Introduction
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Animal and plant microRNAs - similarities and differences
Similarities:
Biogenesis and Processing:
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Some miRNAs, such as those involved in essential cellular processes like growth and differentiation, are conserved across both plants and animals. For instance, the miR-156/157 family in plants and the let-7 family in animals are key regulators of developmental timing.
Differences:
| Animals | Plants |
|---|---|---|
Target recognition and binding mechanism | miRNAs often recognize target mRNAs through imperfect base pairing, particularly in the 3’ untranslated region (3’ UTR) of the mRNA. The “seed region” (nucleotides 2-8) at the 5’ end of the miRNA plays a crucial role in target recognition. Due to the imperfect base pairing, a single miRNA can regulate many target genes. | miRNAs generally have near-perfect or perfect complementarity to their target mRNAs, usually within the coding region. This leads to direct cleavage and degradation of the target mRNA. Plant miRNAs often have a one-to-one relationship with their targets. |
Biogenesis and processing pathways | The primary miRNA (pri-miRNA) is processed in the nucleus by the Drosha-DGCR8 complex into a pre-miRNA. The pre-miRNA is then exported to the cytoplasm, where it is further processed by the enzyme Dicer to produce the mature miRNA. | Both the processing of pri-miRNAs into mature miRNAs and the loading into RISC take place mainly in the nucleus. The enzyme Dicer-like 1 (DCL1) is responsible for cleaving the pri-miRNA and pre-miRNA in a single-step process. |
RISC Composition and Argonaute Proteins | The RISC is typically composed of an Argonaute protein (AGO1 being the most common) and the miRNA. There are multiple AGO proteins with diverse functions. | While AGO1 is the predominant Argonaute protein in plant miRNAs, some plants have additional AGO proteins with specialized roles, such as AGO2 and AGO7. |
Function and Location of Target Sites | miRNAs usually target the 3’ UTR of mRNAs, leading to translational repression or, less commonly, mRNA degradation. Rarely, they can target the 5’ UTR or coding regions. | miRNAs predominantly target the coding regions or the 5’ UTRs of mRNAs, which often results in mRNA cleavage. |
Length and Structure of Precursor miRNAs | Precursor miRNAs are typically 70-100 nucleotides long and have a characteristic hairpin structure. | Precursor miRNAs tend to be longer, ranging from 70 to 200 nucleotides, and the hairpin structures are often more variable. |
Evolutionary Conservation | miRNAs are highly conserved across species, reflecting their critical roles in regulating fundamental biological processes. | While many miRNAs are conserved among closely related plant species, there is generally less conservation at broader taxonomic levels. |
Overall characteristics
In Mammals: AGO2 is the key catalytic AGO protein with slicing activity, while AGO3 and AGO4 are primarily involved in translational repression and gene regulation.
In Plants: AGO2 functions in antiviral defense, AGO4 and AGO6 are central to RNA-directed DNA methylation, AGO5 regulates reproductive tissues, and AGO7 plays an essential role in the ta-siRNA pathway and leaf development.
The diversity in AGO proteins reflects the specialized functions that have evolved in both animals and plants to fine-tune gene expression through small RNA-mediated pathways.
Advantages of Small RNA Sequencing
Generate miRNA sequencing libraries directly from total RNA to understand the role of noncoding RNA.
Understand how post-transcriptional regulation contributes to phenotype
Identify novel biomarkers
Capture the complete range of small RNA and miRNA species
Global community for nextflow Bioinformatics pipelines
nf-core is a community-led project to develop a set of best-practice pipelines built using Nextflow. Pipelines are governed by a set of guidelines, enforced by community code reviews and automatic linting (code testing). A suite of helper tools aim to help people run and develop pipelines.
nf-core small RNAseq pipeline https://nf-co.re/smrnaseq/2.2.3Let’s now go to hands on excercises: