Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b
- 10 December 2007
- journal article
- research article
- Published by Cold Spring Harbor Laboratory in Genome Research
- Vol. 18 (2), 252-260
- https://doi.org/10.1101/gr.6929408
Abstract
Despite its recognized utility, the extent to which evolutionary sequence conservation-based approaches may systematically overlook functional noncoding sequences remains unclear. We have tiled across sequence encompassing the zebrafish phox2b gene, ultimately evaluating 48 amplicons corresponding to all noncoding sequences therein for enhancer activity in zebrafish. Post hoc analyses of this interval utilizing five commonly used measures of evolutionary constraint (AVID, MLAGAN, SLAGAN, phastCons, WebMCS) demonstrate that each systematically overlooks regulatory sequences. These established algorithms detected only 29%–61% of our identified regulatory elements, consistent with the suggestion that many regulatory sequences may not be readily detected by metrics of sequence constraint. However, we were able to discriminate functional from nonfunctional sequences based upon GC composition and identified position weight matrices (PWM), demonstrating that, in at least one case, deleting sequences containing a subset of these PWMs from one identified regulatory element abrogated its regulatory function. Collectively, these data demonstrate that the noncoding functional component of vertebrate genomes may far exceed estimates predicated on evolutionary constraint.Keywords
This publication has 40 references indexed in Scilit:
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectNature, 2007
- Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE dataGenome Research, 2007
- In vivo enhancer analysis of human conserved non-coding sequencesNature, 2006
- ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elementsGenome Research, 2006
- Evaluating the biological relevance of putative enhancers using Tol2 transposon-mediated transgenesis in zebrafishNature Protocols, 2006
- Close sequence comparisons are sufficient to identify human cis-regulatory elementsGenome Research, 2006
- Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomesGenome Research, 2005
- A common sex-dependent mutation in a RET enhancer underlies Hirschsprung disease riskNature, 2005
- Transcription regulation and animal diversityNature, 2003
- Stages of embryonic development of the zebrafishDevelopmental Dynamics, 1995