igorulitsky.bsky.social
Associate Professor, Weizmann Institute of Science. RNA biologist, interested in what (long) RNA molecules do and how. Father of 4.
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אני בגדול נמנע מזה מאז בערך ינואר 2024. עדיף להפריד
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Most importantly, we now have a new route for how ASOs, that are traditionally used for down-regulation of transcription, can be in some instances used for effective up-regulation. Which is something to be excited about (rather than doom scrolling!).
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In a mouse model of CHD2 haploinsufficiency we show that ASO1 administration increases CHD2 expression and alleviates phenotypes of CHD2 haploinsufficiency. Lastly, we show that the concept of fusion transcript induction can be translated to other genes, and we are hard at work on other genes.
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We describe a new mouse model where we deleted the conserved sites and that has constitutive fusion transcript production, which we link to differential gene regulation in neurons.
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and identify additional ASOs, trans-acting factors, and NMD, that can all be targeted and lead to more fusion transcript formation, suggesting this is a tightly regulated event.
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This fusion transcript still has the full CHD2 ORF, so can produce full-length protein, but CHASERR substitutes most of the CHD2 5'UTR (=different translational control). We provide a lot of data to show this transcript is indeed exported and translated
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Scrutinizing RNA-seq data, we found that while in regular conditions CHASERR and CHD2 are separate transcripts, when CHASERR-targeting ASOs are used, a "fusion" transcript containing the beginning of CHASERR followed by most of CHD2 sequence emerges.
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But what do these motifs do? We spent a couple of years testing the hypothesis that these form part of an elusive "active site" of CHASERR, which helps it to repress CHD2, possibly via RNA-RNA interactions. Turns out that is not the case!
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Caro showed that antisense oligos (ASOs) blocking these highly conserved sites led to increase in CHD2 expression. This is exciting as CHD2+/- individuals have epilepsy and ASD, so there is interest in clinically-relevant ways to up-regulate CHD2 levels in the brain.
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In the beginning of her postdoc, Caro developed lncLOOM, a computational tool for discovering short conserved elements in lncRNAs, which led to the discovery of short "RRAUGG" conserved motifs in the last exon of CHASERR
link.springer.com/article/10.1...
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As with all lncRNAs we care about, we were most strongly interested in a) How it works? b) Can we somehow adapt it for therapeutic use? The new paper is the culmination of our efforts on both fronts.
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We initially studied Chaserr in mouse, but @vijayganesh.bsky.social and a broad team of collaborators reported recently in @nejm.org
that CHASERR deletion in humans leads to a syndromic neurodevelopmental disorder, the first involving a lncRNA fragment deletion
www.nejm.org/doi/full/10....
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We love all lncRNAs, but more so the highly conserved ones. These are rare gems, and CHASERR is a shiny gem found in all vertebrate species. We found it is essential for viability and it represses CHD2, a gene found immediately downstream of it.
www.nature.com/articles/s41...
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First, it's a collaboration between Caro, a star postdoc now faculty at Cape Town, Yael, a PhD student and mouse neuro aficionado, and research scientist Yoav, with
the lab of Moran Rubinstein at Tel Aviv, who taught us everything we know about modeling CHD2 haploinsufficiency.
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Congrats Daniel!!
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This is aweful
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Last year, it turned out that @mendell-lab.bsky.social lab also stumbled upon this lncRNA/snoRNA (NORAD deja vu!). While both of us converge on roles in nucleolar biology, there are differences, possibly due to the very different sets of systems/assays. www.cell.com/cell/fulltex... 11/fin
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TIGA1 is likely produced only by a minor isoform of the lncRNA as it starts upstream of the major transcription start site. As usual, while this is possibly the most data-rich manuscript we ever had, there is much remaining to be explored! 10/n
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In any case, there are at least 4 separate functional elements within 1 gene - a snoRNA, a cis-acting positive transcriptional regulator, a trans-acting nucleolar regulator. And and a small protein, TIGA1, previously described. 9/n
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and the effects we are observing result from the action of the lncRNA rather than the snoRNA (function of a nascent snoRNA is also possible). 8/n
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The snoRNA itself, however, is not sufficient to rescue the phenotypes we are observing, and fittingly, its expression is not affected by the transient EPB41L4A-AS1 perturbations, so we believe the snoRNA is required for proper processing/localization of EPB41L4A-AS1 7/n
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We identify SUB1, an abundant nuclear single-strand binding protein, as a major binding partner of EPB41L4A-AS1, whose perturbation mimics EPB41L4A-AS1 loss. This loss can be rescued by exogenous EPB41L4A-AS1 expression, but only in an intact form, including the snoRNA. 6/n
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By RNA-seq Alan found many genes dysregulated by EPB41L4A-AS1 KD, enriched in nucleolar biology. He also found that snoRNAs are up-regulated when EPB41L4A-AS1 is perturbed. This is accompanied by additional changes such as the distribution of proteins within the nucleus. 5/n
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It sits at a TAD boundary, and KD, using different methods, disrupts transcription across the EPB41L4A while reducing some (but not all) other genes in the two broad TADs that flank it, including NREP. It does not seem to affect nearby CTCF cluster. But that's not all it does! 4/
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We can across the breezily pronounceably EPB41L4A-AS1 as part of a screen Alan did for lncRNAs that are correlated in expression and regulation with adjacent genes. Indeed, our first finding is that these lncRNAs act in cis to promote the expression of EPB41L4A. 3/n
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snoRNA host genes are really cool genes - they are very highly and typically broadly transcribed, so there are evolutionary reasons for them to acquire functions beyond just hosting snoRNAs. www.cell.com/trends/genet... 2/n