micrornas ( mirnas ) are single - stranded , short ( 1527 nucleotides ) rna sequences that repress protein synthesis via base pairing to some portion of a messenger rna ( mrna ) , such as the 3 untranslated region ( 3utr ) , the 5 untranslated region ( 5utr ) , or the coding region [ 1 , 2 ] . endogenous mirnas have been found in various organisms , including animals , plants , and viruses . in mammals , precursor mirnas ( pre - mirnas ) 60100 nucleotides in length form a hairpin stem - loop structure and are processed by dicer , a highly conserved rnase iii family endonuclease that is found in almost all eukaryotic organisms [ 3 , 4 ] . this processing yields a mirna  : mirna duplex that is approximately 21 nucleotides long . one or both of the duplex 's short rna strands is incorporated into rna - induced silencing complexes ( riscs , which are composed of dicer , argonaute , and other nonspecified proteins ) and functions as a mature mirna that can base pair with mrna targets , inducing either the degradation or translational repression of the mrna [ 3 , 4 ] . the regulation of mirna is essential for organisms because mirna plays critical roles in numerous biological processes , including the proliferation and differentiation of cells , as well as apoptosis . it is predicted that mammalian mirnas can regulate approximately 30% of protein - coding genes . the dysfunctional posttranscriptional modulation of gene expression caused by mirnas has been related to diseases such as cancer and neurodegenerative disorders [ 58 ] . the investigation of mirnas and their gene targets has thus attracted much attention in recent years and has become a major focus of research in medicine and molecular biology [ 7 , 913 ] . for this study , the author explored the base composition of mature mirnas from the six mammalian species that contain the largest number of known mirnas . position - specific base dominance in certain mirnas has been investigated by other researchers ; for example , gkirtzou et al . discussed the sequence composition on and around mature mirnas for humans and mice , and wang et al . however , this paper provides more complete , detailed , and updated information regarding the base composition characteristics of mature mirnas in four primates and two rodents , thus providing additional knowledge regarding mammalian mirnas . we found that the mammalian mirnas are evolutionarily conserved and gu - rich , where u residues are more frequent than other bases . adenosine residues are generally a less frequent occupant , except at positions 2 and 3 in the 5 seed region of these mirnas . this characteristic may explain the specificity of pairing and target recognition by the 5 seed region in mirnas . the sequences of mature mirnas were obtained from mirbase ( http://www.mirbase.org/ ) , a database that contains experimentally supported base sequences for various mirnas [ 1619 ] . the mirna data for homo sapiens , pongo pygmaeus , pan troglodytes , macaca mulatta , mus musculus , and rattus norvegicus were exported from the mirbase database and then transferred into microsoft excel . in excel , the mirna sequences were arranged such that each excel column contained only the nucleotides at a specific position of the mirnas studied ( e.g. , column b contained nucleotides at position 1 of the 5 end of all human mirnas ; column c contained nucleotides at position 2 of the 5 end of all human mirnas studied ) . the nucleotides in each column were copied and pasted into an online rna base composition calculator ( http://www.currentprotocols.com/wileycda/curpro3tool/toolid-7.html/ ) in order to determine the number and percentage of a , g , u , and c at every position of each mirna of each species studied . the six largest mirna pools were exported from the mirbase database , including homo sapiens ( 1921 mirnas ) , mus musculus ( 1157 mirnas ) , rattus norvegicus ( 680 mirnas ) , pongo pygmaeus ( 600 mirnas ) , pan troglodytes ( 525 mirnas ) , and macaca mulatta ( 488 mirnas ) . a small number of human mirnas were found to have slightly different names but identical sequences . the names of mirnas in mirbase are first assigned to their hairpin precursors and then inherited by the mature mirnas . the naming problem is caused by the occasional existence of multiple mirna members in the same family , where the mature sequence from one stem of the hairpin precursor is slightly different from the same sequence in a mirna family member , while the sequences from the other stem of the hairpin precursor are identical . after deleting these redundant sequences , 1897 out of 1921 of human mirnas were included for investigation in this study . column 3 in table 1 provides the total base composition , including total numbers and percentages of a , g , u , and c in all mature mirnas of each species studied . overall , g and u residues are more abundant than a and c residues in the mirna sequences investigated . more us than gs are present in five of the six species , with human mirnas being the exception . based on canonical watson - crick base pairing , this bias in mirna composition indicates the abundance of a residues in the target mrna regions . david bartel 's research team discovered the high frequency of u and low occurrence of g at the 5 end of caenorhabditis elegans mirnas . data shown in table 1 , column 4 , confirmed this tendency in mammalian species . at position 1 of all experimentally confirmed mirnas in each species studied , the frequency of u residues ranges from 36% to 44% ( shown in red in table 1 ) , whereas g residues range from 11% to 14% ( shown in green in table 1 ) . in addition , c residues are less frequent at the 5 end of mammalian mirnas , indicating a preference for base pairs with lower thermodynamic stability ( i.e. , favoring au rather than gc base pairs ) at position 1 . data presented in table 1 , column 5 , provide the base composition at the 3 end of the mirnas studied . interestingly , the 3 end demonstrates the same abundance of u residues as found in the 5 end of mirnas , indicating an enrichment of a residues within the 5 end of mrna targets . g and c residues are less frequent in the 3 end of