Nature Genetics: Insertion and deletion accumulate over the regulatory regions of neurons, year by year

Research teams led by institutions such as Harvard Medical School and Boston Children's Hospital recently adopted a new single-cell DNA sequencing method and found that human neurons accumulate relatively low-frequency indels year by year, which seems to be particularly common
in regulatory elements.

The findings were published in the journal Nature Genetics on
September 26.

Accurately detecting somatic mutations through single-cell DNA sequencing is challenging because expansion creates some illusions
.

In this study, the researchers first compared single-cell genome sequences produced by two amplification methods: MDA (Multiple Reset Swap Amplification) and PTA
.

"Our study establishes a new method for somatic mutation detection for single-cell DNA sequencing of PTA-amplified whole genomes," the authors write, noting that "our method analyzes genomes with low mutation load and cases where
multiple cells do not have common somatic mutations.

With this approach, the researchers started with 52 PFC neurons from more than a dozen individuals and generated new genomic sequence data with an average sequencing depth of 30 to 60 times
.

The researchers explain that single nucleotide variants (SNVs) accumulate more slowly
than small indels.

Even so, the single-cell sequence data showed a large number of insertion deletions in the regulatory region of the neuron being analyzed, prompting the research team to examine the gene expression consequences
of this regulatory change.

"Our catalog confirms previously discovered age-related SNV signatures and shows that somatic mutations (specifically insertions and deletions) are enriched in transcriptional genes and brain-specific regulatory elements," the researchers wrote, noting that "this enrichment suggests that somatic cell insertions may interfere with neuronal regulatory programs.

On a larger level, the authors believe that this strategy of increasing PTA amplification to increase single-cell DNA sequencing promises to advance broader research, including somatic mutation analysis of neurons in patients with neurodegenerative diseases, characterization of mutations caused by mutagenic compound exposure, and determination of the efficiency and accuracy
of CRISPR editing at the single-cell level.

Source text search

Luquette, L.
J.
, Miller, M.
B.
, Zhou, Z.
et al.
Single-cell genome sequencing of human neurons identifies somatic point mutation and indel enrichment in regulatory elements.
Nat Genet (2022).
https://doi.
org/10.
1038/s41588-022-01180-2