Protein structures can provide invaluable information, both for reasoning about biological processes and for enabling interventions such as structure-based drug development or targeted mutagenesis. After decades of effort, 17% of the total residues in human protein sequences are covered by an experimentally-determined structure1. Here we dramatically expand structural coverage by applying the state-of-the-art machine learning method, AlphaFold2, at scale to almost the entire human proteome (98.5% of human proteins). The resulting dataset covers 58% of residues with a confident prediction, of which a subset (36% of all residues) have very high confidence. We introduce several metrics developed by building on the AlphaFold model, and use them to interpret the dataset, identifying strong multi-domain predictions as well as regions likely to be disordered. Finally, we provide some case studies illustrating how high-quality predictions may be used to generate biological hypotheses. Importantly, we are making our predictions freely available to the community via a public database (hosted by the European Bioinformatics Institute at https://alphafold.ebi.ac.uk/
 ). We anticipate that routine large-scale and high-accuracy structure prediction will become an important tool, allowing new questions to be addressed from a structural perspective.

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Highly accurate protein structure prediction for the human proteome

http://manuscript.elsevier.com/S1097276522004968/pdf/S1097276522004968.pdf

Hidden codes in mRNA: Control of gene expression by m6A.

Dynamic control of chromatin-associated m6A methylation regulates nascent RNA synthesis.

The Mediator complex, which in humans is 1.4 MDa in size and includes 26 subunits, controls many aspects of RNA polymerase II (Pol II) function. Apart from its size, a defining feature of Mediator is its intrinsic disorder and conformational flexibility, which contributes to its ability to undergo phase separation and to interact with a myriad of regulatory factors. In this Review, we discuss Mediator structure and function, with emphasis on recent cryogenic electron microscopy data of the 4.0-MDa transcription preinitiation complex. We further discuss how Mediator and sequence-specific DNA-binding transcription factors enable enhancer-dependent regulation of Pol II function at distal gene promoters, through the formation of molecular condensates (or transcription hubs) and chromatin loops. Mediator regulation of Pol II reinitiation is also discussed, in the context of transcription bursting. We propose a working model for Mediator function that combines experimental results and theoretical considerations related to enhancer–promoter interactions, which reconciles contradictory data regarding whether enhancer–promoter communication is direct or indirect. We conclude with a discussion of Mediator’s potential as a therapeutic target and of future research directions. The Mediator complex is an important regulator of RNA polymerase II. This Review discusses recent structural insights into Mediator function and proposes a model that reconciles contradictory data on whether enhancer–promoter communication during transcription is direct or indirect. 

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The Mediator complex as a master regulator of transcription by RNA polymerase II

The multifaceted effects of YTHDC1-mediated nuclear m6A recognition

Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation.

The Cdk8 kinase module (CKM) in Mediator, comprising Med13, Med12, CycC, and Cdk8, regulates RNA polymerase II transcription through kinase-dependent and -independent functions. Numerous pathogenic mutations causative for neurodevelopmental disorders and cancer congregate in CKM subunits. However, the structure of the intact CKM and the mechanism by which Cdk8 is non-canonically activated and functionally affected by oncogenic CKM alterations are poorly understood. Here, we report a cryo-electron microscopy structure of Saccharomyces cerevisiae CKM that redefines prior CKM structural models and explains the mechanism of Med12-dependent Cdk8 activation. Med12 interacts extensively with CycC and activates Cdk8 by stabilizing its activation (T-)loop through conserved Med12 residues recurrently mutated in human tumors. Unexpectedly, Med13 has a characteristic Argonaute-like bi-lobal architecture. These findings not only provide a structural basis for understanding CKM function and pathological dysfunction, but also further impute a previously unknown regulatory mechanism of Mediator in transcriptional modulation through its Med13 Argonaute-like features.

Guojie Li

Papers

Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation.

Structure and noncanonical Cdk8 activation mechanism within an Argonaute-containing Mediator kinase module