Ensembl TrainingEnsembl Home

<- Back to exercise page

Arabidopsis MIR395 region

MicroRNAs (miRNAs) are small non-coding RNA molecules (ca. 22 nucleotides) found in plants and animals, which function in transcriptional and post-transcriptional regulation of gene expression. A well-studied miRNA family in plants is the MIR395 family.

(a) How many members has the MIR395 family in Arabidopsis thaliana?

(b) How are the MIR395 genes organised? Are they clustered? Are they all located on the same strand of the genome? How are they positioned relative to each other?

(a) Go to the Ensembl Plants homepage.

Select Arabidopsis thaliana from the drop down and type mir395 in the search box. Click Go.

There are six MIR395 family members in Arabidopsis thaliana, i.e. MIR395A, -B, -C, -D, -E and -F.

(b) The six MIR395 genes are organised in two clusters, one in the genomic region from base pair 9363196 to 9367179 on chromosome 1 (MIR395A, -B and –C) and one from base pair 26269979 to 26273969 on chromosome 1 (MIR395D, -E and –F).

Click on the genomic coordinates of the MIR395A gene, 1:9363196-9363288. Select the region containing the MIR395A, -B and –C genes. Click on Jump to region in the pop-up menu.

The MIR395A gene is located on the reverse strand, while the -B and -C genes are located on the forward strand.

Repeat the above for the other gene cluster.

The MIR395D and -E genes are located on the reverse strand, while the -F gene is located on the forward strand.

The position of the genes relative to each other is identical within both clusters: two genes in opposite orientation to each other roughly 1 kb apart and the third gene roughly 2.5 kb away. Therefore, it has been hypothesised that the two clusters have evolved by tandem duplications, followed by an intrachromosomal duplication (Maher et al. Evolution of Arabidopsis microRNA families through duplication events. Genome Res 2006; 16:510-519).