Types of RNA

• mRNA: Messenger RNA. Encodes amino acids sequences.
• tRNA: Transfer RNA. Carries amino acids to ribosome during translation.
• rRNA: Ribosomal RNA. Makes up ribosomes.
• snRNA: Small Nuclear RNA (U1, U2, U4, U5, and U6).
• sRNA: Small RNA. Binds to protein or mRNA targets, and regulates gene expression.
• miRNA: Micro RNA. A family of sRNA that regulates gene expression in a sequence-specific manner.
• siRNA:  Small Interfering RNA.
• dsRNA: Double-Stranded RNA
• pre-mRNA: Precursor mRNA. Contains both exons and introns.
• mature mRNA: All introns removed.

Homologs, Orthologs, and Paralogs

Homologs, Orthologs, and Paralogs - these 3 terms are conceptually related. It is necessary to understand the distinction among them.

Homology means that two genes are related by descent i.e. they have a common ancestral DNA sequence. Homology can be divided into two parts - Orthology and Paralogy. Orthologs are results of speciation, while Paralogs are results of gene duplication.

Orthology and Paralogy can easily be determined from the ancestral tree. You have to track along the vertical line of descent and find the place where the pair of genes join. If they join at an upside-down 'Y' node, then they are orthologs. In contrast, if they join at a horizontally connected node, then they are paralogs.

Here is an example [1]. In Fig. (a):

• A1 has 5 Orthologs - B1, B2, C1, C2, C3, as all five orthologs join with A1 at an inverted 'Y' node, where speciation occurred.
• B1 & B2 are paralogs, as they meet horizontally, where gene duplication took place.
• B1 & C1 are orthologs.
• C1, C2 & C3 are paralogs to each other.

Fig. (b) and Fig. (c) are actually same. (c) is actually a detailed illustration of (b). Here:

• A1 & A2 (and also B1 & B2) are orthologs.
• A1 & B1; A1 & B2; A2 & B1; A2 & B2 are all paralogs.

Identification of orthologs can play a significant role to determine evolutionary history. Usually, orthologs have the same function as their common ancestor, while paralogs do not. Bioinformaticians often take advantage of this behavior to differentiate orthologs from paralogs. But, functional similarity (or dissimilarity) does not necessarily imply orthologs (or paralogs).

Reference:

1. Jensen,R.A. (2001) Orthologs and paralogs - we need to get it right. Genome Biol., 2(8). [link]

Other Sources:

1. http://homepage.usask.ca/~ctl271/857/def_homolog.shtml
2. http://biology.stackexchange.com/questions/4962/what-is-the-difference-between-orthologs-paralogs-and-homologs

Deciphering Nature's Alphabet

Few days ago, GenomeTV uploaded an inspiring documentary on major discoveries of molecular biology. Each of the five parts contains stories behind a set of major discoveries. Great scientists themselves tell their own history, which is amazing. Here is the playlist in youtube: http://www.youtube.com/playlist?list=PL1ay9ko4A8smA2OjHMSeJPqrhJwYaH-Aa.