Ancient Noncoding Elements Conserved in the Human Genome

@article{Venkatesh2006AncientNE,
  title={Ancient Noncoding Elements Conserved in the Human Genome},
  author={Byrappa Venkatesh and Ewen Kirkness and Yong-Hwee Eddie Loh and Aaron L. Halpern and Alison P. Lee and Justin Johnson and Nidhi Dandona and Lakshmi D Viswanathan and Alice Tay and J. Craig Venter and Robert Strausberg and Sydney Brenner},
  journal={Science},
  year={2006},
  volume={314},
  pages={1892 - 1892}
}
Cartilaginous fishes represent the living group of jawed vertebrates that diverged from the common ancestor of human and teleost fish lineages about 530 million years ago. We generated ~1.4× genome sequence coverage for a cartilaginous fish, the elephant shark (Callorhinchus milii), and compared this genome with the human genome to identify conserved noncoding elements (CNEs). The elephant shark sequence revealed twice as many CNEs as were identified by whole-genome comparisons between teleost… 
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112 Citations
Highly Influential Citations
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Background Citations
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Methods Citations
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Results Citations
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112 Citations

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Citation Type

Rapidly evolving fish genomes and teleost diversity.
  • V. Ravi, B. Venkatesh
  • Biology, Environmental Science
    Current opinion in genetics & development
  • 2008
Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes.
TLDR
Analysis of vertebrate CNEs in human, dog, chicken, Xenopus, and four teleost fishes using elephant shark, a cartilaginous vertebrate, as the base genome, shows that aCNEs have been evolving at different rates in different bony vertebrate lineages.
The Divergent Genomes of Teleosts.
TLDR
Several divergent features of the teleost genomes include an accelerated evolutionary rate of protein-coding and nucleotide sequences, a higher rate of intron turnover, loss of many potential cis-regulatory elements and shorter conserved syntenic blocks, and a combination of these might have contributed to the evolution of the amazing phenotypic diversity and morphological innovations of teleosts.
Organization of conserved elements near key developmental regulators in vertebrate genomes.
Survey Sequencing and Comparative Analysis of the Elephant Shark (Callorhinchus milii) Genome
TLDR
Survey sequencing and comparative analysis of the elephant shark genome are described, showing the degree of conserved synteny and conserved sequences between the human and elephant shark genomes are higher than that between human and teleost fish genomes.
Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution
TLDR
Analyses of the assembly indicate that two whole-genome duplications likely occurred before the divergence of ancestral lamprey and gnathostome lineages, and help define key evolutionary events within vertebrate lineages.
Reptiles and Mammals Have Differentially Retained Long Conserved Noncoding Sequences from the Amniote Ancestor
TLDR
The results show that the rate of retention of LCNS from the amniote ancestor differs between mammals and Reptilia (including birds), and that this may reflect differing roles and constraints in gene regulation.
Evolutionary growth process of highly conserved sequences in vertebrate genomes.
The evolutionary origin of developmental enhancers in vertebrates: Insights from non‐model species
  • Koh Onimaru
  • Biology
    Development, growth & differentiation
  • 2020
TLDR
The evolutionary origin of conserved non‐coding elements (CNEs) is examined, which often function as tissue‐specific developmental enhancers, and how CNEs are related to gene regulatory changes that caused the major morphological transitions of vertebrates are discussed.
Early Evolution of Conserved Regulatory Sequences Associated with Development in Vertebrates
TLDR
Emerging genomic sequence data for the sea lamprey is exploited to explore the depth of conservation of this type of element in the earliest diverging extant vertebrate lineage, the jawless fish (agnathans), and identified lamprey elements associated with all but two of these gene regions.
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CORRECTIONS &CLARIFICATIONS Brevia: “Ancient noncoding elements conserved in the human genome
  • 2006