A tRNA/rRNA can be cleaved into different small RNAs with distinct functions depending on the cut site, yet abundance-based small RNA analysis is blind to it. Tong Zhou & us built a tool to read that hidden layer. Meet qMAP & the 'RNA fragmentome' @molsystbiol.org link.springer.com/article/10.1...

qMAP decodes RNA fragmentation dynamics in development and disease - Molecular Systems Biology

Noncanonical small RNAs, such as tRNA-derived (tsRNAs) and rRNA-derived (rsRNAs) fragments, are more abundant than microRNAs and arise from selective cleavage events rather than random degradation. Wh...

link.springer.com

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/s41... It's Fascinating to see how nature always repurposes molecules for new functions! ♾

Science Magazine@science.org · last mo.

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: https://scim.ag/4whygtn #ScienceMagArchives

A tRNA/rRNA can be cleaved into different small RNAs with distinct functions depending on the cut site, yet abundance-based small RNA analysis is blind to it. Tong Zhou & us built a tool to read that hidden layer. Meet qMAP & the 'RNA fragmentome' @molsystbiol.org link.springer.com/article/10.1...

qMAP decodes RNA fragmentation dynamics in development and disease - Molecular Systems Biology

Noncanonical small RNAs, such as tRNA-derived (tsRNAs) and rRNA-derived (rsRNAs) fragments, are more abundant than microRNAs and arise from selective cleavage events rather than random degradation. Wh...

link.springer.com

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

Decoding the origins of cellular self-organization for engineered biology - Nature Biotechnology

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 ...

go.nature.com

After years of crystallization, in @natbiotech.nature.com, @zernickagoetz.bsky.social and I discuss the evolutionary origins of multicellularity & how physical constraints inevitably drive cellular self-organization. Harnessing these rules may help us better understand & engineer life rdcu.be/flTKa

Decoding the origins of cellular self-organization for engineered biology - @qichen-lab.bsky.social @zernickagoetz.bsky.social go.nature.com/4e1m3Br

Decoding the origins of cellular self-organization for engineered biology - Nature Biotechnology

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 ...

go.nature.com

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. bsky.app/profile/qich...

Qi Chen@qichen-lab.bsky.social · 7mo ago

1/5 It took us some time to connect the dots...now in @embojournal.org 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/10.1...

A molecular "aging clock" has been identified in human sperm RNA, showing progressive changes with age that may influence offspring health and metabolism. doi.org/hbkmvf

Scientists discover a hidden RNA 'aging clock' in human sperm

Increasing paternal age has been linked to elevated health risks for the next generation, including higher risks of obesity and stillbirth.

phys.org

Fascinating research! Qi Chen and colleagues have identified a potential "aging cliff" in sperm RNA (rsRNA) that is associated with the increased health risks for the next generation that accompany advancing paternal age. Read on uofuhealth.utah.edu/newsroom/new...

Scientists Discover a Hidden RNA “Aging Clock” in Human Sperm

The molecular contents of sperm go through similar shifts over time in both mice and humans, which may lead to a rapid, dramatic shift at mid-life.

uofuhealth.utah.edu

Qi Chen@qichen-lab.bsky.social · 7mo ago

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. bsky.app/profile/qich...

What underlies the impact of sperm aging on fertility and offspring health? small ncRNA profiling by Kenneth Aston, Tong Zhou, @qichen-lab.bsky.social and colleagues reveals a drastic shift in RNA complements able to affect recipient cell metabolism link.springer.com/article/10.1...

Conserved shifts in sperm small non-coding RNA profiles during mouse and human aging - The EMBO Journal

Sperm aging impacts male fertility and offspring health, highlighting the need for reliable aging biomarkers to guide reproductive decisions. However, the molecular determinants of sperm fitness durin...

link.springer.com

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. bsky.app/profile/qich...

Qi Chen@qichen-lab.bsky.social · 7mo ago

1/5 It took us some time to connect the dots...now in @embojournal.org 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/10.1...