mirnas as well , however , to a lesser degree than in the 5 end . it has been reported that the presence of an a residue in the mrna target , across from position 1 of the 5 end of a mirna , improves binding between the mirna and its target . this occurs even though actual base pairing between the a residue and the nucleotide at position 1 of the 5 end of the mirna is not necessary [ 3 , 4 , 2124 ] . the strong bias toward u residues at position 1 of both ends of mirnas in the six mammalian species studied in this paper implies that both ends , rather than just the 5 end , may participate in target recognition . one study demonstrated that mirna can simultaneously interact with both the 3utr and 5utr of a mrna target via complementary base pairing using its 5 and 3 regions , respectively , thus providing evidence for the possibility that both ends of mirnas are involved in target recognition . in metazoans , the second - through - seventh nucleotides at 5 end of a mirna are known as the seed region , which is the most important region for mirna complementarity and target recognition [ 23 , 26 ] . in this study , we investigated the base composition ( i.e. , the percentages of a , g , u , and c ) for two areas of every mature mirna of each species in our study . we examined the sequences both the 5 seed region and the nucleotide immediately following it ( i.e. , the eighth nucleotide at the 5 end ) ; our results are presented in table 2 . the corresponding regions at the 3 end were also studied , and those results are also presented in table 2 . in the 5 seed region , there is a preference for a at positions 2 and 3 ( shown in red in table 2 ) , followed by a preference for g at positions 46 ( shown in magenta in table 2 ) . the base preference at positions 7 and 8 is not consistent across the six species . in the corresponding 3 regions , there is a strong preference for g at position 2 ( shown in orange in table 2 ) , followed by a preference for u at position 3 ( shown in green in table 2 ) . position 4 at the 3 end of these mirnas is more frequently g in primates and u in rodents ( shown in blue in table 2 ) . position 5 at the 3 end of these mirnas is most frequently u ( shown in purple in table 2 ) ; u is also the most frequent occupant of position 7 ( shown in purple in table 2 ) , except in human mirnas . the base preferences at positions 6 and 8 of the 3 end of mirnas are not consistent across the six species studied . the specificity of mirna targeting in mammals is not necessarily restricted to the 5 and 3 ends of the seed pairing regions , and previous reports suggest that seed matches are not always sufficient for the repression of targets in mammals . therefore , base composition beyond the eighth nucleotide from the 5 end of mirnas was also investigated in this study . base composition information for the ninth - through - sixteenth nucleotides from the 5 end of the mirnas is presented in table 3 . positions 9 , 13 , and 16 demonstrate a strong preference for u ; whereas position 15 shows a strong preference for g in all six species investigated . the base preferences at positions 10 , 11 , 12 , and 14 from the 5 end of the mirnas are not consistent in these six species . previous studies suggest that the presence of an a or u residue in the mrna target , across from position 9 of the 5 end of a mirna , improves binding between the mirna and its target . this occurs even though the a or u does not need to base pair with the nucleotide at position 9 of the 5 end of the mirna [ 3 , 4 , 22 ] . our study demonstrates that at position 9 of the mirnas , there is a strong preference for u ( ranging from 29% to 35% in the six species investigated ) , which is able to base pair with the a residue in the mrna target . this finding implies that the nucleotide at position 9 of the 5 end of a mirna plays an important role in improving both the recognition of specific targets and the functional efficiency of the mirna . it has been reported that residues at positions 1316 of the 5 end of the mirnas are also important for stabilizing mirna - mrna interactions , especially when base pairing in the 5 seed region is suboptimal [ 3 , 4 , 22 ] . the lengths of the mature mirnas investigated in this study range from 15 to 27 nucleotides . for some short mirnas , residues at positions 1316 are located in the 3 half of the mirnas ; however , for some long mirnas , these residues are situated in the central region of the mirnas . therefore , whether nucleotide pairing at positions 1316 of the 5 end of a mirna is important may , at least partially , depend on their exact locations in the mirna investigated . overall , mammalian mirnas are evolutionarily conserved and gu - rich , where u residues are more frequent than other bases . another interesting finding is that , in the mirna sequences investigated , a residues are clearly the most frequent occupants of positions 2 and 3 of the 5 end of mirnas . unlike g and u residues that may pair with c / u and a / g , respectively , a residues can only pair with u residues of target mrnas , which may augment the recognition specificity of the 5 seed region .
micrornas ( mirnas ) are short rna sequences that repress protein synthesis by either inhibiting the translation of messenger rna ( mrna ) or increasing mrna degradation . 
 endogenous mirnas have been found in various organisms , including animals , plants , and viruses . 
 mammalian mirnas are evolutionarily conserved , are scattered throughout chromosomes , and play an important role in the immune response and the onset of cancer . for this study , the author explored the base composition characteristics of mirna genes from the six mammalian species that contain the largest number of known mirnas . 
 it was found that mammalian mirnas are evolutionarily conserved and gu - rich . 
 interestingly , in the mirna sequences investigated , a residues are clearly the most frequent occupants of positions 2 and 3 of the 5 end of mirnas . unlike g and u residues that may pair with c / u and a / g , respectively , a residues can only pair with u residues of target mrnas , which may augment the recognition specificity of the 5 seed region .