Many repetitive regions of the genome have been considered “junk DNA” because the available technologies did not allow them to be studied with sufficient resolution. Now, new evidence suggests that some of these segments, such as the SST1/NBL2 macrosatellites, could have a more complex and determinative biological role than previously thought in nucleus organization, genome regulation, chromosomal vulnerability, and even cancer. This is according to an article published in the journal Trends in Genetics, led by researchers Sonia V. Forcales, from the Faculty of Medicine and Health Sciences of the UB and IDIBELL, and Gabrijela Dumbović, from Goethe University (Germany).
The new research, published in the journal’s Forum section, integrates evidence accumulated over the years with the most recent advances in structural genomics on these rather unknown components of the human genome. As SST1/NBL2 are primate-specific sequences, the work may also contribute to solving questions of evolutionary interest about the biological function of the repeating genome in humans and other primates.
Repetitive and altered regions in human tumours
SST1/NBL2 satellites have been associated with cancer, especially through epigenetic and transcriptional alterations. They are located mainly in acrocentric chromosomes (those with arms of different lengths) and are a very valuable model “because they concentrate many of the extreme characteristics of the human repetitive genome: they are large sequences repeated in tandem, with a high structural complexity, dynamic epigenetic regulation and production of non-coding RNAs”, explains Sonia V. Forcales, from the Department of Pathology and Experimental Therapeutics of the UB and researcher in the Immunity, inflammation and cancer group of IDIBELL.
In cancer, these repetitive regions of the genome are frequently demethylated – without methyl chemical groups – one of the most frequent epigenetic alterations in human tumours. The team has contributed to characterising epigenetic dysregulation in these macrosatellites and to describing a type of non-coding RNA (TNBL, derived from NBL2 regions frequently poorly methylated in tumours). This transcript can interact with factors involved in splicing, response to genomic damage, and nucleolar function.
“This suggests possible connections between the repeating genome and functional molecular processes in tumor biology. However, we still do not know to what extent SST1/NBL2 sequences participate directly in these processes or what the exact mechanism involved is,” says the researcher from the UB and IDIBELL.
Recent studies have also placed regions containing SST1/NBL2 among the points in the genome involved in Robertsonian translocations, i.e., the most common chromosomal rearrangements in humans. When these rearrangements involve chromosome 21, they can result in a form of trisomy 21, which is responsible for a minority of cases of Down syndrome. “These data do not indicate that SST1/NBL2 is the sole cause, but they do reinforce the idea that these regions could contribute to the structural vulnerability of acrocentric chromosomes,” says Dr. Forcales.
Other human diseases have also been linked to macrosatellite families and repetitive sequences of the genome, considered “junk DNA.” For example, the macrosatellite D4Z4 is involved in facioscapulohumeral muscular dystrophy, and alterations in the methylation of repetitive regions such as SST1/NBL2 and D4Z4 have been described in ICF syndrome, a rare disease associated with immunodeficiency, chromosomal instability and facial abnormalities.
A revolution in the study of the human repetitive genome
Current techniques make it possible to study these “junk” regions of the genome, which until now had been considered irrelevant simply because the tools to analyse their biological complexity weren’t available. “The great challenge is no longer just to completely sequence the human genome, but to understand the function of the repetitive regions that for decades were left out of the focus of genomics,” says Sonia V. Forcales.
Long-read sequencing technologies – such as Oxford Nanopore and PacBio – and the new telomere-to-telomere (T2T) assemblies of the human genome are what have revolutionized the ability to reconstruct regions such as SST1/NBL2, which until now were absent, fragmented or poorly represented with more conventional technologies. At the same time, traditional techniques – RNA-FISH, DNA-FISH, RNA pull-down or Northern blot – have been key to studying their nuclear location, the expression of RNAs derived from these sequences and their molecular interactions.
This new level of resolution is already completely transforming the way we can study the human repetitive genome. For example, they will make it possible to study the variability between individuals, between tumours, their epigenetic marks and the RNAs derived from SST1/NBL2 in a more reliable way, the authors point out.
In the future, the team wants to characterize possible variants of these RNAs, as well as their regulation and epigenetic modifications. The aim is to determine whether these RNAs have a functional role in tumour processes, and are not just a consequence of epigenetic dysregulation of cancer.
“We are still in a basic research phase, but if we confirm that these RNAs contribute functionally to tumour processes, future avenues could be opened to explore their role as biomarkers or therapeutic vulnerabilities,” concludes the researcher.