Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II

A large-scale curated and filterable dataset for cryo-EM foundation model pre-training

Cryo-electron microscopy (cryo-EM) is a transformative imaging technology that enables near-atomic resolution 3D reconstruction of target biomolecule, playing a critical role in structural biology and drug discovery. Cryo-EM faces significant challenges due to its extremely low signal-to-noise ratio (SNR) where the complexity of data processing becomes particularly pronounced. To address this challenge, foundation models have shown great potential in other biological imaging domains. However, their application in cryo-EM has been limited by the lack of large-scale, high-quality datasets. To fill this gap, we introduce CryoCRAB, the first large-scale dataset for cryo-EM foundation models. CryoCRAB includes 746 proteins, comprising 152,385 sets of raw movie frames (116.8 TB in total). To tackle the high-noise nature of cryo-EM data, each movie is split into odd and even frames to generate paired micrographs for denoising tasks. The dataset is stored in HDF5 chunked format, significantly improving random sampling efficiency and training speed. CryoCRAB offers diverse data support for cryo-EM foundation models, enabling advancements in image denoising and general-purpose feature extraction for downstream tasks.

Regulation of RNA polymerase II transcription through re-initiation and bursting

The regulation of RNA polymerase II (RNAPII) activity requires orchestrated responses among genomic regulatory sequences and an expansive set of proteins and protein complexes. Despite intense study over five decades, mechanistic insights continue to emerge. Within the past 10 years, live-cell imaging and single-cell transcriptomics experiments have yielded new information about enhancer-promoter communication, transcription factor dynamics, and the kinetics of RNAPII transcription activation. These insights have established RNAPII re-initiation and bursting as a common regulatory phenomenon with widespread implications for gene regulation in health and disease. Here, we summarize regulatory strategies that help control RNAPII bursting in eukaryotic cells, which is defined as short periods of active transcription followed by longer periods of inactivity. We focus on RNAPII re-initiation (i.e., a "burst" of two or more polymerases that initiate from the same promoter), with an emphasis on molecular mechanisms, open questions, and controversies surrounding this distinct regulatory stage.

Real-time visualization of reconstituted transcription reveals RNA polymerase II activation mechanisms at single promoters

RNA polymerase II (RNAPII) is regulated by sequence-specific transcription factors (TFs) and the pre-initiation complex (PIC): TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, Mediator. TFs and Mediator contain intrinsically-disordered regions (IDRs) and form phase-separated condensates, but how IDRs control RNAPII function remains poorly understood. Using purified PIC factors, we developed a Real-time In-vitro Fluorescence Transcription assay (RIFT) for second-by-second visualization of RNAPII transcription at hundreds of promoters simultaneously. We show rapid RNAPII activation is IDR-dependent, without condensate formation. For example, the MED1-IDR can functionally replace a native TF, activating RNAPII with similar (not identical) kinetics; however, MED1-IDR squelches transcription as a condensate, but activates as a single-protein. TFs and Mediator cooperatively activate RNAPII bursting and re-initiation and surprisingly, Mediator can drive TF-promoter recruitment, without TF-DNA binding. Collectively, RIFT addressed questions largely intractable with cell-based methods, yielding mechanistic insights about IDRs, condensates, enhancer-promoter communication, and RNAPII bursting that complement live-cell imaging data.

Transcription start site scanning requires the fungi-specific hydrophobic loop of Tfb3

RNA polymerase II (pol II) initiates transcription from transcription start sites (TSSs) located ∼30-35 bp downstream of the TATA box in metazoans, whereas in the yeast Saccharomyces cerevisiae, pol II scans further downstream TSSs located ∼40-120 bp downstream of the TATA box. Previously, we found that removal of the kinase module TFIIK (Kin28-Ccl1-Tfb3) from TFIIH shifts the TSS in a yeast in vitro system upstream to the location observed in metazoans and that addition of recombinant Tfb3 back to TFIIH-ΔTFIIK restores the downstream TSS usage. Here, we report that this biochemical activity of yeast TFIIK in TSS scanning is attributable to the Tfb3 RING domain at the interface with pol II in the pre-initiation complex (PIC): especially, swapping Tfb3 Pro51-a residue conserved among all fungi-with Ala or Ser as in MAT1, the metazoan homolog of Tfb3, confers an upstream TSS shift in vitro in a similar manner to the removal of TFIIK. Yeast genetic analysis suggests that both Pro51 and Arg64 of Tfb3 are required to maintain the stability of the Tfb3-pol II interface in the PIC. Cryo-electron microscopy analysis of a yeast PIC lacking TFIIK reveals considerable variability in the orientation of TFIIH, which impairs TSS scanning after promoter opening.

