Skip to main content
Premium Trial:

Request an Annual Quote

Sequencing Implies Compound Heterozygous Splicing Gene Mutations in Rare Developmental Condition

NEW YORK (GenomeWeb) – A rare congenital condition called Roifman syndrome can be caused by variants affecting the activity of the transcript splicing gene RNU4ATAC, according to a Nature Communications study published this week.

An international team led by investigators at the University of Toronto performed genome sequencing on two siblings with Roifman syndrome, uncovering distinct single nucleotide changes affecting each copy of the small nuclear RNA gene RNU4ATAC, which codes for a minor spliceosome component that has a role in minor intron splicing. Similar compound heterozygous mutations in RNU4ATAC turned up when the team sequenced the gene in four children from three more families affected by Roifman syndrome.

With the help of RNA sequencing, the researchers found that the Roifman syndrome-associated alterations in RNU4ATAC shift the way that minor introns are spliced. Rare mutations in the same gene were previously implicated in a distinct growth condition known as microcephalic osteodysplastic primordial dwarfism, type 1 (MOPD1), they noted, hinting at the variable conditions that can arise from such splicing changes.

"Roifman syndrome is phenotypically distinct from MOPD1 and presents a unique pattern of compound heterozygosity," senior author Stephen Scherer, a genetics and genome biology researcher affiliated with the University of Toronto and the King Abdulaziz University in Saudi Arabia, and his co-authors wrote.

"While Roifman syndrome and MOPD1 are extremely rare, recurrent spontaneous abortions or congenital disorders with a broader phenotypic spectrum may be caused by homozygous or compound heterozygous variants altering any of the RNU4ATAC structural elements critical for splicing," they explained, "with an estimated prevalence up to one in 30,000 pregnancies."

Roifman syndrome is a rare condition characterized by developmental and other symptoms — from cognitive and growth delay to skeletal abnormalities, immune problems, wide set eyes, an upturned nose, and other dysmorphic facial features. Based on some of the physical features found in those with the condition, some suspected that Roifman syndrome might stem from mutations affecting the cells' cilia.

In their new search for a Roifman syndrome culprit, Scherer and his colleagues had the company Complete Genomics generate whole-genome sequences for two brothers with Roifman syndrome.

The team's analysis of these sequences did not uncover suspicious X-linked or autosomal homozygous mutations. But it did see heterozygous substitutions in structural regions of RNU4ATAC.

When they sequenced the gene in four children with Roifman syndrome from three more families, the researchers again found compound heterozygous mutations clustering in similar parts of the gene. On the other hand, homozygous or compound heterozygous glitches in the gene did not turn up when they considered genome sequences from hundreds of unaffected individuals.

The team then delved into the transcriptional consequences of the RNU4ATAC variants, using the Illumina HiSeq 2500 instrument to sequence mononuclear blood RNA from two individuals with Roifman syndrome and three members of their family who do not have the disease.

As anticipated from RNU4ATAC's role in minor intron splicing, the affected children's RNA more often retained minor introns, showing a slight uptick in expression of genes containing minor introns.

The expression change "is expected to successfully compensate the increased minor intron retention only for a minority of the genes," the study's authors noted. "This suggests a compensatory transcriptional up-regulation of minor intron genes, which however is not fully successful at restoring optimal levels of correctly spliced transcripts."

Such hiccups may explain some of the features found in individuals with Roifman syndrome and other conditions marked by RNU4ATAC mutations, they explained, since minor intron-containing genes contribute to a broad swath of skeletal, developmental, cognitive, and other processes.