Thread by @muju79

Ever wondered if and how #recombination of #retroelements contributes to #somatic #mosaicism? Read about it in our new pre-print:

Non-allelic homologous recombination of Alu and LINE-1 elements generates somatic complexity in human genomes. biorxiv.org/content/10.110…

1/ Background: pathogenic non-allelic homologous recombination (NAHR) of Alu and LINE-1 has been found in several genomic disorders and #cancer types. We thought this could be just the tip of the iceberg of a physiological recombinogenic activity of retroelements.

2/ The excellent Martin Frith developed a fresh pipeline to identify non-allelic homologous recombination (NAHR) in short and long-reads libraries: 🦖TE-reX🦖. It smartly focuses on split reads that join repeat elements at homologous positions.

3/ We optimized capture-seq of Alu and LINE-1 (you can now go from gDNA to sequencing-ready libraries in1⃣day!) and sequenced 5 tissues from 10 post-mortem donors: kidney, liver and 3 brain cortical regions -frontal/temporal/parietal- separated by FANS in NeuN-/NeuN+ fractions.

4/ TE-reX identified thousands of NAHR events in capture-seq libraries, confirming that NAHR is an extensive feature of normal genomes. The brain has less total NAHR events than other tissues but it is characterized by a very specific recombination signature...

5/ ...Compared to liver/kidney, the brain has:

✅ Higher rate of intra-chromosomal NAHR (figure below)
✅ Higher intra-chromosomal NAHR rate of proximal Alu and LINE-1...
✅ ...that is also strongly biased for repeats in inverted configuration

6/ We confirmed NAHR of Alu/LINE-1 in 3 ways:

➡️ PCR + Sanger sequencing of 100+ NAHR events
➡️ Capture-free Illumina libraries
➡️ Capture-free and PCR-free @nanopore libraries.

@nanopore data confirmed intra- and inter-chromosomal NAHR events spanning a wide range of sizes:

7/ We identified hundreds of retroelements acting as NAHR hotspots enriched in structural variants from the @1000genomes project, in COSMIC #cancer genes and in subtelomeres and peri-centromeres of several chromosomes.

Here's a cluster of very hot REs in subtelomere of chr4:

8/ We differentiated human iPSCs into neurons, performed Alu/LINE-1 capture-seq and found with TE-reX that ~50 days of differentiation are enough to trigger a neuron-specific intra-chromosomal NAHR profile. This indicates that somatic NAHR accompanies cell-fate determination.

9/ Finally, we applied our workflow to equal sample sets from donors with sporadic #Alzheimer's and #Parkinson's disease. Compared to control donors, we found altered intra-chromosomal NAHR profiles and a region-specific increase of NAHR in #Alzheimer's temporal cortex.

Big thanks to @carninci for supporting this project through the years, to Martin Frith for being a wonderful collaborator and for help shaping this work together and to all authors for their contribution!