Genome-wide identification of conserved intronic non-coding sequences using a Bayesian segmentation approach

Abstract

BackgroundComputational identification of non-coding RNAs (ncRNAs) is a challenging problem. We describe a genome-wide analysis using Bayesian segmentation to identify intronic elements highly conserved between three evolutionarily distant vertebrate species: human, mouse and zebrafish. We investigate the extent to which these elements include ncRNAs (or conserved domains of ncRNAs) and regulatory sequences.ResultsWe identified 655 deeply conserved intronic sequences in a genome-wide analysis. We also performed a pathway-focussed analysis on genes involved in muscle development, detecting 27 intronic elements, of which 22 were not detected in the genome-wide analysis. At least 87% of the genome-wide and 70% of the pathway-focussed elements have existing annotations indicative of conserved RNA secondary structure. The expression of 26 of the pathway-focused elements was examined using RT-PCR, providing confirmation that they include expressed ncRNAs. Consistent with previous studies, these elements are significantly over-represented in the introns of transcription factors.ConclusionsThis study demonstrates a novel, highly effective, Bayesian approach to identifying conserved non-coding sequences. Our results complement previous findings that these sequences are enriched in transcription factors. However, in contrast to previous studies which suggest the majority of conserved sequences are regulatory factor binding sites, the majority of conserved sequences identified using our approach contain evidence of conserved RNA secondary structures, and our laboratory results suggest most are expressed.Functional roles at DNA and RNA levels are not mutually exclusive, and many of our elements possess evidence of both. Moreover, ncRNAs play roles in transcriptional and post-transcriptional regulation, and this may contribute to the over-representation of these elements in introns of transcription factors. We attribute the higher sensitivity of the pathway-focussed analysis compared to the genome-wide analysis to improved alignment quality, suggesting that enhanced genomic alignments may reveal many more conserved intronic sequences.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3645-2) contains supplementary material, which is available to authorized users.

Detection and identification of cis-regulatory elements using change-point and classification algorithms

“…We extend the analysis from the previous work of Algama [ 16 ] and proceed by using the same dataset. A zebrafish referenced multiz 8-way alignment in.maf format was obtained from the University California Santa Cruz (UCSC) genome browser at http://hgdownload-test.cse.ucsc.edu/goldenPath/danRer7/multiz8way/ and split into 25 data sets corresponding to zebrafish chromosomes, where alignment blocks that overlapped with RefSeq genes were removed.…”

“…changept considers characters on either side of a gap to be adjacent, so a segment containing long gaps or a large proportion of gaps may not be indicative of real genomic structure. These criteria were a slight modification of those used previously by Algama et al [ 16 ], where changpt was used to identify conserved non-coding regions. We have opted for a more relaxed value of minimum segment length and profile value to allow for more potential candidates for conserved non-coding regions and a more aggressive criteria for the gap size to compensate.…”

“…We proceed by using a Bayesian segmentation-classification algorithm changept rooted in comparative genomics. This algorithm has been previously successful in the identification of conserved non-coding regions [ 16 ]. In summary, this method delineates an alignment and classifies segments according to their structure within the alignment.…”

Cis-regulatory elements in conserved non-coding sequences of nuclear receptor genes indicate for crosstalk between endocrine systems

“…Introns are a major proportion of DNA in both the plant and mammalian genome and are considered relevant components for genome adaptation [ 4 ]. They are not simply removed after RNA processing and are responsible for chromatin modification, transcription, RNA splicing, editing, translation, and gene expression [ 4 , 5 , 6 , 7 ]. The presence of introns elevates gene expression in a wide range of organisms including mammals [ 6 , 8 , 9 ].…”

“…The same high abundance of regulatory binding sites has not been observed in exons [ 12 ]. This, therefore, suggests that the prevalence of conserved non-coding sequences (CNSs) among species is related to the preservation of a specific function and/or gene regulation and RNA splicing [ 5 , 13 ].…”