Biology subjects

Kornberg, R. D.

Publications and source records attributed to Kornberg, R. D..

6 recordsLinked to original sources

bioRxiv2026

A Structural Model of Transcriptional Activation by Mediator

Mediator integrates regulatory signals from transcription factors (TFs) and controls RNA polymerase II (Pol II) activity in eukaryotes. Its Tail module serves as the primary hub for TF activation domains (ADs), but the mechanistic logic coupling this distal engagement to transcriptional output is unclear. Here we model an extensive set of human AD-Tail interactions with AlphaFold 3 and infer how they may influence the architecture of the Mediator-Pol II complex. Across the ensemble, ADs recurrently engage a restricted set of surfaces spanning multiple Tail subunits, revealing several previously unrecognized sites. The ensemble map recovers established activator-binding regions and is consistent with prior biochemical and structural data. Our modeling suggests how multivalent AD binding modulates the conformational landscape of the Tail to favor an initiation-competent Pol II state, providing a structural framework for tunable gene activation through Mediator.

molecular biology↗

bioRxiv2026

Reconstitution of +1 nucleosome transcription reveals coordinated functions of SAGA, Mediator, and TFIIH

The +1 nucleosome has emerged as a key regulator of eukaryotic transcription, but how it controls transcription initiation remains poorly understood. Here we reconstitute transcription through the +1 nucleosome using eleven purified yeast factors: RNA polymerase II (Pol II), the six general transcription factors (GTFs), TFIIS, the activator Pho4, and the SAGA and Mediator complexes. The system recapitulates key features of regulation observed in vivo. SAGA, acting with Pho4, directs pre-initiation complex (PIC) assembly to the correct position through its TBP-loading activity. Mediator stimulates transcription when the +1 nucleosome imposes a barrier to PIC formation, consistent with stabilization of productive TFIIH-DNA engagement. Contrary to the prevailing model, SAGA remains bound to the PIC after TBP loading and acetylates the +1 nucleosome within the assembled complex. The isolated PIC-Mediator-SAGA-nucleosome complex is transcriptionally active, and the repressive effect of the nucleosome is relieved by the DNA translocase activity of Ssl2, the TFIIH subunit that opens promoter DNA. TFIIH thus couples promoter melting to remodeling of the +1 nucleosome.

biochemistry↗

bioRxiv2022

Structure of the histone acetyltransferase NuA4 complex

NuA4, one of two major histone acetyltransferase complexes in Saccharomyces cerevisiae, specifically acetylates histone H4 and H2A, and therefore loosen the histone-DNA contacts, resulting in increased transcriptional activity. Here we present a near-atomic resolution structure of NuA4 complex through cryonic electron microscopy. The structure comprises six subunits and a total of 5,000 amino acids, within which Eaf1 and Eaf2 twist against each other and span from Actin-Arp4 module to the platform subunit Tra1, forming the backbone of NuA4. The locations of four missing components including Yaf9, and Esa1, Yng2 and Eaf6 of Piccolo module were indicated based on the structure. Intriguingly, our biochemical data showed that NuA4 doesnt bind nucleosome in vitro, whereas possesses strong histone acetyltransferase activity. Its Piccolo module, which has long been regarded as the catalytic module of NuA4, acetylates the nucleosome substrate at almost the same efficiency, but is capable of binding nucleosome. Combining the structural and biochemical data give rise to a model in which the entire NuA4 adopts an auto-inhibited conformation, and undergoes structural rearrangements upon substrate and co-factor additions, restoring its capacity of nucleosome-binding and activity of hyper-acetylation.

biochemistry↗

bioRxiv2021

Mitotic Chromosome Condensation Driven by a Volume Phase Transition

Procedures were devised for the reversible decondensation and recondensation of purified mitotic chromosomes. Computational methods were developed for the quantitative analysis of chromosome morphology in high throughput, enabling the recording of condensation behavior of thousands of individual chromosomes. Established physico-chemical theory for ionic hydrogels was modified for application to chromosomal material and shown to accurately predict the observed condensation behavior. The theory predicts a change of state (a "volume phase transition") in the course of condensation, and such a transition was shown to occur. These findings, together with classical cytology showing loops of chromatin, lead to the description of mitotic chromosome structure in terms of two simple principles: contraction of length of chromatin fibers by the formation of loops, radiating from a central axis; and condensation of the chromosomal material against the central axis through a volume phase transition. One sentence summaryThe mitotic chromosome is an axially scaffolded ionic hydrogel, undergoing a volume phase transition to achieve a condensed state.

biophysics↗

bioRxiv2020

Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator

Gene activator proteins comprise distinct DNA-binding and transcriptional activation domains (ADs). Because few ADs have been described, we tested domains tiling all yeast transcription factors for activation in vivo and identified 150 ADs. By mRNA display, we showed that 73% of ADs bound the Med15 subunit of Mediator, and that binding strength was correlated with activation. AD-Mediator interaction in vitro was unaffected by a large excess of free activator protein, pointing to a dynamic mechanism of interaction. Structural modeling showed that ADs interact with Med15 without shape complementarity ("fuzzy" binding). ADs shared no sequence motifs, but mutagenesis revealed biochemical and structural constraints. Finally, a neural network trained on AD sequences accurately predicted ADs in human proteins and in other yeast proteins, including chromosomal proteins and chromatin remodeling complexes. These findings solve the longstanding enigma of AD structure and function and provide a rationale for their role in biology.

molecular biology↗

bioRxiv2017

Polycomb-Mediated Chromatin Loops Revealed by a Sub-Kilobase Resolution Chromatin Interaction Map

The locations of chromatin loops in Drosophila were determined by Hi-C (chemical cross-linking, restriction digestion, ligation, and high-throughput DNA sequencing). Whereas most loop boundaries or \"anchors\" are associated with CTCF protein in mammals, loop anchors in Drosophila were found most often in association with the polycomb group (PcG) protein Polycomb (Pc), a subunit of Polycomb Repressive Complex 1 (PRC1). Loops were frequently located within domains of PcG-repressed chromatin. Promoters located at PRC1 loop anchors regulate some of the most important developmental genes and are less likely to be expressed than those not at PRC1 loop anchors. Although DNA looping has most commonly been associated with enhancer-promoter communication, our results indicate that loops are also associated with gene repression.

molecular biology↗