Alternate RNA variations of genes might form autism | Spectrum
Alternate Game: Over half of the genes expressed in the human cortex, including some associated with autism, have more than one transcript isoform.
Researchers have discovered thousands of new alternative versions of RNA, or isoforms, of genes expressed in the brain, including some implicated in autism, according to a new study.
Several of the RNA isoforms are expressed at different levels during brain development, as a separate analysis shows. Isoforms affected by autism-related “loss of function” mutations – which destroy a protein or disrupt its activity – are usually expressed before birth and are typically involved in essential neuronal processes.
Together, the results confirm that alternative splicing – in which the RNA transcripts of a gene are cut and assembled into different proteins – is key to regulating gene expression in the brain. They also emphasize the importance of studying the different isoforms of a gene to understand how certain variants contribute to conditions like autism.
“Both studies tell us that looking at the gene level means looking at a low resolution and overlooking a lot of things,” says Sagiv Shifman, a professor of genetics at the Hebrew University of Jerusalem in Israel who was not involved in any of the studies.
Isoforms of the same gene can have different properties and interact with different protein partners, as previous research has shown.
“This tells us that what goes on in the cell is determined by isoforms, not genes,” says Lilia Iakoucheva, associate professor of psychiatry at the University of California at San Diego, who led the first study. “It goes without saying that we should look at the isoform-level data and not the gene-level data.”
TThousands of isoforms are expressed at different levels during brain development, Iakoucheva and her team found during an analysis with the online database BrainSpan. Many genes associated with autism have isoforms, the level of expression of which changes during the early development of the fetus, supporting the idea that this is a key period for autism.
Isoforms affected by autism-related loss of function mutations are typically involved in essential neural processes and tend to be expressed before birth, the study also showed. And these isoforms often carry “microexons”, small pieces of DNA in genes that are abnormally regulated in people with autism.
Isoforms with similar expression patterns in brain tissue tend to share similar functions, according to statistical analysis. Networks of isoforms involved in splicing and the function of neural connections have been enriched by loss of function mutations associated with autism.
Four genes linked to autism and other neurodevelopmental disorders, including DYRK1A and SCN2A, carry mutations with loss of function at the splice sites – where enzymes cut the RNA molecule that is made into proteins. Introducing mutations at the splice site in these genes in cells grown in a dish usually resulted in isoforms with altered biological properties, but in some cases the mutations were harmless.
Software analyzes typically classify mutations that affect splice sites as pathogenic, as they can lead to shortened proteins, for example. However, Iakoucheva’s results suggest that this is not always the case. The results appeared in Cell Reports in August.
“In some cases, these mutations do not result in the loss of all expression of the gene,” says Shifman. “If you want to understand the mechanism of disease, that is very important.”
The BrainSpan data that Iakoucheva’s study used was obtained using sequencing technology that reads several hundred base pairs at a time. Putting together long isoforms from such short reads can be challenging, and some isoforms may not assemble correctly, she warns.
Newer methods can sequence an entire transcript at once, says Jonathan Mill, professor of epigenetics at the University of Exeter in the UK who led the second study. “That means you can see the structure of this transcript and find out if there are any quirks in the sequence that could be interesting from a functional point of view,” he says.
Mill and his team used such “long-read” sequencing approaches to characterize RNA isoforms in samples from the fetal and adult human cortex – the outer layer of the brain. They identified transcripts that map to nearly 13,000 genes expressed in this region of the brain.
More than half of the genes, including some involved in some forms of autism, have more than one transcript isoform, the team found. For example, TCF4, a gene associated with an autism-associated syndrome, has 33 different isoforms that are expressed in the human cortex.
Almost 40 percent of the transcripts found, including some from genes associated with autism, had not previously been described. And nine autism genes, including FOXG1, have been involved in “fusion” events in which two adjacent genes are transcribed into a single RNA molecule. Fusion transcripts are a common type of mutation in several cancers.
The study, published in Cell Reports in November, provides a reference map of RNA isoforms expressed in the cerebral cortex throughout development, Mill says.
Looking at isoforms is “the future,” says Manuel Irimia, group leader at the Center for Genomic Regulation in Barcelona, Spain, who was not involved in either study. Although long-read sequencing can provide insight into the sequence and structure of RNA transcripts, there is room for improvement, says Irimia. Compared to short-read approaches, long-read sequencing results in fewer reads so that not all of the transcripts expressed in a cell may be recorded.
“In five years, long-read sequencing analyzes will certainly be much more accurate,” he says.
Mill started a larger study of brain samples from 50 people to identify the differences between people and understand how genetic variants affect alternative splicing. The researchers also plan to sequence RNA isoforms from individual populations of brain cells to profile gene expression patterns in different cell types.
“We are just beginning to use these technologies to characterize the complete heterogeneity of the expressed transcripts,” says Mill. Ultimately, he adds, the identification of specific isoforms that are deregulated in diseases such as autism could have therapeutic applications , as technologies already exist to correct splice defects using short RNA snippets.
Cite this article: https://doi.org/10.53053/ZLPB9063
