Arttu Jolma
@ArttuJolma
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Research Associate in lab. of Tim Hughes. Studying transcription factor target specificities, gene regulation and RNA binding proteins.
Toronto, ON, Canada
Joined January 2018
(8/8) . @IvanDKoz, @nikitagryzunov, @VorontsovIE, @halfacrocodile, @legoushque, @AntoniGralak, @ZinkevichA, @JKribelbauer and see also
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(7/8) Kudos to the Codebook and GRECO-BIT consortium members including @BartDeplancke, @MakeevSeva, @EPD_SIB, @OFornes, @ImYellan, . .
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(6/8) 1,421 human TFs now have a characterized DNA-binding specificity, and nearly all 1,638 have been assayed. Analyses in indicate, however, that many previously characterized TF binding specificities may be inaccurate.
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(5/8) Collectively the uncharacterized TFs bind directly to tens of thousands of conserved sequences, providing biochemical functions for these sites. Intriguingly, many of these sites are in genomic “dark matter”. Explored further in
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(4/8) Methods for PWM discovery and benchmarking are explored in detail in an accompanying manuscript:
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(3/8) Of the 332 uncharacterized TFs, PWMs were identified for 177, the vast majority of which have unique and previously unseen motifs.
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(2/8) We applied five different assays to 332 uncharacterized TFs (i.e., Codebook TFs) and 61 control TFs, including a new assay, GHT-SELEX, described in:
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(1/8) Thrilled to reveal the results of the Codebook Project, an international effort to identify accurate DNA-binding motifs and genomic binding loci for the >300 uncharacterized human transcription factors (TFs)
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I was going to make a Tweetorial describing our new paper, but it looks like Hamed covered it already very well. Enjoy!.
Super excited to finally share the results of a massive effort with @ProfTimHughes to characterize the intrinsic sequence binding specificities of human transcription factors, led by @ArttuJolma, @ahcorcha, @AliFathi125, Ally Yang, and Kaitlin Laverty 1/n.
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Nice to see my new work getting some publicity, I'll try to get a Tweetorial done for this in the near future.
GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors (Jolma et al., 2024) .▶️TFs possess sufficient intrinsic specificity to independently delineate cellular targets
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RT @generegulation: Extensive binding of uncharacterized human transcription factors to genomic dark matter (Razavi et al., 2024) https://t….
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So here is a brand new study with my second author contribution. It is a cool story about how most of the RNA binding observed in mass spec studies for a large fraction of all proteins is in fact is nonspecific.
✨New paper alert✨. We assayed the binding specificities of 492 unconventional RBPs (ucRBPs) with RNAcompete and found that most bind non-specifically.
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Yey, our new paper is finally out! Congratulations Kaitlin and Sara!.
Check out our new RBP motif algorithm: .PRIESSTESS 🧙♀️.- fits RNA sequence and structure models .- is trivially interpretable.- generalizes as well or better as black-box models.
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RT @quaidmorris: Check out our new RBP motif algorithm: .PRIESSTESS 🧙♀️.- fits RNA sequence and structure models .- is trivially interpret….
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Yarr, congratulations to my boss!.
Congratulations to all @UofT faculty who won Canada Research Chairs but above all to our amazing Prof Tim Hughes!. The goal of his research is to be able to read the genome the way cells do. Find out more:. @CRC_CRC @uoftmedicine
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Tsirpy, tsirp!.(that is what Finnish birds say when publishing an article).
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My ex-boss Jussi Taipale and and another Swedish Professor Sten Linnarson are proposing a very sensible strategy for combatting Covid-19. We should make testing a massively parallel high throughput process and perform it repeatedly on the scale of whole population.
”To stop COVID-19, test everyone, repeatedly.” Me and Jussi Taipale propose a simple strategy to defeat coronavirus, and pose a challenge to the scientific community.
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RT @Gene_Regulation: Strong binding activity of few transcription factors is a major determinant of open chromatin .
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Yey! Katja's paper just came out in eLife (-: .(I'm there also, deep in the author ranks).It's a cool story about the mechanism that a transcription factor (HOXB13) uses to recognise two kinds of distinctly different binding sites CTCGTAAA and CCAATAAA.
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