Uncoupling the TFIIH Core and Kinase Modules Leads To Misregulated RNA Polymerase II CTD Serine 5 Phosphorylation

TFIIH is an essential transcription initiation factor for RNA polymerase II (RNApII). This multi-subunit complex comprises two modules that are physically linked by the subunit Tfb3 (MAT1 in metazoans). The TFIIH Core Module, with two DNA-dependent ATPases and several additional subunits, promotes DNA unwinding. The TFIIH Kinase Module phosphorylates Serine 5 of the C-terminal domain (CTD) of RNApII subunit Rpb1, a modification that coordinates exchange of initiation and early elongation factors. While it is not obvious why these two disparate activities are bundled into one factor, the connection may provide temporal coordination during early initiation. Here we show that Tfb3 can be split into two parts to uncouple the TFIIH modules. The resulting cells grow slower than normal, but are viable. Chromatin immunoprecipitation of the split TFIIH shows that the Core Module, but not the Kinase, is properly recruited to promoters. Instead of the normal promoter-proximal peak, high CTD Serine 5 phosphorylation is seen throughout transcribed regions. Therefore, coupling the TFIIH modules is necessary to localize and limit CTD kinase activity to early stages of transcription. These results are consistent with the idea that the two TFIIH modules began as independent functional entities that became connected by Tfb3 during early eukaryotic evolution.

Three-step mechanism of promoter escape by RNA polymerase II

The transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how interactions between RNA polymerase II (RNA Pol II) and initiation factors are broken to enable promoter escape. Here, we reconstitute RNA Pol II promoter escape in vitro and determine high-resolution structures of initially transcribing complexes containing 8-, 10-, and 12-nt ordered RNAs and two elongation complexes containing 14-nt RNAs. We suggest that promoter escape occurs in three major steps. First, the growing RNA displaces the B-reader element of the initiation factor TFIIB without evicting TFIIB. Second, the rewinding of the transcription bubble coincides with the eviction of TFIIA, TFIIB, and TBP. Third, the binding of DSIF and NELF facilitates TFIIE and TFIIH dissociation, establishing the paused elongation complex. This three-step model for promoter escape fills a gap in our understanding of the initiation-elongation transition of RNA Pol II transcription.

A Revision of Herpes Simplex Virus Type 1 Transcription: First, Repress; Then, Express

The herpes virus genome bears more than 80 strong transcriptional promoters. Upon entry into the host cell nucleus, these genes are transcribed in an orderly manner, producing five immediate-early (IE) gene products, including ICP0, ICP4, and ICP22, while non-IE genes are mostly silent. The IE gene products are necessary for the transcription of temporal classes following sequentially as early, leaky late, and true late. A recent analysis using precision nuclear run-on followed by deep sequencing (PRO-seq) has revealed an important step preceding all HSV-1 transcription. Specifically, the immediate-early proteins ICP4 and ICP0 enter the cell with the incoming genome to help preclude the nascent antisense, intergenic, and sense transcription of all viral genes. VP16, which is also delivered into the nucleus upon entry, almost immediately reverses this repression on IE genes. The resulting de novo expression of ICP4 and ICP22 further repress antisense, intergenic, and early and late viral gene transcription through different mechanisms before the sequential de-repression of these gene classes later in infection. This early repression, termed transient immediate-early protein-mediated repression (TIEMR), precludes unproductive, antisense, intergenic, and late gene transcription early in infection to ensure the efficient and orderly progression of the viral cascade.

Structural visualization of transcription initiation in action

Transcription initiation is a complex process, and its mechanism is incompletely understood. We determined the structures of de novo transcribing complexes TC2 to TC17 with RNA polymerase II halted on G-less promoters when nascent RNAs reach 2 to 17 nucleotides in length, respectively. Connecting these structures generated a movie and a working model. As initially synthesized RNA grows, general transcription factors (GTFs) remain bound to the promoter and the transcription bubble expands. Nucleoside triphosphate (NTP)-driven RNA-DNA translocation and template-strand accumulation in a nearly sealed channel may promote the transition from initially transcribing complexes (ITCs) (TC2 to TC9) to early elongation complexes (EECs) (TC10 to TC17). Our study shows dynamic processes of transcription initiation and reveals why ITCs require GTFs and bubble expansion for initial RNA synthesis, whereas EECs need GTF dissociation from the promoter and bubble collapse for promoter escape.

