Super excited to share our latest #preprint on the TE classification/annotation and regulatory evolution from our lab @guilbourque at @Ashbi_KyotoU. Check it out here! 🧵. Cryptic endogenous retrovirus subfamilies in the primate lineage.

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RT @JakobssonLab: New preprint from our lab! Why is not everyone working on Transposons?. Loss of H3K9me3 maintenance in human neural proge….

RT @CellGenomics: Capturing cell-type-specific activities of cis-regulatory elements from peak-based single-cell ATAC-seq .

RT @Nature: Why don't humans have tails? . A genetics study finds that a mobile genetic sequence inserted into a gene for tail development….

RT @CellGenomics: Locus-level L1 DNA methylation profiling reveals the epigenetic and transcriptional interplay between L1s and their integ….

RT @wayomayo: Our paper on the ancestral genome-assisted TE annotation method/resource is out in @CellGenomics! Enhanced annotation is now….

RT @guilbourque: #Pangenome graphs improve the analysis of SVs for rare genetic diseases. Our new study is out! . Great collaboration with….

RT @lpachter: I've gotten several requests recently for permission to use the notes from my computational biology class: ..

RT @Ashbi_KyotoU: [News release] ASHBi researchers identify and selectively manipulate the neural circuits underlying the balance of risk v….

RT @CellGenomics: Genome-wide classification of epigenetic activity reveals regions of enriched heritability in immune-related traits https….

RT @AkankshaThawani: 🔥🔥How does the LINE-1 retrotransposon jump around in the human genome? Super excited to present my postdoctoral work….

RT @KathleenHBurns: Check out our latest review | LINE-1 retrotransposition and its deregulation in cancers: implications for therapeutic o….

RT @CedricFeschotte: “Transposable elements contribute to nearly 80% of human-specific candidate cis-regulatory elements in cortical cells”….

RT @xielablife: Very happy to share our new paper on how SOX2 instructs pluripotency program transition in vivo in mouse E3.5-E7.5 embryos.….

RT @CellGenomics: Multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci .

RT @CedricFeschotte: 💥 New preprint! Really excited about this work brilliantly led by Manu @manvendr7 & Sabrina Leddy in collab with @TheN….

In the end, we applied the approach to other simian-specific LTR subfamilies. Among 53 subfamilies analyzed, we corrected 30% instances from 26 subfamilies. We found that the phyletic groups we characterized were enriched for different epigenetic marks TFs and KRAB-ZNFs.

Focusing on the youngest phyletic group “MER11_G4”, we revealed the gain of SOX-related motif in this phyletic group was due to a single-nucleotide deletion and occurred in humans and chimpanzees but not in macaques. It also significantly increased their regulatory potential.

We further found that the phyletic groups are highly conserved in the primate lineage even though the instances spread independently.

Using lenti-MPRA, we validated the regulatory activity of phyletic groups and identified motifs at single-nucleotide resolution with a TE-wide motif association approach. The phyletic groups also have a higher TF motif enrichment compared to the original subfamily annotations.

We found a high epigenetic heterogeneity per subfamily which was well rearranged by the rooted tree and phyletic groups. And the reconstituted MER11 phyletic groups display a more consistent epigenetic profile compared to the original subfamily annotations.