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Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features

Seki, Ryohei, Li, Cai, Fang, Qi, Hayashi, Shinichi, Egawa, Shiro, Hu, Jiang, Xu, Luohao, Pan, Hailin, Kondo, Mao, Sato, Tomohiko, Matsubara, Haruka, Kamiyama, Namiko, Kitajima, Keiichi, Saito, Daisuke, Liu, Yang, Gilbert, M. Thomas P., Zhou, Qi, Xu, Xing, Shiroishi, Toshihiko, Irie, Naoki, Tamura, Koji, Zhang, Guojie·2017·Nature Communications
DOI 10.1038/ncomms14229PMC PMC5473641
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Abstract

Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One of these magnificent examples is the transition from non-avian dinosaurs to birds that has created numerous evolutionary innovations such as self-powered flight and its associated wings with flight feathers. By analysing 48 bird genomes, we identified millions of avian-specific highly conserved elements (ASHCEs) that predominantly (>99%) reside in non-coding regions. Many ASHCEs show differential histone modifications that may participate in regulation of limb development. Comparative embryonic gene expression analyses across tetrapod species suggest ASHCE-associated genes have unique roles in developing avian limbs. In particular, we demonstrate how the ASHCE driven avian-specific expression of gene Sim1 driven by ASHCE may be associated with the evolution and development of flight feathers. Together, these findings demonstrate regulatory roles of ASHCEs in the creation of avian-specific traits, and further highlight the importance of cis -regulatory rewiring during macroevolutionary changes.

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  • The emergence of lineage-specific elements has been proposed as a key driver of morphological diversification during vertebrate evolution.

    “The emergence of lineage-specific elements has been proposed as a key driver of morphological diversification during vertebrate evolution.29,36,37,38”

    From A genomic compendium of hundreds of teleost fishes reveals their evolutionary landscape (2026) · cites this paper as [29]

  • Studies in mammals and birds have shown that highly conserved elements are enriched for transcriptional regulation and organ development pathways.

    “studies in both mammals and birds have shown that highly conserved elements are enriched for transcriptional regulation and organ development pathways.9,29”

    From A genomic compendium of hundreds of teleost fishes reveals their evolutionary landscape (2026) · cites this paper as [29]

  • Conserved elements play pivotal roles in shaping specific traits, often being under strong evolutionary constraint and involved in crucial regulatory functions.

    “Previous studies have indicated that conserved elements play pivotal roles in shaping specific traits, often being under strong evolutionary constraint and involved in crucial regulatory functions.28,29”

    From A genomic compendium of hundreds of teleost fishes reveals their evolutionary landscape (2026) · cites this paper as [29]

  • Evolutionary rates on microchromosomes and sex chromosomes differ from those on autosomes in vertebrates.

    “Previous studies have shown that the evolutionary rates on microchromosomes and sex chromosomes differ from those on autosomes in vertebrates.29,30”

    From A genomic compendium of hundreds of teleost fishes reveals their evolutionary landscape (2026) · cites this paper as [29]

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Research works printed but not linked: 62

