Maja Kuzman
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majakuzman.bsky.social
Maja Kuzman
@majakuzman.bsky.social
110 followers 290 following 14 posts
computational biologist. all things genomic. working on cfDNA, cancer genomics, early detection, prenatal testing, epigenetics, transposable elements. building reproducible computational pipelines. seeking academic partners for collaboration.
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#DoOrDie #DNADamageResponse

Thats a cool story :

When a cells DNA is damaged, and needs a quick reaction, its actually the buildup of (errorenous) RNA that through ribosome confusion and bumping into each other actually signals the quick response for apoptosis. Makes a lot of sense.
RNA Is the Cell’s Emergency Alert System | Quanta Magazine
How does a cell know when it’s been damaged? A molecular alarm, set off by mutated RNA and colliding ribosomes, signals danger.
www.quantamagazine.org
#baseEditing #personalizedMedicine
#precisionGeneEditing

We are there!! 💛🧬

As of June, at least 20 clinical trials with base or prime editors are underway. The newer base and prime editing medicines modify or insert specific nucleotides into the DNA without creating double-stranded breaks.
Precision gene editing medicine makes history, and it’s just getting started - Nature Biotechnology
Despite their astounding success, custom-made base editors and prime editors will need time to broaden their clinical impact.
www.nature.com
Reposted by Maja Kuzman
we recently found some really neat RNA-guided DNA-cutting systems in phages. Despite remarkable similarities to CRISPR systems, including encoding guide RNAs in arrays, they appear entirely evolutionarily distinct (but definitely related to snoRNAs 🤓)
We decided to call them TIGR-Tas systems 🐯
#TransposableElements altho abundant in the human genome, are repressed by methylation and chromatin modifications.

Here authors show another mechanism of repression; hierarchical chromatin topology (TADs) - when disrupted they can lead to co-option of LTRs as alternative promotors of #oncogenes!
Disruption of TAD hierarchy promotes LTR co-option in cancer - Nature Genetics
NIPBL perturbation activates long terminal repeat (LTR)-derived alternative promoters due to reorganization of chromatin’s hierarchical structure, leading to LTR co-option and oncogene activation in m...
www.nature.com
LOVE to encounter a good review! Feels like reading what should become a textbook in comparative immunology!

Different organisms make intentional changes to their DNA, relying on similar mechanisms, function usually for immune defens or pathogenicity.

Thanks authors
@sebastianevda.bsky.social
How and when organisms edit their own genomes - Nature Genetics
This Review describes the changes that some organisms make to their own DNA sequences, linking many to common genetic mechanisms built around canonical DNA repair and to a set of functional circumstan...
www.nature.com
Another day, another wonder;

Archea parasite with a circular genome of only 238Kbp (!) found within a dinoflagellate.

It only encodes for replicative machinery: can replicate but not sustain itself, making that line between life and non-life blurry! What a life

www.biorxiv.org/content/10.1...
You do understand you might be my only follower, right? :))
Op op!

Google introduces AlphaGenome - their tool to predict effect of mutations, including gene expression, splicing patterns, chromatin accessability, 3d genome structure.

Also first model to predict splice junctions from sequence.

Lets see how it works!

#AlphaGenome #google #genomics
AlphaGenome: AI for better understanding the genome
Introducing a new, unifying DNA sequence model that advances regulatory variant-effect prediction and promises to shed new light on genome function — now available via API.
deepmind.google
Reposted by Maja Kuzman
One last thanks to the #TCTeAC organisers, especially @svobodalab.bsky.social‬. And shoutout to all whom I met throughout the killing game: @majakuzman.bsky.social for organising, @da-bar.bsky.social for bodyguarding, @valeriyk1.bsky.social for scouting, @itaiyanai.bsky.social for enabling, /1
Would you trust a single base edit to rewrite your future? :)

this could be a cool thing to follow up in few years.

Eli Lilly just spent a billion dollars for a single base editing drug that lowers LDL levels by 50% by silencing PCSK9 gene in the liver with a single-course therapy.
please add me as well!