ArticlePloS one2011
Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation.Nature communications · 2017Article
- A single nucleotide polymorphism associated with isolated cleft lip and palate, thyroid cancer and hypothyroidism alters the activity of an oral epithelium and thyroid enhancer near FOXE1.Human molecular genetics · 2015Article
- Article
- Deep conservation of cis-regulatory elements in metazoans.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Review
- The mystery of extreme non-coding conservation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Review
- Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression.BMC genomics · 2012Article
- Using BAC transgenesis in zebrafish to identify regulatory sequences of the amyloid precursor protein gene in humans.BMC genomics · 2012Article
- Transcription factor binding at enhancers: shaping a genomic regulatory landscape in flux.Frontiers in genetics · 2012Article
- Article
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Authors and funding
8 authors.
Funding
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Abstract
Non-coding DNA conservation across species has been often used as a predictor for transcriptional enhancer activity. However, only a few systematic analyses of the function of these highly conserved non-coding regions (HCNRs) have been performed. Here we use zebrafish transgenic assays to perform a systematic study of 113 HCNRs from human chromosome 16. By comparing transient and stable transgenesis, we show that the first method is highly inefficient, leading to 40% of false positives and 20% of false negatives. When analyzed in stable transgenic lines, a great majority of HCNRs were active in the central nervous system, although some of them drove expression in other organs such as the eye and the excretory system. Finally, by testing a fraction of the HCNRs lacking enhancer activity for in vivo insulator activity, we find that 20% of them may contain enhancer-blocking function. Altogether our data indicate that HCNRs may contain different types of cis-regulatory activity, including enhancer, insulators as well as other not yet discovered functions.
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