  1. Sereno, P. Birds as dinosaurs. Acta Zool. Sinica 50, 991–1001 (2004).
  2. Dyke, G. & Kaiser, G. W. Living Dinosaurs: The Evolutionary History of Modern Birds Wiley-Blackwell (2011). · DOI
  3. O'Connor, P. M. & Claessens, L. P. Basic avian pulmonary design and flow-through ventilation in non-avian theropod dinosaurs. Nature 436, 253–256 (2005). · DOI
  4. Zhang, G. et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346, 1311–1320 (2014). · DOI · Paper page
  5. Jarvis, E. D. et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320–1331 (2014). · DOI · Paper page
  6. King, M. C. & Wilson, A. C. Evolution at two levels in humans and chimpanzees. Science 188, 107–116 (1975). · DOI · Paper page
  7. Wong, G. K. et al. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 432, 717–722 (2004). · DOI
  8. Mattick, J. S. RNA regulation: a new genetics? Nat. Rev. Genet. 5, 316–323 (2004). · DOI · Paper page
  9. Masui, S. et al. Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells. Nat. Cell Biol. 9, 625–635 (2007). · DOI
  10. Zhou, V. W., Goren, A. & Bernstein, B. E. Charting histone modifications and the functional organization of mammalian genomes. Nat. Rev. Genet. 12, 7–18 (2011). · DOI · Paper page
  11. Cotney, J. et al. The evolution of lineage-specific regulatory activities in the human embryonic limb. Cell 154, 185–196 (2013). · DOI
  12. Hamburger, V. & Hamilton, H. L. A series of normal stages in the development of the chick embryo. J. Morphol. 88, 49–92 (1951). · DOI
  13. Ernst, J. & Kellis, M. ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods 9, 215–216 (2012). · DOI
  14. Creyghton, M. P. et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl Acad. Sci. USA 107, 21931–21936 (2010). · DOI · Paper page
  15. Mahoney, Z. X. et al. Discs-large homolog 1 regulates smooth muscle orientation in the mouse ureter. Proc. Natl Acad. Sci. USA 103, 19872–19877 (2006). · DOI
  16. Wang, Z. et al. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat. Genet. 45, 701–706 (2013). · DOI
  17. Irie, N. & Kuratani, S. Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis. Nat. Commun. 2, 248 (2011). · DOI
  18. Fastovsky, D. & Weishampel, D. The Evolution and Extinction of the Dinosaurs Cambridge University Press (2005).
  19. Seki, R. et al. Evolutionary and developmental aspects of avian-specific traits in limb skeletal pattern. Zoolog. Sci. 29, 631–644 (2012). · DOI
  20. Tamura, K., Nomura, N., Seki, R., Yonei-Tamura, S. & Yokoyama, H. Embryological evidence identifies wing digits in birds as digits 1, 2, and 3. Science 331, 753–757 (2011). · DOI
  21. Kardong, K. V. Vertebrates: Comparative Anatomy, Function, Evolution McGraw-Hill (2006).
  22. Lee, S.-i., Kim, J., Park, H., Jabłoński, P. G. & Choi, H. The function of the alula in avian flight. Sci. Rep. 5, 9914 (2015). · DOI
  23. Peters, H., Neubuser, A., Kratochwil, K. & Balling, R. Pax9-deficient mice lack pharyngeal pouch derivatives and teeth and exhibit craniofacial and limb abnormalities. Genes Dev. 12, 2735–2747 (1998). · DOI
  24. Kist, R., Greally, E. & Peters, H. Derivation of a mouse model for conditional inactivation of Pax9. Genesis. 45, 460–464 (2007). · DOI
  25. Coumailleau, P. & Duprez, D. Sim1 and Sim2 expression during chick and mouse limb development. Int. J. Dev. Biol. 53, 149–157 (2009). · DOI
  26. Nohno, T. et al. Involvement of the Sonic hedgehog gene in chick feather formation. Biochem. Biophys. Res. Commun. 206, 33–39 (1995). · DOI
  27. Patel, K., Makarenkova, H. & Jung, H. S. The role of long range, local and direct signalling molecules during chick feather bud development involving the BMPs, follistatin and the Eph receptor tyrosine kinase Eph-A4. Mech. Dev. 86, 51–62 (1999). · DOI
  28. Domyan, E. T. et al. Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species. Elife 5, e12115 (2016). · DOI
  29. Zhou, Z.-H., Wang, X.-L., Zhang, F.-C. & Xu, X. Important features of Caudipteryx-evidence from two nearly complete new specimens. Vertebrat. PalAsiatic. 38, 241–254 (2000).
  30. Xu, X. et al. Four-winged dinosaurs from China. Nature 421, 335–340 (2003). · DOI · Paper page
  31. Xu, X. & Guo, Y. The origin and early evolution of feathers: insights from recent paleontological and neontological data. Vertebrat. PalAsiatic. 47, 311–329 (2009).
