The genome of hexaploid wheat (2n = 6X = 42; genomes AABBDD) is one of the largest in the grass family. The 2C DNA content of hexaploid wheat is 33.1 pg, about 37 and 165 times the genome size of rice (Oryza sativa) and Arabidopsis thaliana, respectively . Based on DNA re-association studies the non-repetitive DNA fraction is estimated to be about 17% of the wheat genome , or hypothesized to be as low as 1% based on available sequence data analysis and genome size in relation to other plant genomes . The repetitive, non-genic regions of wheat, as in many plant genomes, primarily consist of transposable elements (TEs) [4–7] and to a much lesser extent of pseudogenes [8–11]. During the past few years, about 1,500 Triticeae TE sequences have been discovered and deposited in the database for Triticeae repeats (TREP; http://wheat.pw.usda.gov/ITMI/Repeats).
First discovered by Barbara McClintock (1950) in maize, TEs have been reported to be present in all genomes analyzed, with similarities even among life kingdoms . TEs are discrete sequences in the genome that can multiply and/or move within a host genome . Class I TEs, which include long terminal repeat (LTR) retrotransposons and non-LTR transposons, are transcribed into mRNA that is subsequently reverse transcribed into DNA by a reverse transcriptase. Class II TEs, which are DNA transposons, including terminal inverted repeats (TIR) transposons, miniature inverted repeat transposable elements (MITEs) and Helitrons, move as DNA molecules that are excised from a genomic position and integrate elsewhere . TEs are now recognized as important contributors to genomic organization and as major drivers of genome evolution. Centromeric and pericentromeric regions mainly consist of TEs [15–17], which may play an important role in centromeric stability and heterochromatin maintenance [18, 19]. Induced activation of TEs resulted in altered chromosome segregation and meiotic disruption in mouse , loss of sister chromatid cohesion in yeast  and loss of centromere condensation in A. thaliana .
Active TEs constitute a major source of mutations in the genome. Transposition of a TE can result in altered gene expression [23–30], generation of novel regulatory networks , gene deletions [32, 33], gene duplications , increases in genome size [6, 35, 36], illegitimate recombination  and chromosome breaks and rearrangements [38, 39]. Because of the potential harmful effects of active TEs, the expression of most TEs in the genome is suppressed so that, even if whole and capable of autonomous transposition, most TEs remain silent throughout the plant's life cycle . Only few naturally active TEs have been identified so far [12, 40]. Nonetheless, TE-derived sequences are abundant in wheat cDNA libraries  and activation of TEs has been observed under conditions of biotic and abiotic stresses [42, 43]. TE expression is silenced both at transcription and after transcription through epigenetic mechanisms .
TEs can be transcriptionally silenced by DNA methylation and repressive chromatin formation, involving modifications of histone tails and altered chromatin packing [12, 44, 45]. Post-transcriptional silencing of TEs is achieved by the degradation of TE transcripts by RNA-degrading complexes [12, 46–48]. Small non-coding RNAs (sRNAs), generated when double-stranded RNA (dsRNA) is cleaved by proteins belonging to the Dicer family, guide the sequence-specific silencing after transcription . sRNAs are also involved in DNA methylation of homologous DNA sequences in the nucleus (RNA-directed DNA methylation) and heterochromatin formation, guiding the silencing of TE at the transcriptional level [50, 51]. The function of sRNAs is related to their length: if 21-nt long, silencing is post-transcriptional, whereas if 24-nt long, silencing is mediated by RNA-dependent DNA methylation and heterochromatin maintenance [19, 51]. TEs are mobilized in Caenorhabditis elegans mutants that are defective in RNAi [52, 53] and in mutants of A. thaliana that are deficient in DNA methylation and chromatin structure regulation [45, 54–56]. Beside TE-silencing, the sRNAs are involved in a wide variety of biological phenomena, ranging from developmental processes to responses to biotic and abiotic stresses .
High-throughput sequencing has greatly facilitated the analysis of sRNA sequences. Massively-parallel sequencing platforms allow the identification of hundreds of thousands of sRNAs in any organism [58–66]. Profiles of sRNA collected from 22 species of higher plants, including wheat, are now publically available http://smallrna.udel.edu/.
In wheat, fast rates of TE insertion and deletion result in rapid turnover of intergenic regions, which can affect neighbouring genes . This fast mutation frequency, together with the high tolerance to mutations of a polyploid genome, accounts for the genomic dynamism and adaptability of wheat . Regulation of TE expression in the wheat genome has not been studied in detail. In this study, we report the analysis of the different classes of sRNAs originated from the different known classes of TEs in wheat, their target regions within the repetitive elements, and their impact on the methylation patterns of the targeted regions.