ArticleGenome research2008
Multigenome DNA sequence conservation identifies Hox cis-regulatory elements.
Article in Genome research, 2008. 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, 29 citations in OpenAlex.
- Cell-specific variant-to-gene mapping identifies conserved neural and glial regulators of sleep.bioRxiv : the preprint server for biology · 2026Article
- Evolutionary plasticity in nematode Hox gene complements and genomic loci arrangement.Scientific reports · 2024Article
- Genome-wide profiling of angiogenic cis-regulatory elements unravels cis-regulatory SNPs for vascular abnormality.Scientific data · 2024Article
- The GATA factor ELT-3 specifies endoderm in Caenorhabditis angaria in an ancestral gene network.Development (Cambridge, England) · 2022Article
- The anterior Hox gene ceh-13 and elt-1/GATA activate the posterior Hox genes nob-1 and php-3 to specify posterior lineages in the C. elegans embryo.PLoS genetics · 2022Article
- Genome-wide discovery of active regulatory elements and transcription factor footprints inGenome research · 2017Article
- Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks.Genome biology · 2015Article
- Multiple transcription factors directly regulate Hox gene lin-39 expression in ventral hypodermal cells of the C. elegans embryo and larva, including the hypodermal fate regulators LIN-26 and ELT-6.BMC developmental biology · 2014Article
- Article
- Evolution of coding and non-coding genes in HOX clusters of a marsupial.BMC genomics · 2012Article
- Scaffolding a Caenorhabditis nematode genome with RNA-seq.Genome research · 2010Article
- Phylogenetic conservation of the cell-type-specific Lan3-2 glycoepitope in Caenorhabditis elegans.Development genes and evolution · 2010Article
- New tools for investigating the comparative biology of Caenorhabditis briggsae and C. elegans.Genetics · 2010Article
- Systems biology of embryogenesis.Reproduction, fertility, and development · 2010Article
- The C. elegans tailless/Tlx homolog nhr-67 regulates a stage-specific program of linker cell migration in male gonadogenesis.Development (Cambridge, England) · 2009Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
To learn how well ungapped sequence comparisons of multiple species can predict cis-regulatory elements in Caenorhabditis elegans, we made such predictions across the large, complex ceh-13/lin-39 locus and tested them transgenically. We also examined how prediction quality varied with different genomes and parameters in our comparisons. Specifically, we sequenced approximately 0.5% of the C. brenneri and C. sp. 3 PS1010 genomes, and compared five Caenorhabditis genomes (C. elegans, C. briggsae, C. brenneri, C. remanei, and C. sp. 3 PS1010) to find regulatory elements in 22.8 kb of noncoding sequence from the ceh-13/lin-39 Hox subcluster. We developed the MUSSA program to find ungapped DNA sequences with N-way transitive conservation, applied it to the ceh-13/lin-39 locus, and transgenically assayed 21 regions with both high and low degrees of conservation. This identified 10 functional regulatory elements whose activities matched known ceh-13/lin-39 expression, with 100% specificity and a 77% recovery rate. One element was so well conserved that a similar mouse Hox cluster sequence recapitulated the native nematode expression pattern when tested in worms. Our findings suggest that ungapped sequence comparisons can predict regulatory elements genome-wide.
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Registered trials
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.