ATP-dependent chromatin remodelers reorganize promoter nucleosomes to create accessible, transcription-ready chromatin. Remodelers such as RSC clear nucleosomes, others like INO80 position the +1 nucleosome, SWR1 swaps H2A for H2A.Z, and ISWI spaces arrays. Their coordinated, nonsequential actions balance nucleosome removal, positioning, and restoration during transcription, supporting efficient RNA polymerase passage.

DNA double-strand breaks are repaired by NHEJ, which forms a long-range synaptic complex that shifts to a DNA-PKcs free short-range state. Cryo-EM reveals three transitional complexes with distinct DNA-PKcs dimers. Autophosphorylation triggers outward rotation of Ku and DNA-PKcs, exposing breaks and releasing DNA-PKcs. An inactive dimer suggests a full regulatory cycle.

RNA polymerase III transcribes 5S rRNA, tRNAs, and other short RNAs. Cryo-EM of yeast TFIIIA-TFIIIC on the 5S promoter shows TFIIIA bridging DNA to recruit TFIIIC. Visualizing Brf1-TBP DNA binding by TFIIIB reveals the full length 5S gene wrapping the complex, illuminating initiation assembly and contrasting with Pol II transcription mechanisms.

DNA double strand breaks are cytotoxic lesions whose misrepair promotes cancer. We used single-particle cryo-EM to visualize human NHEJ assemblies in which Ku, DNA-PKcs, LigIV, XRCC4, and XLF first form a long-range complex holding DNA ends apart, then transition to a short-range, LigIV-mediated alignment for ligation to complete accurate end joining.

Eukaryotic transcription assembles a Pol II preinitiation complex. Cryo-EM of human Mediator-bound PIC shows Mediator, recruited by transcription factors, scaffolds PIC formation and promotes TFIIH/CDK7 phosphorylation of the Pol II CTD. Transcription factor sites are tethered to the tail; Mediator stabilizes CDK7 and presents two CTD binding sites enabling phosphorylation.

SWI/SNF is a conserved ATP-dependent chromatin remodeler that slides/evicts nucleosomes to create accessible DNA. Cryo-EM of yeast SWI/SNF-nucleosome reveals an ARP module between ATPase and body, linked by Snf2 HSA. The body’s Snf12-Snf5-Swi3 scaffold centers Swi1. Snf5 engages the acidic patch, rationalizing cancer mutations and +1 nucleosome remodeling mechanism.

Parainfluenza virus 5, a paramyxovirus, packages its RNA in a nucleoprotein template. The L protein performs RNA synthesis, capping, and methylation, requiring P as a cofactor. We present a near-atomic structure of the complete L-P complex, an antiviral target, revealing methyltransferase/CTD rearrangements relative to RdRp that may switch between replication and transcription.

Pol III initiation is TFIIIB-dependent and tightly regulated. Cryo-EM structures of Pol III pre-initiation complexes show TFIIIB encircling upstream promoter DNA and engaging Pol III to stabilize C34 winged helix domains over the active site cleft. The PIC architecture resembles Pol II. An elongation complex scaffold reveals facilitated recycling before transcription reinitiation events.

Pol I initiation relies on Core Factor (CF) to recognize promoter DNA and build the pre-initiation complex. A 3.8-Å cryo-EM structure of yeast Pol I-CF-DNA shows bipartite CF binding from -27 to -16. CF mobility tunes Pol I cleft states and stabilizes Rrn7 NTD or A49 winged helices, supporting an ATP-independent ratchet that melts promoter DNA, unlike Pol II translocation.

Eukaryotic Pol II transcription initiates when a multi-subunit pre-initiation complex assembles at promoters to open DNA and define the start site. Cryo-EM structures capture the human PIC in closed, open, and initially transcribing states. Newly resolved elements include TFIIE, TFIIH, and segments of TFIIA, TFIIB, and TFIIF. Comparisons reveal stepwise rearrangements, highlight TFIIB’s bubble-stabilizing role, and support XPB’s translocase activity.