ArticleGenome biology2006
Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage.
Article in Genome biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 50 citations in OpenAlex.
- Conservation of regulatory elements with highly diverged sequences across large evolutionary distances.Nature genetics · 2025Article
- Developmental and evolutionary comparative analysis of a regulatory landscape in mouse and chicken.Development (Cambridge, England) · 2022Article
- 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
- C2H2 zinc finger proteins greatly expand the human regulatory lexicon.Nature biotechnology · 2015Article
- Conserved noncoding elements follow power-law-like distributions in several genomes as a result of genome dynamics.PloS one · 2014Article
- Deep conservation of cis-regulatory elements in metazoans.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Review
- Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development.Nucleic acids research · 2013Article
- Article
- Fishing for function: zebrafish BAC transgenics for functional genomics.Molecular bioSystems · 2011Review
- Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos.Nature methods · 2009Article
- Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention.Genome research · 2009Article
- Identification of direct T-box target genes in the developing zebrafish mesoderm.Development (Cambridge, England) · 2009Article
- Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend.BMC genomics · 2009Article
- Conservation of core gene expression in vertebrate tissues.Journal of biology · 2009Article
- Evolution of the mammalian transcription factor binding repertoire via transposable elements.Genome research · 2008Article
- Dispensability of mammalian DNA.Genome research · 2008Article
- Article
- Identification and analysis of a conserved Tcfap2a intronic enhancer element required for expression in facial and limb bud mesenchyme.Molecular and cellular biology · 2008Article
- TFCONES: a database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements.BMC genomics · 2007Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
backgroundAll vertebrates share a remarkable degree of similarity in their development as well as in the basic functions of their cells. Despite this, attempts at unearthing genome-wide regulatory elements conserved throughout the vertebrate lineage using BLAST-like approaches have thus far detected noncoding conservation in only a few hundred genes, mostly associated with regulation of transcription and development.
resultsWe used a unique combination of tools to obtain regional global-local alignments of orthologous loci. This approach takes into account shuffling of regulatory regions that are likely to occur over evolutionary distances greater than those separating mammalian genomes. This approach revealed one order of magnitude more vertebrate conserved elements than was previously reported in over 2,000 genes, including a high number of genes found in the membrane and extracellular regions. Our analysis revealed that 72% of the elements identified have undergone shuffling. We tested the ability of the elements identified to enhance transcription in zebrafish embryos and compared their activity with a set of control fragments. We found that more than 80% of the elements tested were able to enhance transcription significantly, prevalently in a tissue-restricted manner corresponding to the expression domain of the neighboring gene.
conclusionOur work elucidates the importance of shuffling in the detection of cis-regulatory elements. It also elucidates how similarities across the vertebrate lineage, which go well beyond development, can be explained not only within the realm of coding genes but also in that of the sequences that ultimately govern their expression.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.