@qichen_lab
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Associate Professor @UUtah @UofUMedicine | sperm RNA-mediated epigenetic inheritance, embryo development, small RNAs, RNA modifications & diseases
Salt Lake City, UT
Joined November 2015
- Tweets1.5K
- Following848
- Followers1.6K
- Likes11.8K
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Perhaps our boldest hypothesis… we propose a model for RNA Structural Memory propagation @NatureCellBio, where RNA conformation is reshaped by stress, locked by RBPs, copied prion-like in condensates & passed across generations—all without altering DNA.🧵
rdcu.be/eBwPJ
A tRNA or rRNA can be cut in different places and produce fragments with different meanings. Abundance analysis is blind to that map.
We @tongzhoulab call the map the 'RNA fragmentome'.
qMAP reads it in iPSC reprogramming, ulcerative colitis, implantation failure, and sperm aging.
RNA sequencing can reveal more than RNA abundance. qMAP analyzes RNA fragmentation patterns that may uncover regulatory changes linked to development, disease, reproduction, and aging. - @unevadareno - @unrmed rna-seqblog.com/qmap-reveals…
Qi Chen retweeted
A single tRNA or rRNA can be cleaved at different sites, generating small RNAs with distinct functions depending on where the cuts are made. That fragmentation pattern is itself a regulatory layer beyond abundance — the "RNA fragmentome".
With @tongzhoulab, we built qMAP, a tool to read this hidden information across development, disease & aging — for both mechanistic discovery and translational applications.
Qi Chen retweeted
After years of crystallization, now in @NatureBiotech, @ZernickaGoetz and I discuss the evolutionary origins of multicellularity and how physical constraints inevitably drive cellular self-organization.
Harnessing these rules may help us better understand and engineer life – Build to understand. rdcu.be/flTKa
Qi Chen retweeted
Perhaps the most puzzling part:
We see a paradox: the rsRNA length shift is progressive⏳yet the global RNA profile shows an "Aging Cliff"📉.
Cliff or Progression? Maybe the gradual shift is the forerunner—accumulating silently until it triggers the cliff.
nitter.cf/qichen_lab/status/2013…
1/5 It took us some time to connect the dots...now in @embojournal we use PANDORA-seq to start decoding the 'sperm RNA code of aging'
We find a conserved rsRNA length shift that reflects aging in both mouse & human sperm, and an 'aging cliff' at mid-life🧵
link.springer.com/article/10…
Qi Chen retweeted
1/5 It took us some time to connect the dots...now in @embojournal we use PANDORA-seq to start decoding the 'sperm RNA code of aging'
We find a conserved rsRNA length shift that reflects aging in both mouse & human sperm, and an 'aging cliff' at mid-life🧵
link.springer.com/article/10…
Qi Chen retweeted
RNA Day Special: With Ru-Juan Liu’s lab & @IliasSkeparnias @NasosSh, we review in @NatRevMCB how structurally degenerate mitochondrial #tRNAs drove evolutionary adaptations in their biogenesis machinery, modifications and mitoribosomes— and how this unique biology shapes disease.
Adding to the intriguing story of Vault structures & their component Vault RNAs, we highlighted that Vault RNA-derived small RNAs (vtsRNAs) also bear biological functions: nature.com/articles/s41556-0…
It's Fascinating to see how nature always repurposes molecules for new functions! ♾
Leonard Rome’s lab discovered an odd, abundant component of cells in the 1980s—and he’s still trying to figure out what it does.
Learn more: scim.ag/3Tczhok #ScienceMagArchives
ALT Graphic of the structure of cell vaults.
Qi Chen retweeted
Our toolchain developed over the years to explore the expanding small RNA universe:
PANDORA-seq (see the once invisible)
nature.com/articles/s41556-0…
nature.com/articles/s41596-0…
SPORTS (comprehensive annotation)
sciencedirect.com/science/ar…
FUSION (robust comparison)
academic.oup.com/bioinformat…
qMAP (read the fragmentome)
link.springer.com/article/10…
Along with:
Our thoughts on exploring the expanding universe of small RNAs with new tools:
nature.com/articles/s41556-0…
&
Our reflections on small RNA origins & their functions beyond RNAi (aptamer-like)
cell.com/trends/biochemical-…
jbc.org/article/S0021-9258(2…
cell.com/molecular-cell/full…
cell.com/trends/biochemical-…
Qi Chen retweeted
Human embryos are often mosaics of normal and abnormal cells. Can “they” sense and decide which cells should stay and do all lineages play by the same rules?
Our new study @natcomms.nature.com uncovers lineage-specific quality control after implantation.
nature.com/articles/s41467-0…
A single tRNA or rRNA can be cleaved at different sites, generating small RNAs with distinct functions depending on where the cuts are made. That fragmentation pattern is itself a regulatory layer beyond abundance — the "RNA fragmentome".
With @tongzhoulab, we built qMAP, a tool to read this hidden information across development, disease & aging — for both mechanistic discovery and translational applications.
Our toolchain developed over the years to explore the expanding small RNA universe:
PANDORA-seq (see the once invisible)
nature.com/articles/s41556-0…
nature.com/articles/s41596-0…
SPORTS (comprehensive annotation)
sciencedirect.com/science/ar…
FUSION (robust comparison)
academic.oup.com/bioinformat…
qMAP (read the fragmentome)
link.springer.com/article/10…
Along with:
Our thoughts on exploring the expanding universe of small RNAs with new tools:
nature.com/articles/s41556-0…
&
Our reflections on small RNA origins & their functions beyond RNAi (aptamer-like)
cell.com/trends/biochemical-…
jbc.org/article/S0021-9258(2…
cell.com/molecular-cell/full…
cell.com/trends/biochemical-…
Qi Chen retweeted
This Perspective positions cellular self-organization as a foundational principle for the origin of multicellular life and discusses how decoding this concept with stem cell-based models will advance biological engineering go.nature.com/4e1m3Br
rdcu.be/ftZeL
Qi Chen retweeted
Sharing this perspective reinforced for me the idea that constraints are not obstacles. In biology, they can drive self-organization and the emergence of complexity. I suspect similar principles may operate far beyond biology, in the organization of cultures, ideas, and societies
After years of crystallization, now in @NatureBiotech, @ZernickaGoetz and I discuss the evolutionary origins of multicellularity and how physical constraints inevitably drive cellular self-organization.
Harnessing these rules may help us better understand and engineer life – Build to understand. rdcu.be/flTKa
Qi Chen retweeted
Decoding the origins of cellular self-organization for engineered biology go.nature.com/4e1m3Br
After years of crystallization, now in @NatureBiotech, @ZernickaGoetz and I discuss the evolutionary origins of multicellularity and how physical constraints inevitably drive cellular self-organization.
Harnessing these rules may help us better understand and engineer life – Build to understand. rdcu.be/flTKa
Qi Chen retweeted
I’m thrilled to share that our paper is out in Molecular Cell! We developed Ribo-Tweezer, a new technology that lets us rapidly and reversibly remove specific proteins from mature ribosomes to ask what they actually do in translation.
I fed this post/picture to Gemini's new Lyria 3 model, asking for a soundtrack based on the vibe.
I wasn't prepared for the result... it captures the weight of this journey so beautifully that I'm almost in tears...
What a time to be alive...
Qi Chen retweeted
Scientists discover a hidden RNA ‘aging clock’ in human sperm.
New research from @UofUHealth sheds light on connection between paternal age and elevated health risks for the unborn.
attheu.utah.edu/facultystaff…
