Investigation Of Novel ORFs In Mouse Cell Line And Human Tissues

Abstract

It has become quite apparent that the genomes of many organisms are much more complex than thought before the usage of routine high throughput sequencing of genomes of various organisms. It is quite well known that there are coding regions of the genome that are transcribed and translated to form functional proteins. The transcription and translation is not restricted to these regions but other non coding regions are also transcribed and translated. These noncoding transcriptional events have been claimed to be ‘transcriptional noise’ but we think otherwise. We show that these noncoding transcriptional events are not noise by studying Nascent RNA sequences from Mus musculus and think that they can play an important role in various cell functions. The work done in the project shows that in Nascent RNA sequences from Mus musculus, there was no differential expression between knock-out of a histone variant (which would leave the enhancers and chromatin open for non-specific transcriptions to happen and therefore increasing noisy transcription) when compared to wild type. This analysis rules out that transcription of sORFs occurs due to noisy transcriptional events. Having established that sORFs are not biological noise and we want to try and aim to further strengthen this argument by finding expression of sORFs in healthy tissues by analyzing GTEx datasets. The GTEx dataset, being a huge collection of mRNA data from normal human tissues, helped us understand and quantify the expression of sORFs and other Novel ORFs at a large scale. The project then goes on to study how various noncoding regions like sORFs, altORFs, pseudogenes and de novo genes are expressed in 53 healthy human tissue types from the GTEx database and quantifies their expression in these tissues.