMedCentralGoogle Scholar
  4. Bonaccorsi S, Lohe A (1991) Fine mapping of satellite DNA sequences along the Y chromosome of Drosophila melanogaster: relationships between satellite sequences and fertility factors. Genetics 129:177–189PubMedPubMedCentralGoogle Scholar
  5. Camacho JPM, Sharbel TF, Beukeboom LW (2000) B-chromosome evolution. Philos T Roy Soc B 355:163–178CrossRefGoogle Scholar
  6. Carchilan M, Delgado M, Ribeiro T, Costa-Nunes P, Caperta A, Morais-Cecilio L, Jones RN, Viegas W, Houben A (2007) Transcriptionally active heterochromatin in rye B chromosomes. Plant Cell 19:1738–1749CrossRefPubMedPubMedCentralGoogle Scholar
  7. Carchilan M, Kumke K, Mikolajewski S, Houben A (2009) Rye B chromosomes are weakly transcribed and might alter the transcriptional activity of A chromosome sequences. Chromosoma 118:607–616CrossRefPubMedGoogle Scholar
  8. Czech B, Hannon GJ (2016) One loop to rule them all: the ping-pong cycle and piRNA-guided silencing. Trends Biochem Sci 41:324–337CrossRefPubMedPubMedCentralGoogle Scholar
  9. Dej KJ, Spradling AC (1999) The endocycle controls nurse cell polytene chromosome structure during Drosophila oogenesis. Development 126:293–303PubMedGoogle Scholar
  10. Eickbush DG, Eickbush TH, Werren JH (1992) Molecular characterization of repetitive DNA-sequences from a B-chromosome. Chromosoma 101:575–583CrossRefPubMedGoogle Scholar
  11. Femino AM, Fay FS, Fogarty K, Singer RH (1998) Visualization of single RNA transcripts in situ. Science 280:585–590CrossRefPubMedGoogle Scholar
  12. Ferree PM, Fang C, Mastrodimos M, Hay BA, Amrhein H, Akbari OS (2015) Identification of genes uniquely expressed in the germ-line tissues of the Jewel wasp Nasonia vitripennis. G3-Genes Genom Genet 5:2647–2653Google Scholar
  13. Ferree PM, Gomez K, Rominger P, Howard D, Kornfeld H, Barbash DA (2014) Heterochromatin position effects on circularized sex chromosomes cause filicidal embryonic lethality in Drosophila melanogaster. Genetics 196:1001–1005CrossRefPubMedPubMedCentralGoogle Scholar
  14. Ferree PM, Prasad S (2012) How can satellite DNA divergence cause reproductive isolation? Let us count the chromosomal ways. Genetics Research International 2012:430136CrossRefPubMedPubMedCentralGoogle Scholar
  15. Hewitt GM (1976) Meiotic drive for B-chromosomes in primary oocytes of Myrmeleotettix-maculatus (Orthoptera-Acrididae). Chromosoma 56:381–391CrossRefPubMedGoogle Scholar
  16. Holoch D, Moazed D (2015) RNA-mediated epigenetic regulation of gene expression. Nat Rev Genet 16:71–84CrossRefPubMedPubMedCentralGoogle Scholar
  17. Huang, W., Y. Du, X. Zhao, and W.W. Jin. 2016. B chromosome contains active genes and impacts the transcription of A chromosomes in maize (Zea mays L.). Bmc Plant Biol. 16Google Scholar
  18. Jones RN (1991) B-chromosome drive. Am Nat 137:430–442CrossRefGoogle Scholar
  19. Jones RN, Viegas W, Houben A (2008) A century of B chromosomes in plants: so what? Ann Bot-London 101:767–775CrossRefGoogle Scholar
  20. Kim VN, Han J, Siomi MC (2009) Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10:126–139CrossRefPubMedGoogle Scholar
  21. Klemme S, Banaei-Moghaddam AM, Macas J, Wicker T, Novak P, Houben A (2013) High-copy sequences reveal distinct evolution of the rye B chromosome. New Phytol 199:550–558CrossRefPubMedGoogle Scholar
  22. Ku HY, Lin HF (2014) PIWI proteins and their interactors in piRNA biogenesis, germline development and gene expression. Natl Sci Rev 1:205–218CrossRefPubMedPubMedCentralGoogle Scholar
