Happy to share our preprint showing how transposons/mobile elements (MEs) make us who we are. Highlights:.🧬A LINE-1 insertion causes increased keloid risk.🧬ME variants coherently regulate gene expression.🧬Population-specific patterns of Alu insertion.

I hope I’ll have time to make a thread about the merits of this work soon. But for now, @Faulkner_Lab's criticism highlights that there is much work to be done to bring the field of mobile DNA into the bright light of rigorous statistical genetics.

We needed to catalog hundreds of MEVs that strongly associate with differential expression of nearby genes to demonstrate this point.

"L1 often acts as an enhancer" as we show in the eQTL section. I agree, this point has not been convincingly argued in the literature previously, due at least in part to the limitations of prior tools for genotyping MEVs.

and where they insert in germlines before selection (as far as we can tell using population sequencing, rather than sequencing individual gametes). Our work addresses this last point, and it's where we saw some of the biggest surprises (e.g. population differences).

There are many ways to look at distributions of mobile element insertions. There may be differences in where we observe mobile elements to be enriched in reference genomes (a product of evolution), where they insert experimentally in cultured cells,.

The point of our PCR validation was to test genotyping accuracy, so we only used MEVs for which PCR gave credible genotypes. You’re most familiar with PCR being used to ask if an MEV is real or not AT ALL, in which case it doesn’t make sense to drop the ones that don’t PCR well.

In contrast to false positive rate, Mendelian error rate compares MEGAnE’s MEV calls in parents to MEGAnE’s calls in their children. There’s a reason raw Mendelian error rates are not published as claims of de novo ME insertion rates; it’s not fair to conflate these two.

Thanks for reading the paper!.Calculating the false positive rate involves comparing MEGAnE MEV calls to gold-standard calls generated using multiple technologies. No need to wonder if the rate is higher than 3% based on these other analyses. It’s a calculation, not rhetoric.

Incredible #scicomm by super-postdoc @ShoheiKojima and colleagues in collaboration with @mextjapan. Huge honor for him to represent @RIKEN_JP and @RIKEN_IMS and the SPDR program (, not to mention my team, in this way!.

RT @RIKEN_IMS: 本日4月11日（火）理化学研究所が企画した文部科学省の学習資料「一家に一枚　ウイルス」の特設サイト、PR動画、解説動画が公開！.

This is the result of collaboration between many groups at @RIKEN_JP @riken_en @RIKEN_IMS @RIKEN_CPR. I would sincerely appreciate critical feedback on this work; please DM or email me if you have any!.

These findings were enabled by a new tool for accurate ME discovery/genotyping using short-read data. Before now, statistical genetics approaches have been limited to common variants already sequence-resolved by long-reads. Get MEGAnE (👓) here:

RT @sasaki_kotaro: Our paper is finally out at biorxiv. Hominoid-specific endogenous retrovirus in human primordial germ cell-like cells.….

RT @jampei2: 研究成果をbioRxivに公開しました. ゲノム中には古代のウイルス感染によって生じた内在性レトロウイルス(ERV)が多数存在します. 本研究では, 類人猿に特異的に挿入されたERVがエンハンサーとして働き, 生殖細胞の遺伝子発現制御において重要な役割….

RT @SystemsVirology: Our new study "A hominoid-specific endogenous retrovirus has rewired the gene regulatory network shared between primor….

RT @J_191206: Thank you for sharing your exciting research at the EVE study club!. This study club is cohosted by @Masayuki_Horie and @nick….

RT @SalehLabParis: Happy to finish 2020 with the publication of our discovery of transgenerational antiviral immunity in drosophila and mos….

RT @WilenLab: We havent forgotten our other favorite virus: #norovirus. We asked what cell types were murine norovirus infected. We deleted….

RT @J_191206: Our latest work, “One hundred million years history of bornavirus infections hidden in vertebrate genomes”, is out in @biorxi….