Monday, February 2, 2015

Runs of short exons in Titin gene are conserved across all Mammals

Titin gene more commonly known as Connectin is an elastic muscle protein. The complete gene sequence for this gene has been known since 2001. 

Here we compare the exon structure of Titin transcripts across multiple species with special focus on the cluster of short exons(< 100 bp) in the middle of the gene. Exon ranks of these exons is from ~100 to 180.  These exons correspond to the PEVK segments that are thought to provide the protein "spring" like properties. Comparison of the Titin gene across multiple species has previously been performed across large evolutionary distances. 

All four rodent species [Kangaroo rat (Dipodomys ordii), Mouse (Mus musculus), Pika (Ochotona princeps) and Rabbit(Oryctolagus cuniculus)] from Ensembl show the PEVK exons in phase 1 followed by a pair of 3 exons as seen the human titin gene. 

Mouse
Rabbit
Kangroo Rat
Pika

Similarly, all 12 species from Laurasiatheria[Alpaca (Vicugna pacos), Cat (Felis catus),Cow (Bos taurus), Dog (Canis lupus familiaris), Dolphin (Tursiops truncatus), Ferret (Mustela putorius furo), Hedgehog (Erinaceus europaeus), Horse (Equus caballus), Megabat (Pteropus vampyrus), Microbat (Myotis lucifugus), Panda (Ailuropoda melanoleuca), Sheep (Ovis aries)] also have the PEVK cluster.


Alpaca

Cat
Cow
Dog


Dolphin
Ferret

Horse
Megabat



Microbat


Panda

Sheep
The European Hedgehog has only 30 exons annotated in Ensembl release 78. This might change in later releases. So Functional characterization or some other form of validation is required before considering the possibility of the loss of large number of exons.

All 8 primate genomes [Chimpanzee(Pan troglodytes), Gibbon (Nomascus leucogenys), Gorilla (Gorilla gorilla gorilla), Marmoset (Callithrix jacchus), Olive baboon (Papio anubis), Orangutan (Pongo abelii), Tarsier (Tarsius syrichta) and  Vervet-AGM (Chlorocebus sabaeus)] are very similar to the Human titin. The Gibbon TTN gene is not showing the characteristic run of short exons, but this could be due to the Gibbon genome being relatively new.


Gorilla

Chimp

Gibbon
Marmoset

Olive babbon
Tasrsier
Vervet-AGM

Orangutan















While we have looked at birds before, it has not been a complete coverage. Moreover the ortholog for the TTN gene has been named the SPEG complex locus. So here we use the SPEG complex locus transcripts instead of the transcript from the gene annotated as Titin. We can see that the Chinese Turtle (Pelodiscus sinensis) shows the characteristic pattern of the PEVK exons. However, none of the transcripts annotated in birds [falbicollis_ENSFALG00000003453,ggallus_ENSGALG00000028386,acarolinensis_ENSACAG00000013938,mgallopavo_ENSMGAG00000011306 tguttata_ENSTGUG00000006089]
Chinese Turtle
show the pattern.


Another post dealing with Fish, insects and other species might be able to find other interesting changes in the Titin gene during the course of evolution.



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