Lesion recognition by XPC, TFIIH and XPA in DNA excision repair

Nucleotide excision repair removes DNA lesions caused by ultraviolet light, cisplatin-like compounds and bulky adducts1. After initial recognition by XPC in global genome repair or a stalled RNA polymerase in transcription-coupled repair, damaged DNA is transferred to the seven-subunit TFIIH core complex (Core7) for verification and dual incisions by the XPF and XPG nucleases2. Structures capturing lesion recognition by the yeast XPC homologue Rad4 and TFIIH in transcription initiation or DNA repair have been separately reported3-7. How two different lesion recognition pathways converge and how the XPB and XPD helicases of Core7 move the DNA lesion for verification are unclear. Here we report on structures revealing DNA lesion recognition by human XPC and DNA lesion hand-off from XPC to Core7 and XPA. XPA, which binds between XPB and XPD, kinks the DNA duplex and shifts XPC and the DNA lesion by nearly a helical turn relative to Core7. The DNA lesion is thus positioned outside of Core7, as would occur with RNA polymerase. XPB and XPD, which track the lesion-containing strand but translocate DNA in opposite directions, push and pull the lesion-containing strand into XPD for verification.

Structural basis of a transcription pre-initiation complex on a divergent promoter

Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. Here, the Saccharomyces cerevisiae Mediator complexed with a PIC (Med-PIC) was assembled on a divergent promoter and analyzed by cryoelectron microscopy. The structure reveals two distinct Med-PICs forming a dimer through the Mediator tail module, induced by a homodimeric activator protein localized near the dimerization interface. The tail dimer is associated with ∼80-bp upstream DNA, such that two flanking core promoter regions are positioned and oriented in a suitable form for PIC assembly in opposite directions. Also, cryoelectron tomography visualized the progress of the PIC assembly on the two core promoter regions, providing direct evidence for the role of the Med-PIC dimer in divergent transcription.

Structural insights into assembly of transcription preinitiation complex

RNA polymerase II (Pol II)-mediated transcription in eukaryotic cells starts with assembly of preinitiation complex (PIC) on core promoter, a DNA sequence of ∼100 base pairs. The transcription PIC consists of Pol II and general transcription factors TFIID, TFIIA, TFIIB, TFIIF, TFIIE, and TFIIH. Previous structural studies focused on PIC assembled on TATA box promoters with TFIID replaced by its subunit, TATA box-binding protein (TBP). However, the megadalton TFIID complex is essential for promoter recognition, TBP loading onto promoter, and PIC assembly for almost all Pol II-mediated transcription, especially on the TATA-less promoters, which account for ∼85% of core promoters of human coding genes. The functions of TFIID could not be replaced by TBP. The recent breakthrough in structure determination of TFIID-based PIC complexes in different assembly stages revealed mechanistic insights into PIC assembly on TATA box and TATA-less promotes and provided a framework for further investigation of transcription initiation.

Structural insights into nuclear transcription by eukaryotic DNA-dependent RNA polymerases

The eukaryotic transcription apparatus synthesizes a staggering diversity of RNA molecules. The labour of nuclear gene transcription is, therefore, divided among multiple DNA-dependent RNA polymerases. RNA polymerase I (Pol I) transcribes ribosomal RNA, Pol II synthesizes messenger RNAs and various non-coding RNAs (including long non-coding RNAs, microRNAs and small nuclear RNAs) and Pol III produces transfer RNAs and other short RNA molecules. Pol I, Pol II and Pol III are large, multisubunit protein complexes that associate with a multitude of additional factors to synthesize transcripts that largely differ in size, structure and abundance. The three transcription machineries share common characteristics, but differ widely in various aspects, such as numbers of RNA polymerase subunits, regulatory elements and accessory factors, which allows them to specialize in transcribing their specific RNAs. Common to the three RNA polymerases is that the transcription process consists of three major steps: transcription initiation, transcript elongation and transcription termination. In this Review, we outline the common principles and differences between the Pol I, Pol II and Pol III transcription machineries and discuss key structural and functional insights obtained into the three stages of their transcription processes.

Assembly of RNA polymerase II transcription initiation complexes

The first step of eukaryotic gene expression is the assembly of RNA polymerase II and general transcription factors on promoter DNA. This highly regulated process involves ∼80 different proteins that together form the preinitiation complex (PIC). Decades of work have gone into understanding PIC assembly using biochemical and structural approaches. These efforts have yielded significant but partial descriptions of PIC assembly. Over the past few years, cryo-electron microscopy has provided the first high-resolution structures of the near-complete mammalian PIC assembly. These structures have revealed that PIC assembly is a highly dynamic process. This review will summarize recent structural findings and discuss their implications for understanding cell type-specific gene expression.