ArticleGenome biology and evolution2012
Identification and characterization of lineage-specific highly conserved noncoding sequences in Mammalian genomes.
Article in Genome biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 28 citations in OpenAlex.
- Extensive Loss and Gain of Conserved Noncoding Elements During Early Teleost Evolution.Genome biology and evolution · 2024Article
- dbCNS: A New Database for Conserved Noncoding Sequences.Molecular biology and evolution · 2021Article
- Article
- The Dynamics, Causes, and Impacts of Mammalian Evolutionary Rates Revealed by the Analyses of Capybara Draft Genome Sequences.Genome biology and evolution · 2020Article
- Pairs of Adjacent Conserved Noncoding Elements Separated by Conserved Genomic Distances Act as Cis-Regulatory Units.Genome biology and evolution · 2018Article
- Conserved noncoding sequences conserve biological networks and influence genome evolution.Heredity · 2018Article
- Conserved non-coding elements: developmental gene regulation meets genome organization.Nucleic acids research · 2017Review
- Silencing Effect of Hominoid Highly Conserved Noncoding Sequences on Embryonic Brain Development.Genome biology and evolution · 2017Article
- Genome-wide identification of conserved intronic non-coding sequences using a Bayesian segmentation approach.BMC genomics · 2017Article
- GC Content Heterogeneity Transition of Conserved Noncoding Sequences Occurred at the Emergence of Vertebrates.Genome biology and evolution · 2016Article
- Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences.Genome biology and evolution · 2016Article
- Lineage-specific conserved noncoding sequences of plant genomes: their possible role in nucleosome positioning.Genome biology and evolution · 2014Article
- The mystery of extreme non-coding conservation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Review
- Vertebrate paralogous conserved noncoding sequences may be related to gene expressions in brain.Genome biology and evolution · 2013Article
- Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders.Genome biology and evolution · 2013Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Vertebrate genome comparisons revealed that there are highly conserved noncoding sequences (HCNSs) among a wide range of species and many of which contain regulatory elements. However, recently emerged sequences conserved in specific lineages have not been well studied. Toward this end, we identified 8,198 primate and 21,128 specific HCNSs as representative ones among mammals from human-marmoset and mouse-rat comparisons, respectively. Derived allele frequency analysis of primate-specific HCNSs showed that these HCNSs were under purifying selection, indicating that they may harbor important functions. We selected the top 1,000 largest HCNSs and compared the lineage-specific HCNS-flanking genes (LHF genes) with ultraconserved element (UCE)-flanking genes. Interestingly, the majority of LHF genes were different from UCE-flanking genes. This lineage-specific set of LHF genes was more enriched in protein-binding function. Conversely, the number of LHF genes that were also shared by UCEs was small but significantly larger than random expectation, and many of these genes were involved in anatomical development as transcriptional regulators, suggesting that certain groups of genes preferentially recruit new HCNSs in addition to old HCNSs that are conserved among vertebrates. This group of LHF genes might be involved in the various levels of lineage-specific evolution among vertebrates, mammals, primates, and rodents. If so, the emergence of HCNSs in and around these two groups of LHF genes developed lineage-specific characteristics. Our results provide new insight into lineage-specific evolution through interactions between HCNSs and their LHF genes.
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