RESULTS: Expression analysis by RNA-Seq 1
All cells have the same gene content, but cells in different parts of an organism’s body express different genes, which make different kinds of proteins.
So what were these new genes doing? Where were they being expressed?
To an extent, the authors could address those two questions from databases used to locate the denovo genes. However, mostly they used a different set of databases yet again. This time, it was RNA-seq databases. These store data collected via a new methodology called “Whole Transcriptome Shotgun Sequencing” which can take snapshots in time of the various RNAs - messenger, transfer, ribose, and other fragments - circulating in cells at various times.
All these RNAs constitute what is called the transcriptome because they are created at, and associated with transcription. The transcriptome changes enormously in time as genes switch on and off. And naturally the transciptome varies from tissue to tissue.
I couldn’t easily locate a description of RNA-seq which gave me some kind of reasonable understanding of how it works. The technique is very new and very powerful. So rather than attempting to describe it, I’ll simply report on the results of their studies with respect to where those denovo genes were found, and how much they expressed.
By searching RNA-seq databases for 11 tissues: adipose, whole brain, cerebral cortex, breast, colon, heart, liver, lymph node, skeletal muscle, lung and testes, the scientists were able to determine expression levels of the genes in each tissue for for 53 of the 60 denovo genes. For the remaining 7 genes, they found the expression data in some of the other databases used previously. Possibly a reason for not finding all genes on RNA-seq was because the expression levels of denovo genes is generally very low and for these 7 specific genes, the levels were the lowest.
What they did find however, was that the expression level for all tissues was highest in the testes with the cerebral cortex next. And the tissues that had the highest number of denovo genes expressed was the cerebral cortex, followed by the testes. The expression levels can be seen here. The tissues with the highest numbers of genes expressed can be seen at figures 2b and 2c here.
Only when it came to the tissues with the greatest number of genes having the highest expression levels did the cerebral cortex and testes not stand out. Then the adipose, the lung and the breast did better.
Two of these denovo genes were intriguing. One labelled ENSG00000187488 was very highly expressed in the testes, and the other labelled ENSG00000206028 was very highly expressed in the cerebral cortex. In fact in the other tissues the latter gene only registered in the brain, lymph node and lung, and there at extremely low levels relative the the cerebral cortex. ENSG00000187488 did register in all other tissues, often markedly so. Nevertheless, its expression level in the testes was twice that for the next highest tissue, the heart.
Having located these putative denovo genes and determined where they are expressed, the next question the authors tackled was whether or not these genes were under selective pressure.
To be continued ....
All cells have the same gene content, but cells in different parts of an organism’s body express different genes, which make different kinds of proteins.
So what were these new genes doing? Where were they being expressed?
To an extent, the authors could address those two questions from databases used to locate the denovo genes. However, mostly they used a different set of databases yet again. This time, it was RNA-seq databases. These store data collected via a new methodology called “Whole Transcriptome Shotgun Sequencing” which can take snapshots in time of the various RNAs - messenger, transfer, ribose, and other fragments - circulating in cells at various times.
All these RNAs constitute what is called the transcriptome because they are created at, and associated with transcription. The transcriptome changes enormously in time as genes switch on and off. And naturally the transciptome varies from tissue to tissue.
I couldn’t easily locate a description of RNA-seq which gave me some kind of reasonable understanding of how it works. The technique is very new and very powerful. So rather than attempting to describe it, I’ll simply report on the results of their studies with respect to where those denovo genes were found, and how much they expressed.
By searching RNA-seq databases for 11 tissues: adipose, whole brain, cerebral cortex, breast, colon, heart, liver, lymph node, skeletal muscle, lung and testes, the scientists were able to determine expression levels of the genes in each tissue for for 53 of the 60 denovo genes. For the remaining 7 genes, they found the expression data in some of the other databases used previously. Possibly a reason for not finding all genes on RNA-seq was because the expression levels of denovo genes is generally very low and for these 7 specific genes, the levels were the lowest.
What they did find however, was that the expression level for all tissues was highest in the testes with the cerebral cortex next. And the tissues that had the highest number of denovo genes expressed was the cerebral cortex, followed by the testes. The expression levels can be seen here. The tissues with the highest numbers of genes expressed can be seen at figures 2b and 2c here.
Only when it came to the tissues with the greatest number of genes having the highest expression levels did the cerebral cortex and testes not stand out. Then the adipose, the lung and the breast did better.
Two of these denovo genes were intriguing. One labelled ENSG00000187488 was very highly expressed in the testes, and the other labelled ENSG00000206028 was very highly expressed in the cerebral cortex. In fact in the other tissues the latter gene only registered in the brain, lymph node and lung, and there at extremely low levels relative the the cerebral cortex. ENSG00000187488 did register in all other tissues, often markedly so. Nevertheless, its expression level in the testes was twice that for the next highest tissue, the heart.
Having located these putative denovo genes and determined where they are expressed, the next question the authors tackled was whether or not these genes were under selective pressure.
To be continued ....
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