Motif content comparison between monocot and dicot species

Abstract

While a number of DNA sequence motifs have been functionally characterized, the full repertoire of motifs in an organism (the motifome) is yet to be characterized. The present study wishes to widen the scope of motif content analysis in different monocot and dicot species that include both rice species, Brachypodium, corn, wheat as monocots and Arabidopsis, Lotus japonica, Medicago truncatula, and Populus tremula as dicots. All possible existing motifs were analyzed in different regions of genomes such as were found in different sets of sequences in these species: the whole genome, core proximal and distal promoters, 5′ and 3′ UTRs, and the 1st introns. Due to the increased number of species involved in this study compared to previous works, species relationships were analyzed based on the similarity of common motif content. Certain secondary structure elements were inferred in the genomes of these species as well as new unknown motifs. The distribution of 20 motifs common to the studied species were found to have a significantly larger occurrence within the promoters and 3′ UTRs of genes, both being regulatory regions. Motifs common to the promoter regions of japonica rice, Brachypodium, and corn were also found in a number of orthologous and paralogous genes. Some of our motifs were found to be complementary to miRNA elements in Brachypodium distachyon and japonica rice.

Sequence analysis of the Hsp70 family in moss and evaluation of their functions in abiotic stress responses

“…7 and Supplemental Table S6 ), although there was an obvious difference in the range of cis -elements distributed among the different clusters. Seven clusters were enriched for the MARTBOX, which is the most common element in flowering plants and is suggested to play role in transcriptional regulation 26 . The SORLIP2AT element, which is over-represented in light-induced promoters of phytochrome genes (phyA) in Arabidopsis 27 , was significantly enriched in cluster 3.…”

Motifome comparison between modern human, Neanderthal and Denisovan

“…Building on and refining the methodology of previous work [ 13 , 14 , 22 ], we measured the statistical significance of the motif content of the whole genomes of human, Neanderthal, and Denisovan (as well as mouse for reference). Motifs in specific regions of the genome—core promoters, proximal promoters, distal promoters, all introns, 5’ UTRs and 3’ UTRs—were also determined so that these regions could be examine separately (see Table 1 ).…”

“…The resulting set of statistically significant motifs was normalized by score and was double-filtered to remove general mammalian motifs (by filtering out those motifs, which also occurred in mouse) as well as low-scoring motifs, those whose actual occurrence is close its expected occurrence. For a detailed description of the algorithm, see [ 13 , 14 ]. An overview is given in Fig.…”

“…The method for predicting and scoring motifs in a given sub-genomic set of sequences builds upon the methods of previous works [ 13 , 14 , 21 , 22 ]. The reader is referred to these papers for a detailed description of motif prediction and scoring.…”

“…In this paper, we use an algorithm described in previous works [ 13 , 14 ] to generate and rank a catalogue of all motifs in the whole genomes and several sub-genomic regions in human, Neanderthal, and Denisovan. In part, the algorithm calculates the difference between a given motif’s actual distribution and its expected distribution based on the base pair content of the genome.…”