  32. Xu, X., Zheng, X. T. & You, H. L. Exceptional dinosaur fossils show ontogenetic development of early feathers. Nature 464, 1338–1341 (2010). · DOI
  33. Zhang, J. Evolution by gene duplication: an update. Trends Ecol. Evol. 18, 292–298 (2003). · DOI · Paper page
  34. Ohno, S. Evolution by Gene Duplication Springer (1970). · DOI · Paper page
  35. Kaessmann, H. Origins, evolution, and phenotypic impact of new genes. Genome Res. 20, 1313–1326 (2010). · DOI
  36. Fujita, P. A. et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 39, D876–D882 (2011). · DOI
  37. Li, H. et al. TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 34, D572–D580 (2006). · DOI · Paper page
  38. Harris, R. Improved pairwise alignment of genomic DNA. PhD thesis, Pennsylvania State University (2007).
  39. Kent, W. J., Baertsch, R., Hinrichs, A., Miller, W. & Haussler, D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl Acad. Sci. USA 100, 11484–11489 (2003). · DOI · Paper page
  40. Blanchette, M. et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708–715 (2004). · DOI · Paper page
  41. Hubisz, M. J., Pollard, K. S. & Siepel, A. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief. Bioinform. 12, 41–51 (2011). · DOI · Paper page
  42. Portales-Casamar, E. et al. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 38, D105–D110 (2010). · DOI
  43. Schug, J. Using TESS to predict transcription factor binding sites in DNA sequence. Curr. Protoc. Bioinformatics 2, 15 (2008).
  44. Pedersen, J. S. et al. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput. Biol. 2, e33 (2006). · DOI
  45. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009). · DOI · Paper page
  46. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009). · DOI · Paper page
  47. Landt, S. G. et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22, 1813–1831 (2012). · DOI · Paper page
  48. Bailey, T. et al. Practical guidelines for the comprehensive analysis of ChIP-seq data. PLoS Comput. Biol. 9, e1003326 (2013). · DOI
  49. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008). · DOI · Paper page
  50. Heger, A., Webber, C., Goodson, M., Ponting, C. P. & Lunter, G. GAT: a simulation framework for testing the association of genomic intervals. Bioinformatics 29, 2046–2048 (2013). · DOI
  51. Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010). · DOI · Paper page
  52. Shen, L. et al. diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. PLoS ONE 8, e65598 (2013). · DOI
  53. Flicek, P. et al. Ensembl 2013. Nucleic Acids Res. 41, D48–D55 (2013). · DOI
  54. Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010). · DOI · Paper page
  55. Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010). · DOI · Paper page
  56. Hardcastle, T. J. & Kelly, K. A. baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 11, 422 (2010). · DOI
  57. Yanai, I. et al. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21, 650–659 (2005). · DOI · Paper page
  58. Wang, D., Zhang, Y., Zhang, Z., Zhu, J. & Yu, J. KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genom. Proteom. Bioinformatics 8, 77–80 (2010). · DOI
  59. Noro, M., Uejima, A., Abe, G., Manabe, M. & Tamura, K. Normal developmental stages of the Madagascar ground gecko Paroedura pictus with special reference to limb morphogenesis. Dev. Dyn. 238, 100–109 (2009). · DOI
  60. Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640–6645 (2000). · DOI
  61. Tsukiji, N., Amano, T. & Shiroishi, T. A novel regulatory element for Shh expression in the lung and gut of mouse embryos. Mech. Dev. 131, 127–136 (2014). · DOI
  62. Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007). · DOI · Paper page

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Metadata

Authors
Seki, R., Li, C., Fang, Q., Hayashi, S., Egawa, S., Hu, J., Xu, L., Pan, H., Kondo, M., Sato, T., Matsubara, H., Kamiyama, N., Kitajima, K., Saito, D., Liu, Y., Gilbert, M. T. P., Zhou, Q., Xu, X., Shiroishi, T., Irie, N., Tamura, K., & Zhang, G.
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2017-02-06
Volume
8
Issue
1
ISSN
2041-1723
DOI
10.1038/ncomms14229
PMC
PMC5473641
Cited by
84
References
12
Language
en
Licence

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