Expression of the rice microRNA <i>miR820</i> is associated with epigenetic modifications at its own locus

Abstract

Small RNAs, such as small interfering RNAs (siRNAs) or microRNAs (miRNAs), regulate gene expression at transcriptional and posttranscriptional levels in eukaryotes. miRNAs are processed from duplexes formed on single-stranded RNA. They regulate expression of their target gene either by cleaving mRNA or supressing translation. In general, the primary miRNA transcripts are synthesized by RNA polymerase II and processed similarly to mRNAs. MIRNA genes are usually located in transcriptionally active euchromatic regions. In contrast, siRNAs are processed from duplexes made of two RNA molecules. One of them is often derived from a transposable element (TE) or from repetitive sequences that reside in heterochromatic regions. The other strand is synthesized by the RNAdependent RNA polymerase on the first strand as a template. siRNAs establish epigenetic marks in parasitic DNA such as TEs, thus they usually act in cis. The rice miRNA miR820, encoded by CACTA TEs (five copies, located on different chromosomes), reduces the expression of the de novo DNA methyltransferase gene OsDRM2. Because miR820 is derived from silent TEs, in which the heterochromatic histone modifications are enriched, the mechanism of MIR820 transcription could be expected to differ from typical miRNAs. Here we show that the primary transcript of MIR820 is mainly derived from the CACTA TE copy on chromosome 7 (MIR820b). Histone modification and DNA methylation status around MIR820b differed from that of the other four loci. These unique epigenetic modifications in MIR820b were only found around the miR820 coding region. We conclude that MIR820b transcription may depend on the unique epigenetic modifications, which in turn may be established by the action of miR820 in cis. This suggests a dual function of miR820 in cis and in trans.

Protocol for Artificial MicroRNA Mediated Over-Expression of miR820 in Indica Rice

“…This miR is encoded as two length variants of 21-nt and 24-nt from five different loci [25]. While there is absolute similarity between the mature Osa-mR820 sequences, their precursor sequences share more than 90% similarity.…”

“…It was proposed to be encoded by CACTA transposon family, with its expression being controlled epigenetically at its own locus [24] [25]. Recently, it was shown to be down-regulated under drought [26], salt [27] and arsenic [28] stress.…”

“…The pre-miR820 can be processed by either DCL1 or DCL3 to yield 21-nt and 24-nt long mature miRs, respectively [18]. This suggests a dual function of miR820 with the 21-nt species acting in "trans" by directing the AGO1 mediated cleavage of DNA methyltransferase, OsDRM2, whereas the 24-nt species act through AGO4 mediated pathway to establish and/or maintain epigenetic modifications of OsDRM2 as well as its own locus [18] [25]. The presence of two length variants with common targets poses interesting quest regarding the functional significance of this miR in the biology of the rice plant.…”

Profiling the expression domains of a rice-specific microRNA under stress

“…These represent the canonical 21 nucleotide (nt) miRs that have been named Osa-miR820a-c and their sequences are available as MI0005263, MI0005264, MI0005265 in mirBase version 21 ( Kozomara and Griffiths-Jones, 2014 ). Later it was proposed to be a member of the transposon derived small RNA family, with its expression being controlled epigenetically at its own locus ( Nosaka et al, 2013a , b ). Nosaka et al (2013b) also identified the 24-nt length variants of this family and described two additional family members, Osa-miR820d and Osa-miR820e.…”

“…Later it was proposed to be a member of the transposon derived small RNA family, with its expression being controlled epigenetically at its own locus ( Nosaka et al, 2013a , b ). Nosaka et al (2013b) also identified the 24-nt length variants of this family and described two additional family members, Osa-miR820d and Osa-miR820e. Recently, it has been shown to be down-regulated under arsenic stress in two contrasting arsenic responsive rice cultivars ( Sharma et al, 2015 ).…”