ArticleGenome research2012
Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 33 citations in OpenAlex.
- Article
- Two deeply conserved non-coding sequences control PLETHORA1/2 expression and coordinate embryo and root development.Plant communications · 2025Article
- Identification of clade-wide putativeHorticulture research · 2023Article
- Ultraconserved Elements Occupy Specific Arenas of Three-Dimensional Mammalian Genome Organization.Cell reports · 2018Article
- Reproductive Long Intergenic Noncoding RNAs Exhibit Male Gamete Specificity and Polycomb Repressive Complex 2-Mediated Repression.Plant physiology · 2018Article
- Conserved non-coding elements: developmental gene regulation meets genome organization.Nucleic acids research · 2017Review
- Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics.Systematic biology · 2017Article
- Ultraconserved Sequences Associated with HoxD Cluster Have Strong Repression Activity.Genome biology and evolution · 2017Article
- Silencing Effect of Hominoid Highly Conserved Noncoding Sequences on Embryonic Brain Development.Genome biology and evolution · 2017Article
- GC Content Heterogeneity Transition of Conserved Noncoding Sequences Occurred at the Emergence of Vertebrates.Genome biology and evolution · 2016Article
- Combinatorial Gene Regulatory Functions Underlie Ultraconserved Elements in Drosophila.Molecular biology and evolution · 2016Article
- Highly constrained intergenic Drosophila ultraconserved elements are candidate ncRNAs.Genome biology and evolution · 2015Article
- Abnormal dosage of ultraconserved elements is highly disfavored in healthy cells but not cancer cells.PLoS genetics · 2014Article
- Lineage-specific conserved noncoding sequences of plant genomes: their possible role in nucleosome positioning.Genome biology and evolution · 2014Article
- The most deeply conserved noncoding sequences in plants serve similar functions to those in vertebrates despite large differences in evolutionary rates.The Plant cell · 2014Article
- A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.Applications in plant sciences · 2014Article
- Article
- The mystery of extreme non-coding conservation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Review
- Chromatin and epigenetic features of long-range gene regulation.Nucleic acids research · 2013Review
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Authors and funding
6 authors at 5 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ultraconserved elements (UCEs), stretches of DNA that are identical between distantly related species, are enigmatic genomic features whose function is not well understood. First identified and characterized in mammals, UCEs have been proposed to play important roles in gene regulation, RNA processing, and maintaining genome integrity. However, because all of these functions can tolerate some sequence variation, their ultraconserved and ultraselected nature is not explained. We investigated whether there are highly conserved DNA elements without genic function in distantly related plant genomes. We compared the genomes of Arabidopsis thaliana and Vitis vinifera; species that diverged ∼115 million years ago (Mya). We identified 36 highly conserved elements with at least 85% similarity that are longer than 55 bp. Interestingly, these elements exhibit properties similar to mammalian UCEs, such that we named them UCE-like elements (ULEs). ULEs are located in intergenic or intronic regions and are depleted from segmental duplications. Like UCEs, ULEs are under strong purifying selection, suggesting a functional role for these elements. As their mammalian counterparts, ULEs show a sharp drop of A+T content at their borders and are enriched close to genes encoding transcription factors and genes involved in development, the latter showing preferential expression in undifferentiated tissues. By comparing the genomes of Brachypodium distachyon and Oryza sativa, species that diverged ∼50 Mya, we identified a different set of ULEs with similar properties in monocots. The identification of ULEs in plant genomes offers new opportunities to study their possible roles in genome function, integrity, and regulation.
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