Naef lab – UPNAE Laboratory of Computational and Systems Biology

Current Research Areas
> Circadian gene regulatory networks in mammals > Chronobiology of the liver > Circadian oscillators in single cells > Interactions of circadian oscilators and cell cycle > Transcriptional bursting and noise in mammalian gene transcription
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The latest news
HIGHLIGHTS

Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver
Translation depends on messenger RNA (mRNA)-specific initiation, elongation, and termination rates. While translation elongation is well studied in bacteria and yeast, less is known in higher eukaryotes. Here we combined ribosome and transfer RNA (tRNA) profiling to investigate the relations between translation elongation rates, (aminoacyl-) tRNA levels, and codon usage in mammals. We modeled codon-specific (…)

Modulation of transcriptional burst frequency by histone acetylation
Many mammalian genes are transcribed during short bursts of variable frequencies and sizes that substantially contribute to cell-to-cell variability. However, which molecular mechanisms determine bursting properties remains unclear. To probe putative mechanisms, we combined temporal analysis of transcription along the circadian cycle with multiple genomic reporter integrations, using both short-lived luciferase live microscopy and single-molecule (…)

Clock-dependent chromatin topology modulates circadian transcription and behavior
The circadian clock in animals orchestrates widespread oscillatory gene expression programs, which underlie 24-h rhythms in behavior and physiology. Several studies have shown the possible roles of transcription factors and chromatin marks in controlling cyclic gene expression. However, how daily active enhancers modulate rhythmic gene transcription in mammalian tissues is not known. Using circular chromosome (…)
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Contact
Laboratory of Computational and Systems Biology
Monday to Friday: 08.00 – 16.00
Head of laboratory: Prof. Felix Naef
♦ Office AAB 040
♦ Phone: +41 21 693 16 21
♦ Email: [email protected]
Administrative Assistant: Sophie Barret
♦ Office AAB 038
♦ Phone: +41 21 693 83 58
♦ Email: [email protected]
Mailing Address:
EPFL SV IBI UPNAE
Prof. Felix Naef
AAB 040
Station 15
CH-1015 Lausanne