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Slavov Laboratory @slavovlab.bsky.social · 1d

Yeast metabolic and signaling genes are required for heat-shock survival and have little overlap with the heat-induced genes

www.pnas.org/doi/abs/10.1...

Yeast metabolic and signaling genes are required for heat-shock survival and have little overlap with the heat-induced genes | PNAS

Genome-wide gene-expression studies have shown that hundreds of yeast genes are induced or repressed transiently by changes in temperature; many ar...

www.pnas.org

Slavov Laboratory @slavovlab.bsky.social · 1d

What is the relationship between the transcriptional induction of a gene and the fitness effect of its deletion ?

This study reported remarkably low correlations in the context of heat shock response and survival.

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Reposted by Slavov Laboratory

Nikolai Slavov @slavov-n.bsky.social · 17d

An amazing feat of regulation.

Two very different regulatory mechanisms converge to shape the mitochondrial proteome and keep us alive!

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Reposted by Slavov Laboratory

Nikolai Slavov @slavov-n.bsky.social · 15d

mRNA-mRNA correlations across the single cells from a tissue are rarely interpreted.

They differ from the corresponding protein-protein correlations?

𝐖𝐡𝐲 ❓

www.biorxiv.org/content/10.1...

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Slavov Laboratory @slavovlab.bsky.social · 20d

The regulation of nuclear-encoded mitochondrial proteins is fascinating.

They are synthesized in a fully eukaryotic manner, with introns, splicing, and cytosolic ribosomes.

Yet, they are degraded by proteases that look and act bacterial.

blog.slavovlab.net/2025/09/23/m...

Mixing eukaryotic synthesis with prokaryotic degradation

The Evolutionary Balancing Act Coordinating gene regulation across two fundamentally different systems is one of the great balancing acts of life. Mitochondria embody this challenge: most of their …

blog.slavovlab.net

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Reposted by Slavov Laboratory

Nikolai Slavov @slavov-n.bsky.social · 22d

Some proteins are primarily regulated by one mechanism: RNA abundance, translation, or clearance.

The regulation of most proteins is dominated by different regulatory mechanisms across cell types.

Gratifyingly, this complex regulation defines simple rules ⬇️

www.biorxiv.org/content/10.1...

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Slavov Laboratory @slavovlab.bsky.social · 23d

Protein clearance rates vary across proteins in inverse proportion to the average cell-type doubling rate.

This explains the degree to which protein clearance (degradation) sets protein abundance.

biorxiv.org/content/10.1...

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Slavov Laboratory @slavovlab.bsky.social · 23d

Some proteins are primarily regulated by one mechanism: RNA abundance, translation, or clearance.

The regulation of most proteins is dominated by different regulatory mechanisms across cell types.

Gratifyingly, this complex regulation defines simple rules

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Slavov Laboratory @slavovlab.bsky.social · 23d

Our experimental design aimed for:

- Direct measurements

- Quantitative accuracy supporting confident modeling

- Scalable multiplexing & generalizable approach approach

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Slavov Laboratory @slavovlab.bsky.social · 23d

We quantified mRNA abundance, translation, protein abundance, protein degradation and cell growth across thousands of single cells from a mammalian tissue.

The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:

www.biorxiv.org/content/10.1...

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Slavov Laboratory @slavovlab.bsky.social · Sep 11

A key mechanism controlling mitosis is the precise timing of over 32,000 phosphorylation events.

Below are some of the key regulators of mitosis.

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Slavov Laboratory @slavovlab.bsky.social · Sep 6

Proteins self-organize to build large structures, 100,000-fold larger then the proteins.

It's elegantly dynamic !

Proteins constantly self-assemble and disassemble to build skeletal structures in our cells, shaping and orchestrating life.

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Slavov Laboratory @slavovlab.bsky.social · Sep 1

𝐓𝐨𝐝𝐚𝐲 𝐦𝐚𝐫𝐤𝐬 𝐨𝐮𝐫 𝟏𝟎𝐭𝐡 𝐚𝐧𝐧𝐢𝐯𝐞𝐫𝐬𝐚𝐫𝐲 🎉

A decade of pushing the boundaries in proteomics, systems biology, and data-driven discovery.

🔬 Thank you to our collaborators, alumni & supporters!

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Reposted by Slavov Laboratory

Nikolai Slavov @slavov-n.bsky.social · Aug 29

Our findings (now published in @narjournal.bsky.social‬) identify the first metazoan RNase MRP-specific protein subunits.

