Organization and evolution of a novel cervid satellite DNA with yeast CDEI-like repeats

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• 作者：Lei-Jiau Hsieh ; Ya-Ming Cheng ; Yi-Chun Wang ; Chyi-Chyang Lin…
• 关键词：Indian muntjac ; Centromeric satellite DNA ; Ancient centromeric DNA ; Concerted evolution ; CDEI element ; Chromosome microdissection
• 刊名：Zoological Studies
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：53
• 期：1
• 全文大小：2,607 KB
• 参考文献：1. Alexandrov, IA, Medvedev, LI, Mashkova, TD, Kisselev, LL, Romanova, LY, Yurov, YB (1993) Definition of a new alpha satellite suprachromosomal family characterized by monomeric organization. Nucleic Acids Res 21: pp. 2209-2215 CrossRef
  2. Alexandrov, I, Kazakov, A, Tumeneva, I, Shepelev, V, Yurov, Y (2001) Alpha-satellite DNA of primates: old and new families. Chromosoma 110: pp. 253-266 CrossRef
  3. Bayes, JJ, Malik, HS (2008) The evolution of centromeric DNA sequences. Encyclopedia of Life Sciences, John Wiley & Sons, Ltd, Chichester
  4. Benson, G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27: pp. 573-580 CrossRef
  5. Brinkley, BR, Valdivia, MM, Tousson, A, Brenner, SL (1984) Compound kinetochores of the Indian muntjac: evolution by linear fusion of unit kinetochores. Chromosoma 91: pp. 1-11 CrossRef
  6. Buntjer, JB, Nijman, IJ, Zijlstra, C, Lenstra, JA (1998) A satellite DNA element specific for roe deer (Capreolus capreolus). Chromosoma 107: pp. 1-5 CrossRef
  7. Chiang, PY, Lin, CC, Liao, SJ, Hsieh, LJ, Li, SY, Chao, MC, Li, YC (2004) Genetic analysis for two subspecies of the Reeve’s mantjac (Cervidae: Muntiacus reevesi) by karyotyping and satellite DNA analyses. Zool Stud 43: pp. 9
  8. Chou, SH, Chin, KH (2001) Quadruple intercalated G-6 stack: a possible motif in the fold-back structure of the Drosophila centromeric dodeca-satellite?. J Mol Biol 314: pp. 139-152 CrossRef
  9. Chou, SH, Zhu, L, Reid, BR (1994) The unusual structure of the human centromere (GGA)2 motif: unpaired guanosine residues stacked between sheared G.A pairs. J Mol Biol 244: pp. 259-268 CrossRef
  10. Crooks, GE, Hon, G, Chandonia, JM, Brenner, SE (2004) WebLogo: a sequence logo generator. Genome Res 14: pp. 1188-1190 CrossRef
  11. Ferrer, N, Azorin, F, Villasante, A, Gutierrez, C, Abad, JP (1995) Centromeric dodeca-satellite DNA sequences form fold-back structures. J Mol Biol 245: pp. 8-21 CrossRef
  12. Fronicke, L, Chowdhary, BP, Scherthan, H (1997) Segmental homology among cattle (Bos taurus), Indian muntjac (Muntiacus muntjak vaginalis), and Chinese muntjac (M. reevesi) karyotypes. Cytogenet Cell Genet 77: pp. 223-227
  13. Fry, K, Salser, W (1977) Nucleotide sequences of HS-alpha satellite DNA from kangaroo rat Dipodomys ordii and characterization of similar sequences in other rodents. Cell 12: pp. 1069-1084 CrossRef
  14. Goldberg, IG, Sawhney, H, Pluta, AF, Warburton, PE, Earnshaw, WC (1996) Surprising deficiency of CENP-B binding sites in African green monkey alpha-satellite DNA: implications for CENP-B function at centromeres. Mol Cell Biol 16: pp. 5156-5168
  15. Haaf, T, Ward, DC (1994) Structural analysis of alpha-satellite DNA and centromere proteins using extended chromatin and chromosomes. Hum Mol Genet 3: pp. 697-709 CrossRef
  16. Hernandez Fernandez, M, Vrba, ES (2005) A complete estimate of the phylogenetic relationships in Ruminantia: a dated species-level supertree of the extant ruminants. Biol Rev Camb Philos Soc 80: pp. 269-302 CrossRef
  17. Horvath, JE, Viggiano, L, Loftus, BJ, Adams, MD, Archidiacono, N, Rocchi, M, Eichler, EE (2000) Molecular structure and evolution of an alpha satellite/non-alpha satellite junction at 16p11. Hum Mol Genet 9: pp. 113-123 CrossRef
  18. Jurka, J (2008) LINE1 repeats from dolphin. Repbase Reports 8: pp. 1
  19. Lee, C, Ritchie, DB, Lin, CC (1994) A tande
• 刊物主题：Zoology;
• 出版者：Springer Berlin Heidelberg
• ISSN：1810-522X

文摘

Background It has been proposed that pericentromeric satellite DNA arises from the progressive proximal expansion of ancient centromeric DNA. In an attempt to recover putative ancestral centromeric DNA, we microdissected the pericentromeric/centromeric DNA from the chromosome X-- of Indian muntjac (Muntiacus muntjak vaginalis) and constructed a microclone-library of the X-- centromeric DNA. Results A new cervid satellite DNA element, designated as satellite VI, was isolated from this library. Fluorescence in situ hybridization (FISH) studies revealed that satellite VI is predominately located on the distal pericentromeric region of the Indian muntjac chromosome X-- and on the pericentromeres of several Old World deer species studied. Its sequence is organized as 11-bp monomeric (ATCACGTGGGA) tandem repeats. Further sequencing on a BAC clone of Indian muntjac harboring this repeat showed that an array of this repeat stretches over approximately 5?kb followed by approximately 3?kb of interspersed repetitive sequences, such as long interspersed elements (LINEs), short interspersed elements (SINEs), and long terminal repeats (LTRs). Conclusions Based on the chromosomal localization, genomic and sequence organization, and copy numbers of satellite VI in deer species studied, we postulate that this newly found satellite DNA could be a putative ancient cervidic centromeric DNA that is still preserved in some Old World deer. Interestingly, the first eight nucleotides of the 11-bp monomeric consensus sequences are highly conserved and identical to the CDEI element in the centromere of the budding yeast Saccharomyces cerevisiae. The centromeric/pericentromeric satellite DNA harboring abundant copies of CDEI sequences is the first found in a mammalian species. Several zipper-like d (GGGA)2 motifs were also found in the (ATCACGTGGGA)n repeat of satellite VI DNA. Whether the satellite VI is structurally and functionally correlated with the CDEI of centromere of budding yeast and whether a zipper-like structure forms in satellite VI require further studies.