1/5 It took us some time to connect the dots...now in @embojournal.org 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/10.1...

A road trip to Monument Valley and the wonders of the west, as an anniversary of lab’s 10th year operation…look forward to the journey ahead…

Glad to see this thoughtful piece in @quantamagazine.bsky.social on paternal epigenetic inheritance and the emerging 'Sperm RNA Code', featuring many active colleagues in the field. It’s a reminder that our actions may echo in the next generation(s) & there are immense unknowns to explore...

Quanta Magazine@quantamagazine.org · 8mo ago

In a recent study, the fitness of a father mouse at the time of conception was found to have metabolic and mitochondrial benefits for his offspring. Similar signatures were found in the sperm of well-exercised human men. @ivanamato.bsky.social reports: www.quantamagazine.org/how-dads-fit...

1/ Excited to share our new study with @brumbaugh-lab.bsky.social, out in @natbiotech.nature.com! P-bodies selectively sequester RNAs encoding cell fate regulators, often from the preceding developmental stage. Releasing these RNAs can drive changes in cell identity. 🧵 www.nature.com/articles/s41...

Selective RNA sequestration in biomolecular condensates directs cell fate transitions - Nature Biotechnology

Stem cell differentiation is controlled by manipulating RNA condensates.

nature.com

After developing PANDORA-seq to reveal hidden small RNAs (e.g., tsRNA, rsRNA) and SPORTS to annotate them, we now expand our toolchain with Tong Zhou lab: introducing FUSION, a tool that robustly interprets small RNA changes even in small or 1-on-1 datasets. academic.oup.com/bioinformati...

FUSION: a family-level integration approach for robust differential analysis of small non-coding RNAs

AbstractMotivation. Beyond well-studied microRNAs, noncanonical small non-coding RNAs (sncRNAs) derived from longer parental templates such as tRNAs, rRNAs

academic.oup.com

Perhaps our boldest hypothesis… we propose a model for RNA Structural Memory propagation in @natcellbio.nature.com 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

Our 🌷 May 🌷 issue is online with a broad range of article topics and formats! In their Opinion article (on the cover, too!), @qichen-lab.bsky.social and colleagues describe the interactions between small ncRNAs and Toll-like receptors. Find the issue here: www.cell.com/trends/bioch...

Very glad to see our Sequential Activation Hypothesis highlighted on the cover @cp-trendsbiochem.bsky.social , linking small RNA-TLR interactions to autoimmune disease mechanisms.

Qi Chen@qichen-lab.bsky.social · last yr.

How can abnormal small RNA biogenesis spark autoimmune disease? Our opinion @cp-trendsbiochem.bsky.social discuss a novel two-stage activation hypothesis that may explain why autoimmunity hits women harder, via small RNA-TLR7/8 interactions & augmented by autoantibodies. www.cell.com/trends/bioch...

#NewNProt for #genomewide characterization of a diverse set of #smallnoncodingRNAs in cells and tissues

Optimized identification and characterization of small RNAs with PANDORA-seq - Nature Protocols

This Protocol describes optimized procedures for purification and sequencing of small noncoding RNAs from a variety of samples to characterize these diverse RNA species and map them to the parental RNAs from which they originate.

bit.ly

We put together a step-by-step protocols for PANDORA-seq, now available in Nature Protocols @natprot.bsky.social , including the sample preparation for sperm, sperm heads; and the analyzing software SPORTS optimized for various types of small RNAs including tsRNAs, rsRNAs, and miRNAs. rdcu.be/egk1Z

How can abnormal small RNA biogenesis spark autoimmune disease? Our opinion @cp-trendsbiochem.bsky.social discuss a novel two-stage activation hypothesis that may explain why autoimmunity hits women harder, via small RNA-TLR7/8 interactions & augmented by autoantibodies. www.cell.com/trends/bioch...

go.bsky.app/QkSL6S5

Starting this platform with the excursion to the historic village Shirakawa-go. #tRNA2024 conference at Kanazawa, Japan