We also define the RNA-targeting repertoire of this essential enzyme in mammalian cells.

academic.oup.com/nar/article/...

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Reposted by Slavov Laboratory

Nikolai Slavov @slavov-n.bsky.social · Aug 25

The registration for SCP2026 is open !

Join us next July for the the 9th Single Cell Proteomics Conference.

single-cell.net/proteomics/s...

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Slavov Laboratory @slavovlab.bsky.social · Aug 20

The neighboring gene knockout effects in yeast are even stronger.

In close range (below 1kb), the knockout affects the abundance of mRNA transcribed from nearby genes.

Yeast Data 🔽

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Slavov Laboratory @slavovlab.bsky.social · Aug 20

Neighboring gene effects account for much of the observed phenotypes of gene deletions.

This is a crucial factor to consider in knockout experiments.

Phenotypic similarity is exponentially related to chromosomal proximity in both yeast & human genomes.

Human Data 🔽

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Slavov Laboratory @slavovlab.bsky.social · Aug 20

The epitranscriptome formed by the growing number of modifications occurring within mRNA transcripts.

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Slavov Laboratory @slavovlab.bsky.social · Aug 18

Protein synthesis is among the most energy demanding processes in a cell.

𝐖𝐡𝐲 𝐚𝐫𝐞 𝐭𝐡𝐞𝐧 𝐬𝐨𝐦𝐞 𝐩𝐫𝐨𝐭𝐞𝐢𝐧𝐬 𝐜𝐨𝐧𝐭𝐢𝐧𝐮𝐨𝐮𝐬𝐥𝐲 𝐬𝐲𝐧𝐭𝐡𝐞𝐬𝐢𝐳𝐞𝐝 𝐚𝐧𝐝 𝐢𝐦𝐦𝐞𝐝𝐢𝐚𝐭𝐞𝐥𝐲 𝐝𝐞𝐠𝐫𝐚𝐝𝐞𝐝 ?

blog.slavovlab.net/2025/08/16/p...

Proteins made to die

Protein synthesis is among the most energy-demanding processes in a cell. Yet, some proteins are synthesized and immediately degraded. This may seem like a futile cycle, but it’s a remarkable…

blog.slavovlab.net

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Slavov Laboratory @slavovlab.bsky.social · Aug 12

Spliceosome Dynamics

During splicing, stepwise assembly is one principle by which spliceosomes on the one hand ensure the faithful recognition of splice sites and on the other hand become susceptible to regulatory inputs to implement alternative splicing.

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Slavov Laboratory @slavovlab.bsky.social · Aug 11

Large-Scale, Quantitative Protein Assays on a High-Throughput DNA Sequencing Chip

www.cell.com/molecular-ce...

Large-Scale, Quantitative Protein Assays on a High-Throughput DNA Sequencing Chip

By generating a massive peptide and protein array in situ on an Illumina sequencing flow cell with in vitro translation, Layton et al. demonstrate direct protein assays for enzyme function and antibod...

www.cell.com

Slavov Laboratory @slavovlab.bsky.social · Aug 11

Characterization of activity across the mutational landscape of an enzyme

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Slavov Laboratory @slavovlab.bsky.social · Aug 11

Quantitative protein assays on Illumina chips.

A creative use of the impressive imaging capabilities developed for DNA sequencing by synthesis.
◼️ It allowed quantifying binding and enzyme catalysis

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Reposted by Slavov Laboratory

Nikolai Slavov @slavov-n.bsky.social · Jul 16

Recently, I presented technological progress in single-cell proteomics & the biological analysis that it enables:

𝐒𝐢𝐧𝐠𝐥𝐞-𝐜𝐞𝐥𝐥 𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬: 𝐅𝐫𝐨𝐦 𝐏𝐫𝐨𝐭𝐞𝐢𝐧 𝐕𝐚𝐫𝐢𝐚𝐭𝐢𝐨𝐧 𝐭𝐨 𝐁𝐢𝐨𝐥𝐨𝐠𝐢𝐜𝐚𝐥 𝐅𝐮𝐧𝐜𝐭𝐢𝐨𝐧𝐬

youtu.be/8nhjKSTqeOs?...

Single-cell proteomics: From Protein Variation to Biological Functions

YouTube video by Nikolai Slavov

youtu.be

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Slavov Laboratory @slavovlab.bsky.social · Jul 16

Cell size varies by many orders of magnitude.

The mechanisms that generate and maintain this extraordinary diversity of sizes remain incompletely understood.

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