Single-molecule analysis of transcription activation: dynamics of SAGA co-activator recruitment.
Jongcheol JeonLarry J FriedmanHogyu David SeoAugustus AdelekeBria GrahamEmily PattesonJeff GellesStephen BuratowskiPublished in: bioRxiv : the preprint server for biology (2023)
Transcription activators are said to stimulate gene expression by "recruiting" coactivators to promoters, yet this term fits several different kinetic models. To directly analyze dynamics of activator-coactivator interactions, single-molecule microscopy was used to image promoter DNA, a transcription activator, and the Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex within nuclear extract. SAGA readily, but transiently, binds nucleosome-free DNA without activator, while chromatin template association occurs nearly exclusively when activator is present. On both templates, activator increases SAGA association rates by up to an order of magnitude, and dramatically extends its dwell times. These effects reflect direct interactions with the transactivation domain, as VP16 or Rap1 activation domains produce different SAGA dynamics. Despite multiple bromodomains, acetyl-CoA or histone H3/H4 tail acetylation only modestly improves SAGA binding. Unexpectedly, histone acetylation more strongly affects activator residence. Our studies thus reveal two modes of SAGA interaction with the genome: a short-lived activator-independent interaction with nucleosome-free DNA, and a state tethered to promoter-bound transcription activators that can last up to several minutes.
Keyphrases
- single molecule
- nuclear factor
- gene expression
- transcription factor
- dna methylation
- atomic force microscopy
- living cells
- toll like receptor
- genome wide
- high resolution
- dna damage
- high throughput
- immune response
- oxidative stress
- preterm infants
- binding protein
- mass spectrometry
- fatty acid
- deep learning
- gestational age
- single cell
- nucleic acid
- solid phase extraction