Other errors in genome accompany copy number variation

Such changes are known as copy number variation (CNV) referring to the numbers of copies of a gene. Instead of ‘letters of the DNA alphabet’ being changed or missing, whole sentences, entire paragraphs or even pages/volumes of the encyclopedia of human biological life can be altered.

Now researchers at Baylor College of Medicine say, in a report that appears online in the journal Nature Genetics, that the entire process may be error-prone, generating other, smaller mistakes in the genome. Their studies show that at least in the area near the duplication, small insertions and deletions of the genetic material DNA are common along with single point mutations (single changes in one of the nucleotides that are building blocks of DNA). The mutation rate of those was approximately 10,000 to 100,000-fold greater than for spontaneous mutations generated during formation of human sperm and egg.

Goldilocks genes

The MECP2 gene is one of those Goldilocks genes. The cell tolerates only the right amount of protein associated with it. Boys with MeCP2 duplication syndrome have one of those major duplications, which leaves them with too many copies of the gene MECP2 and, thus, too much of the associated protein. They suffer moderate to severe intellectual disability, weak muscle tone in infancy, feeding difficulties and other problems are common. There is also some individual variability in the expression of their clinical phenotype or symptoms that might be explained by genetic modifiers yet to be found in the genome.

Girls who have mutations that result in too little of the protein associated with the gene have Rett syndrome, a devastating neurological disorder that begins when they are six to 18 months of age, leading to cognitive problems, gait disruption, inability to speak and symptoms of autism.

“Finding the extra errors in the genome was a surprise to us,” said Dr. Claudia M.B. Carvalho, a first author of the report, and an adjunct faculty member at BCM who did her post-doctoral fellowship in the laboratory of Dr. James Lupski, vice chair of the department of molecular & human genetics at BCM. Lupski is corresponding author and holds the Cullen Foundation Endowed Chair in Molecular Genetics.

Breakpoint junction

Carvalho and her colleagues studied 31 unrelated boys who had MECP2 duplication syndrome, looking specifically at 67 breakpoint junctions of the copy number gains. The breakpoint junction is that point where the duplicated genes join in the chromosome.

Usually, the large duplications of genomic material are identified using a so-called gene chip or array, but they do not find these smaller genetic differences. Carvalho and her colleagues only uncovered these by painstaking gene sequencing of the area near the breakpoint junction. In other words, two different methods were critical to identifying the two kinds of changes.

“That means that the mechanism (for DNA replication during cell division) that generates this is error prone,” said Carvalho. The consequence might mean that genes near the breakpoint could be altered by one of these small deletions, insertions or mutations. Because there are several genetic syndromes caused by CNVs spanning different regions of the genome, those findings have implications for the mechanism for formation of other diseases as well.

“Can they be altered without being in the rearrangement?” she said. “This needs to be studied further.”

The changes may be even bigger than her studies show, occurring in parts farther away from the breakpoint, she said.

New mutations

In about 20 percent of the patients they studied, the changes occurred first in the child being sequenced. In the language of genetics, they are de novo or represent new mutations.

“I would like to sequence the whole chromosome arm involved in the arrangement in these patients to see the extent of those mutations,” said Carvalho. “Can we see point mutations and small short deletions or insertions up to the telomere (the ends of the chromosome that important to keeping its integrity and allow the cell to divide). Then I want to go back and check whether the individual clinical phenotype (the symptoms of the boys with the disorder) can be explained by additional mutations (besides the large rearrangement) in the patient’s genome.”

Lupski said, “This is a very important advance in CNV (copy number variation) mutagenesis.” Such work has implications for disease and for understanding evolution.

Others who took part in this work include: Davut Pehlivan, Melissa B. Ramocki, Ping Fang, Benjamin Alleva, Luis M Franco, John W Belmont, P. J. Hastings and Lupski, all of BCM. Ramocki is also with the Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital (www.nri.texaschildrens.org). Alleva was an undergraduate student mentored by Carvalho and is now at Cornell College in Mount Vernon, Iowa.

This work was supported in part by the National Institute of Neurological Disorders and Stroke (NINDS) grants R01 NS058529 to J.R.L. and 5K08NS062711. Carvalho is also a Young Investigator from the Science without Borders Program from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) in Brazil.

Baylor College of Medicine