STAG-CNS

One method for identifying noncoding regulatory regions of a genome is to
quantify rates of divergence between related species, as functional sequence will
generally diverge more slowly. Most approaches to identifying these conserved
noncoding sequences (CNSs) based on alignment have had relatively large minimum
sequence lengths (>/=15 bp) compared with the average length of known
transcription factor binding sites. To circumvent this constraint, STAG-CNS that
can simultaneously integrate the data from the promoters of conserved orthologous
genes in three or more species was developed. Using the data from up to six grass
species made it possible to identify conserved sequences as short as 9 bp with
false discovery rate </=0.05. These CNSs exhibit greater overlap with open
chromatin regions identified using DNase I hypersensitivity assays, and are
enriched in the promoters of genes involved in transcriptional regulation.
STAG-CNS was further employed to characterize loss of conserved noncoding
sequences associated with retained duplicate genes from the ancient maize
polyploidy. Genes with fewer retained CNSs show lower overall expression,
although this bias is more apparent in samples of complex organ systems
containing many cell types, suggesting that CNS loss may correspond to a reduced
number of expression contexts rather than lower expression levels across the
entire ancestral expression domain.

STAG-CNS: An Order-Aware Conserved Noncoding Sequences Discovery Tool for Arbitrary Numbers of Species.

STAG-CNS is a software tool that identifies conserved noncoding sequences (CNSs) in a genome by integrating data from the promoters of conserved orthologous genes in three or more species. It can identify short CNSs as small as 9 bp with a false discovery rate </=0.05 and shows greater overlap with open chromatin regions identified using DNase I hypersensitivity assays. These CNSs are enriched in the promoters of genes involved in transcriptional regulation. STAG-CNS was also used to characterize loss of conserved noncoding sequences associated with retained duplicate genes from the ancient maize polyploidy, where genes with fewer retained CNSs show lower overall expression. This method provides a more sensitive approach to identifying regulatory sequences and can help understand the effects of CNS loss on gene expression in complex organ systems.





STAG-CNS

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