Zeshi Li (Jack)
@lizeshi.bsky.social
Assistant Professor, Chemical Biology and Drug Discovery, Utrecht U. PhD G.-J.Boons Lab; Post-doc C.Joo Lab TUDelft. https://www.uu.nl/medewerkers/ZLi2
There is an interesting read here (posted shortly after the very first preprint): doi.org/10.1242/prel...
April 1, 2025 at 9:49 PM
There is an interesting read here (posted shortly after the very first preprint): doi.org/10.1242/prel...
Hi Dr. Erasmus, here is an updated version: www.biorxiv.org/content/10.1...
RNA-Associated Glycoconjugates Highlight Potential Ambiguities in glycoRNA Analysis
A recent ground-breaking study suggested that small RNA from mammalian cells can undergo N-glycan modifications (termed glycoRNA) 1. The discovery relied upon a metabolic glycan labeling strategy in c...
www.biorxiv.org
March 28, 2025 at 2:57 PM
Hi Dr. Erasmus, here is an updated version: www.biorxiv.org/content/10.1...
An independent study from @nathanaelbkegel.bsky.social et al. has led to alike conclusions. The common RNA prep may not give you the RNA as pure as you think. The results also call for the development of glycoRNA-specific labeling methods… A dual labeling?
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Proteins are a source of glycans found in preparations of glycoRNA
Recent discoveries show that RNA can be modified with sialylated glycans (termed glycoRNA), thus broadening our understanding of cellular glycosylation beyond traditional proteins and lipids. However,...
www.biorxiv.org
March 28, 2025 at 2:33 PM
An independent study from @nathanaelbkegel.bsky.social et al. has led to alike conclusions. The common RNA prep may not give you the RNA as pure as you think. The results also call for the development of glycoRNA-specific labeling methods… A dual labeling?
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Suppose you are ready to load the glycan-labeled glycoRNA samples into gels. Get half of it, mix with RNases/nucleases, incubate, add sample loading buffer, denature, DIRECTLY load the mixture into gel. Do the rest the same as reported. GlycoRNA gets degraded, the N-glycoconjugate remains intact.
March 28, 2025 at 2:33 PM
Suppose you are ready to load the glycan-labeled glycoRNA samples into gels. Get half of it, mix with RNases/nucleases, incubate, add sample loading buffer, denature, DIRECTLY load the mixture into gel. Do the rest the same as reported. GlycoRNA gets degraded, the N-glycoconjugate remains intact.
We hope this serves as a heads-up for the community, and propose a simple checkpoint experiment for whichever protocol you are employing👇
March 28, 2025 at 2:33 PM
We hope this serves as a heads-up for the community, and propose a simple checkpoint experiment for whichever protocol you are employing👇
The non-RNA N-glycoconjugate, is an independent, separate, but potentially co-existing molecular entity in glycoRNA preparations. It even exhibits an apparent RNase sensitivity related to purification methods, but not digestion.
March 28, 2025 at 2:33 PM
The non-RNA N-glycoconjugate, is an independent, separate, but potentially co-existing molecular entity in glycoRNA preparations. It even exhibits an apparent RNase sensitivity related to purification methods, but not digestion.
6. KIR2DL5 does directly bind to RNA. Food for thought: what are other classical membrane glycoproteins that can directly bind to RNA as non-canonical RBPs?
March 24, 2025 at 3:18 PM
6. KIR2DL5 does directly bind to RNA. Food for thought: what are other classical membrane glycoproteins that can directly bind to RNA as non-canonical RBPs?
4. SCOOPS validated HS is essential for hepRNA presentation on cell surface in an orthogonal fashion to the originally described TLR7 probe.
5. SCOOPS enabled unveiling hepRNA identities: high-confidence candidates include mRNA, lncRNA (Huang 2020) and snoRNA.
5. SCOOPS enabled unveiling hepRNA identities: high-confidence candidates include mRNA, lncRNA (Huang 2020) and snoRNA.
March 24, 2025 at 3:18 PM
4. SCOOPS validated HS is essential for hepRNA presentation on cell surface in an orthogonal fashion to the originally described TLR7 probe.
5. SCOOPS enabled unveiling hepRNA identities: high-confidence candidates include mRNA, lncRNA (Huang 2020) and snoRNA.
5. SCOOPS enabled unveiling hepRNA identities: high-confidence candidates include mRNA, lncRNA (Huang 2020) and snoRNA.
3. Exploiting the new chemistry, we establish spatial-selective crosslinking followed by orthogonal organic phase separation (Queiroz 2019), or SCOOPS🍨 to isolate these cell-surface RNA-protein crosslink products for biochemical analysis.
March 24, 2025 at 3:18 PM
3. Exploiting the new chemistry, we establish spatial-selective crosslinking followed by orthogonal organic phase separation (Queiroz 2019), or SCOOPS🍨 to isolate these cell-surface RNA-protein crosslink products for biochemical analysis.
New to this version:
1. A hepRNA-RBP-HS ternary complex model is proposed and validated.
2. A key enabling technique is based on an unexpected finding that photosensitized singlet oxygen can crosslink RNA to RBP.
1. A hepRNA-RBP-HS ternary complex model is proposed and validated.
2. A key enabling technique is based on an unexpected finding that photosensitized singlet oxygen can crosslink RNA to RBP.
March 24, 2025 at 3:18 PM
New to this version:
1. A hepRNA-RBP-HS ternary complex model is proposed and validated.
2. A key enabling technique is based on an unexpected finding that photosensitized singlet oxygen can crosslink RNA to RBP.
1. A hepRNA-RBP-HS ternary complex model is proposed and validated.
2. A key enabling technique is based on an unexpected finding that photosensitized singlet oxygen can crosslink RNA to RBP.
Candidate list kept updating. But if we piece things together, also taking the recent preprint into account, what get pulled down may include: 1. Non-specifically bead-associated RNA; 2. RNA associated with denatured glycoproteins; 3. Real glycoRNA. Complicated. How big is each part in the pool…
March 22, 2025 at 7:58 PM
Candidate list kept updating. But if we piece things together, also taking the recent preprint into account, what get pulled down may include: 1. Non-specifically bead-associated RNA; 2. RNA associated with denatured glycoproteins; 3. Real glycoRNA. Complicated. How big is each part in the pool…