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Liana Merk

@bacteriyay.bsky.social

127 followers 139 following 10 posts

PhD student in Sean Eddy’s lab! I like introns, phages, fermentation, and stamps.

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Liana Merk @bacteriyay.bsky.social · 24/05/2025

(6/7) We highlight a few stories: evidence for retroposition into phage-specific loci, unique CapR domains not reported in group II intron-encoded homing endonucleases, and the presence of a group II intron in an annotated Inovirus, the first group II intron noted in a single stranded DNA organism.

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Liana Merk @bacteriyay.bsky.social · 24/05/2025

(5/7) We use three lines of evidence along with Infernal hits. (1) The presence of full-length intronless homologs of genes the group II’s are inserted in. (2) Identification of pseudoknotted tertiary base-pairing not modeled by Infernal. (3) Similarity of intron-encoded ORFs to known group II ORFs.

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Liana Merk @bacteriyay.bsky.social · 24/05/2025

(4/7) Recent accelerations in Infernal, a profile SCFG-based search and alignment tool from our lab, allow us to find these large RNAs across large genomic and metagenomic datasets.

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Liana Merk @bacteriyay.bsky.social · 24/05/2025

(3/7) We wondered if they haven’t been widely identified in phage because they are challenging to find — they have low primary sequence similarity. Luckily, their splicing mechanism dictates strong conservation in parts of their secondary structure.

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Liana Merk @bacteriyay.bsky.social · 24/05/2025

(2/7) Group II introns are self-splicing RNAs and the speculative ancestor of our own nuclear spliceosomal introns. They are widely known in bacterial, archaeal, and eukaryotic orgenallar genomes, but considered absent in phage.

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