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A tail of gene expression

Imagine trying to fly a kite without a tail. It swoops and loops and wiggles and finally crashes down into the ground. A kite without a tail is unstable, but add a tail at the right place, and your kite will fly steady.

Curiously, a similar connection between possessing a tail and being stable exists in molecules within living cells. Messenger molecules called mRNAs that convey instructions from DNA to protein factories for protein synthesis behave somewhat like kites. The messengers require a special tail to stabilise them so that they can function. Variability in the tail - in length or in their position, affects the function of the mRNAs, and hence influences gene expression.

Now, a team of scientists from the Institute for Stem Cell Biology and Regenerative Medicine (inStem) and the National Centre for Biological Sciences (NCBS) have found that many mRNAs - about 40% of the total - in the flatworm Schmidtea mediterranea have alternate forms that vary in the lengths and positions of their tails.

This study on S. mediterranea is the first of its kind in flatworm model systems, which, due to their incredible regeneration abilities, provide insights to stem cell regulation, cancer and tissue regeneration. This study could further our understanding of how varying mRNA tails could control gene expression in the context of regeneration.

In a typical cell, the expression of a gene encoding for a protein involves two major steps - the coding of a messenger RNA or mRNA from the genetic information in DNA, followed by the translation of the mRNA's message into protein products at the cell's protein factories. However, before translation, a process called 'polyadenylation' adds tails to mRNAs to stabilise these messengers and influence their function.

The addition of these tails generally happens at specific sites - non-coding parts of mRNAs called 3'-untranslated regions or 3'-UTRs. However, through a phenomenon known as 'alternative polyadenylation', these tails can be added on to different sites on the mRNA, affecting its stability and therefore the amount or type of protein product formed.

The work has been a collaborative effort between Dasaradhi Palakodeti's group at inStem and Aswin Seshasayee from NCBS. Apart from using a host of cutting-edge molecular techniques such as Next Generation Sequencing or NGS, the researchers also had to develop specific bioinformatics tools for analysing large amounts of genomic data.

"We know that there are specific patterns in the mRNAs that signal for polyadenylation. But we needed to build a computational pipeline to be able to detect such signals reliably," says Palakodeti.

When searching for a particular pattern in a very large amount of genetic data, the probability of finding such a pattern by pure chance becomes very high. "In order to avoid such false positives, we needed expertise in statistics and bioinformatics, which Aswin Seshasayee and Praveen Anand provided," continues Palakodeti.

The current study, which has focused on defining and characterizing a genome-wide database of the 3'- UTRs in              S. mediterranea could be a very useful resource for researchers in this field. The tools and methods used in the work have been described in a publication in the journal G3:Genes|Genome|Genetics. The authors believe that these tools and methods will lay the foundation for crucial breakthroughs in the flatworm model system and in our understanding of stem cell biology and the process of regeneration.

"One of the most interesting patterns that have emerged from this study is that the same mRNAs with tails at different positions are found in different tissues. The tail at different positions also determine the length of the 3' UTR, which in turn influences the translation. Actively regenerating tissues expressing a gene have mRNAs with shorter 3'UTR, while mature cells expressing that same gene have mRNAs with longer 3' UTR," says Vairavan Lakshmanan, a student in Palakodeti's group and a lead author in the paper detailing these findings.

Praveen Anand, another lead author in this study says, "Many studies focus on what protein an mRNA codes for, but very few actually look at the sequences that are beyond these coding regions. Our work is directed at studying, the signals for polyadenylation on a genome scale that can regulate the stability of mRNAs and can impact the localization of mRNAs and its translation. And all of this has been developed for the first time in the flatworm model system."

 

The work described in this article has been published in a paper titled "Genome-wide analysis of polyadenylation events in Schmidtea mediterranea" in the journal G3: Genes|Genomes|Genetics in August. The paper can be accessed here: http://www.g3journal.org/content/early/2016/08/05/g3.116.031120.abstract

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