What are MicroRNAs and what do they do?


MicroRNAs are small non-coding single-stranded RNA molecules

MicroRNAs (miRNAs) are small non-coding single-stranded RNA molecules consisting of approximately 21 to 22 nucleotides that regulate posttranscriptional gene expression in metazoans and plants. miRNAs are usually generated from noncoding regions of gene transcripts and function to suppress gene expression by translational repression or RNA degradation. miRNAs are now thought to be involved in practically all cell processes via their role in regulating gene expression through translational repression and messenger RNA (mRNA) decay. miRNAs have been found to regulate numerous cell activities, including developmental processes, disease pathogenesis, and host–pathogen interactions. During cell development miRNAs are expressed in a tissue-specific manner. These molecules take part in the regulation of cell-decisions and morphogenesis, the biological process that allows an organism to develop its shape.Therefore the dysregulation of miRNAs can lead to human diseases.

Functions of miRNAs

  • Gene regulation: A miRNA is complementary to a part of one or more mRNAs.
    • Animal miRNAs are usually complementary to a site in the 3′ UTR.
    • Plant miRNAs are usually complementary to coding regions of mRNAs. A perfect or near perfect base pairing with the target RNA promotes cleavage of the RNA.
  • Inhibition of protein translation: microRNAs in animals appear to form only partial base pairs to inhibit protein translation of the target mRNA.
  • DNA methylation: miRNAs occasionally also cause DNA methylation of promoter sites and affect the expression of targeted genes.
  • Targeting of developmental genes: Animal microRNAs target in particular developmental genes. Whereas, genes involved in functions common to all cells, such as gene expression, have very few microRNA target sites.
  • Differentiation and proliferation
  • Stem cell differentiation
  • Notch signalling
  • Programmed cell death
  • Neurogenesis
  • Angiogenesis
  • Hematopoiesis
  • Exocytosis
  • Tumorgenesis
  • Viral defense
  • And potentially many more to be discovered

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Improvements made in instrumental technologies have greatly increased our knowledge of miRNAs in the last decades

It is now well documented that the speed in the advancements of any scientific field depends heavily on the speed of development of new fast and sensitive analytical technologies. The availability of faster and more sensitive DNA sequencing methods has tremendously increased the amount of DNA and RNA sequencing data that can be found in open source databases. Whole genomes and expressed RNA sequences are now available for selected species and total catalogs for polymerase II (Pol II) start sites, protein coding sequences, intron-exon junctions, poly(A) addition sites and transcription units for newly discovered noncoding RNAs have been assembled in recent years.

None of this would have been possible without the continued development of instrumental technologies. Proteins can now be identified routinely using advanced mass spectrometry based methods (e.g. LC-MS/MS for proteomics), and deep-sequencing technologies for DNA and RNA. The development of genetic and cell biological methods has kept pace with developments of molecular and instrumental methods which advanced our understanding of cellular processes at the molecular level in cell biology and medicine tremendously.

Recent research indicates that miRNAs first block translation of their mRNA target and then mediate its decay.

miRNA bind to complementary sequences in the 3’ UTR of multiple target mRNAs, usually resulting in their silencing. It is estimated that miRNAs target ~60% of all genes and are abundantly present in all human cells and are able to repress hundreds of targets each. Experimental results accumulated during the last decade showed that miRNAs are playing significant roles in regulatory mechanisms operating in various organisms, including developmental timing and host-pathogen interactions as well as cell differentiation, proliferation, apoptosis and tumorigenesis.

miRNA are regulatory elements that are coordinatively modulated by multiple effectors when carrying out basic functions, such as single nucleotide polymorphism (SNP), miRNA editing, methylation and regulation of the circadian clock.

The use of modern technologies such as deep-sequencing and  mass spectrometry combined with advanced biochemical methods accelerates miRNA research

In recent years, deep sequencing technologies has allowed scientists to discover many more novel miRNAs. This has led to a sharp increase in the number of known miRNAs. Rules for the annotation  of miRNAs have been developed as well as a web based database containing a collection of miRNA sequences called miRBase.

This database contains over 15, 000 miRNA gene loci in over 140 species, and over 17,000 distinct mature miRNA sequences. Furthermore the database contains maps of reads from short RNA deep-sequencing experiments to microRNAs which are viewable via web interfaces.

The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript that contains information on the location and sequence of the mature miRNA sequence.

Advanced biochemical methods allow for the identification of new miRNAs

The combination of biochemical methods such as immunoprecipitation with sequencing and mass spectrometry based methods and sometimes microarray methods allows researchers now to study an organism at the whole genome level.

A good example is the deep-sequencing of the Hessian fly larval transcriptome by Chen and coworkers. Their work has led to the identification of 89 miRNA species that are either identical or very similar to known miRNAs from other insects. Furthermore, 184 novel miRNAs that have not been reported from other species were also identified. The researchers report that a genome wide search through a draft Hessian fly genome sequence identified a total of 611 putative miRNA-encoding genes based on sequence similarity and the existence of a stem-loop structure for miRNA precursors. Their analysis of the 611 putative genes revealed the dramatic expansion of several miRNA gene families. The largest family contained 91 genes that encoded 20 different miRNAs. Microarray analyses showed that the expression of miRNA genes was strictly regulated during Hessian fly larval development and the abundance of many miRNA genes were affected by host genotypes.

Recently developed novel biochemical approaches for miRNA-target identification

  • High-throughput sequencing of RNA isolated by cross-linking and immunoprecipitation (HITS-CLIP)
  • Modified HITS-CLIP called photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP)

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It is expected that these numbers will increase with the application of the newest high throughput RNA sequencing technologies for the discovery of new noncoding RNAs. Furthermore, miRNA are highly conserved in organisms ranging from the unicellular algae Chlamydomonas reinhardtii to mitochondria suggesting that they are a vital part of genetic regulation with ancient origins.

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References

A book I recommend to read: RNA: Life’s Indispensable Molecule, by Jim Darnell.

Ines Alvarez-Garcia and  Eric A. Miska; MicroRNA functions in animal development and human disease. Development 132, 4653-4662. Published by The Company of Biologists 2005. doi:10.1242/dev.02073.

Bing Liu, Jiuyong Li, and Murray J. Cairns; Identifying miRNAs, targets and functions. Brief Bioinform 2012 : bbs075v1-bbs075.

Chitvan Khajuria, Christie E Williams, Mustapha El Bouhssini, R Jeff Whitworth, Stephen Richards, Jeffrey J Stuart, and Ming-Shun Chen; Deep sequencing and genome-wide analysis reveals the expansion of MicroRNA genes in the gall midge Mayetiola destructor. BMC Genomics. 2013; 14: 187.  Published online 2013 March 18. doi:  10.1186/1471-2164-14-187, PMCID: PMC3608969

Kozomara & Griffiths-Jones 2011: http://www.mirbase.org.

RAMESH S. PILLAI; MicroRNA function: Multiple mechanisms for a tiny RNA? RNA 2005. 11: 1753-1761.



Categories: Bioanalysis, Bioinformatics, Cancer, Cell line authentication, Cell Line Identification, Cell lines, Cellular Reprogramming, Deep sequencing, DNA, DNA Analysis, DNA Editing, DNA finger printing, Gene Expression, Genetics, Genome, Genotyping, High throughput sequencing, lncRNA, Long noncoding RNA, Mass spectrometry, miRNA, Next-generation sequencing, non-coding RNAs, Oligonucleotide Synthesis, Regulatory RNA, RNA, RNA Editing, RNA silencing, RNA Synthesis, RNA World, RNAi, Sequence Annotation, Sequencing

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