  23. Larracuente, A.M., and P.M. Ferree. 2015. Simple method for fluorescence DNA in situ hybridization to squashed chromosomes. Jove-J Vis Exp.Google Scholar
  24. Lohe AR, Hilliker AJ, Roberts PA (1993) Mapping simple repeated DNA sequences in heterochromatin of Drosophila melanogaster. Genetics 134:1149–1174PubMedPubMedCentralGoogle Scholar
  25. Martis MM, Klemme S, Banaei-Moghaddam AM, Blattner FR, Macas J, Schmutzer T, Scholz U, Gundlach H, Wicker T, Simkova H, Novak P, Neumann P, Kubalakova M, Bauer E, Haseneyer G, Fuchs J, Dolezel J, Stein N, Mayer KFX, Houben A (2012) Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences. Proc Natl Acad Sci U S A 109:13343–13346CrossRefPubMedPubMedCentralGoogle Scholar
  26. McAllister BF (1995) Isolation and characterization of a retroelement from B chromosome (PSR) in the parasitic wasp Nasonia vitripennis. Insect Mol Biol 4:253–262CrossRefPubMedGoogle Scholar
  27. McAllister BF, Beukeboom LW, Werren JH (2004) Mapping of paternal-sex-ratio deletion chromosomes localizes multiple regions involved in expression and transmission. Heredity 92:5–13CrossRefPubMedGoogle Scholar
  28. McAllister BF, Werren JH (1997) Hybrid origin of a B chromosome (PSR) in the parasitic wasp Nasonia vitripennis. Chromosoma 106:243–253CrossRefPubMedGoogle Scholar
  29. Menon DU, Meller VH (2012) A role for siRNA in X-chromosome dosage compensation in Drosophila melanogaster. Genetics 191:1023–U1623CrossRefPubMedPubMedCentralGoogle Scholar
  30. Moazed D (2009) Small RNAs in transcriptional gene silencing and genome defence. Nature 457:413–420CrossRefPubMedPubMedCentralGoogle Scholar
  31. Munoz-Pajares A, Martinez-Rodriguez L, Teruel M, Cabrero J, Camacho JPM, Perfectti F (2011) A single, recent origin of the accessory B chromosome of the grasshopper Eyprepocnemis plorans. Genetics 187:853–863CrossRefPubMedPubMedCentralGoogle Scholar
  32. Navarro-Dominguez B, Ruiz-Ruano FJ, Cabrero J, Corral JM, Lopez-Leon MD, Sharbel TF, Camacho JPM (2017) Protein-coding genes in B chromosomes of the grasshopper Eyprepocnemis plorans. Sci Rep-Uk 7Google Scholar
  33. Nur U, Werren JH, Eickbush DG, Burke WD, Eickbush TH (1988) A “selfish” B chromosome that enhances its transmission by eliminating the paternal genome. Science 240:512–514CrossRefPubMedGoogle Scholar
  34. Page BT, Wanous MK, Birchler JA (2001) Characterization of a maize chromosome 4 centromeric sequence: evidence for an evolutionary relationship with the B chromosome centromere. Genetics 159:291–302PubMedPubMedCentralGoogle Scholar
  35. Pal-Bhadra M, Leibovitch BA, Gandhi SG, Rao M, Bhadra U, Birchler JA, Elgin SCR (2004) Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science 303:669–672CrossRefPubMedGoogle Scholar
  36. Palestis BG, Trivers R, Burt A, Jones RN (2004) The distribution of B chromosomes across species. Cytogenet Genome Res 106:151–158CrossRefPubMedGoogle Scholar
  37. Perfectti F, Werren JH (2001) The interspecific origin of B chromosomes: experimental evidence. Evolution 55:1069–1073CrossRefPubMedGoogle Scholar
  38. Perrot-Minnot MJ, Werren JH (2001) Meiotic and mitotic instability of two EMS-produced centric fragments in the haplodiploid wasp Nasonia vitripennis. Heredity 87:8–16CrossRefPubMedGoogle Scholar
  39. Reed KM (1993) Cytogenetic analysis of the paternal sex-ratio chromosome of Nasonia-vitripennis. Genome 36:157–161CrossRefPubMedGoogle Scholar
  40. Rosic S, Kohler F, Erhardt S (2014) Repetitive centromeric satellite RNA is essential for kinetochore formation and cell division (vol 207, pg 335, 2014). J Cell Biol 207:673–673CrossRefPubMedCentralGoogle Scholar
  41. Schulz MH, Zerbino DR, Vingron M, Birney E (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28:1086–1092CrossRefPubMedPubMedCentralGoogle Scholar
  42. Silva DMZD, Pansonato-Alves JC, Utsunomia R, Araya-Jaime C, Ruiz-Ruano FJ, Daniel SN, Hashimoto DT, Oliveira C, Camacho JPM, Porto-Foresti F, Foresti F (2014) Delimiting the origin of a B chromosome by FISH mapping, chromosome painting and DNA sequence analysis in Astyanax paranae (Teleostei, Characiformes). PLoS One 9Google Scholar
  43. Swim MM, Kaeding KE, Ferree PM (2012) Impact of a selfish B chromosome on chromatin dynamics and nuclear organization in Nasonia. J Cell Sci 125:5241–5249CrossRefPubMedGoogle Scholar
  44. Ugarkovic D (2005) Functional elements residing within satellite DNAs. EMBO Rep 6:1035–1039CrossRefPubMedPubMedCentralGoogle Scholar
  45. Usakin L, Abad J, Vagin VV, de Pablos B, Villasante A, Gvozdev VA (2007) Transcription of the 1.688 satellite DNA family is under the control of RNA interference machinery in Drosophila melanogaster ovaries. Genetics 176:1343–1349CrossRefPubMedPubMedCentralGoogle Scholar
  46. Valente GT, Conte MA, Fantinatti BEA, Cabral-de-Mello DC, Carvalho RF, Vicari MR, Kocher TD, Martins C (2014) Origin and evolution of B chromosomes in the cichlid fish Astatotilapia latifasciata based on integrated genomic analyses. Mol Biol Evol 31:2061–2072CrossRefPubMedGoogle Scholar
  47. Van Vugt JJFA, de Jong H, Stouthamer R (2009) The origin of a selfish B chromosome triggering paternal sex ratio in the parasitoid wasp Trichogramma kaykai. P R Soc B 276:4149–4154CrossRefGoogle Scholar
  48. van Vugt JJFA, de Nooijer S, Stouthamer R, de Jong H (2005) NOR activity and repeat sequences of the paternal sex ratio chromosome of the parasitoid wasp Trichogramma kaykai. Chromosoma 114:410–419CrossRefPubMedGoogle Scholar
  49. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SIS, Martienssen RA (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297:1833–1837CrossRefPubMedGoogle Scholar
  50. Werren JH (2011) Selfish genetic elements, genetic conflict, and evolutionary innovation. Proc Natl Acad Sci U S A 108(Suppl 2):10863–10870CrossRefPubMedPubMedCentralGoogle Scholar
  51. Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK (2010) Functional and evolutionary insights from the genomes of three parasitoid Nasonia species (vol 327, pg 343, 2010). Science 327:1577–1577CrossRefGoogle Scholar
  52. Werren JH, Stouthamer R (2003) PSR (paternal sex ratio) chromosomes: the ultimate selfish genetic elements. Genetica 117:85–101CrossRefPubMedGoogle Scholar
  53. Whiting PW (1968) The chromosomes of Mormoniella. The Journal of Heredity 59:19–22CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany 2017
Corrected publication August/2017

Authors and Affiliations

  • Yue Li
    • 1
  • Xueyuan A. Jing
    • 2
  • John C. Aldrich
    • 2
  • C. Clifford
    • 2
  • Jian Chen
    • 1
  • Omar S. Akbari
    • 3
  • Patrick M. Ferree
    • 2
  1. 1.Key Laboratory of Stem Cell Biology Institute of Health Sciences, Shanghai Institute for Biological ScienceChinese Academy of Sciences and Shanghai Jiao-Tong University School of MedicineShanghaiChina
  2. 2.W. M. Keck Science DepartmentClaremont McKenna, Pitzer, and Scripps CollegesClaremontUSA
  3. 3.Department of Entomology and Riverside Center for Disease Vector Research, Institute for Integrative Genome BiologyUniversity of California, RiversideRiversideUSA

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