Nucleic Acids Research

Integrative and conjugative elements (ICEs) are mobile genetic elements that widely disseminate adaptive traits among bacterial populations. Despite their prevalence, the regulatory mechanisms orchestrating ICE integration and excision remain poorly understood. Here, we investigate the transcriptional regulation of the integrase gene (int) in ICEKp1 of Klebsiella pneumoniae. Our results demonstra…

CRISPR/Cas9-induced DNA double-strand breaks (DSBs) trigger diverse repair outcomes, yet the dynamic regulatory networks governing these outcomes remain incompletely understood. Here, we develop indel pattern-guided repair mapping, an integrative framework that deciphers DSB repair mechanisms by integrating repair outcome spectra, kinetic dynamics, and functional gene regulation. Our analysis cat…

Poly(ADP-ribose) (PAR) is a highly charged, intrinsically flexible nucleic-acid-like homopolymer composed of ADP-ribose units. It serves as a critical post-translational modification that is rapidly synthesized in response to DNA damage and participates in diverse important cellular processes, including DNA repair, chromatin remodeling, and RNA biogenesis, often by promoting biomolecular phase se…

Retroviral integration is mediated by viral integrase (IN), which synapses two viral long terminal repeat DNA ends and produces a series of nucleoprotein complexes known as intasomes. While structural studies of mature intasomes have illuminated key aspects of their architecture and provided insights into the integration reaction, the sequence of events driving IN oligomerization and engagement o…

The three-dimensional (3D) genome organization specifies how the distal regulatory elements in the linear genome interact with target genes to regulate transcription. Several experimental methods have been developed to study the 3D genome organization. However, these methods are, in general, expensive, technically challenging, and time-consuming. We present Convolutional Neural Networks-Chromatin…

The ability to precisely control gene expression is fundamental to studying biological processes. Using site-specific recombinases such as FLP, gene expression can be controlled, albeit with limited spatio-temporal precision. We develop a photocaged FLP recombinase, which can be precisely controlled using light, and we demonstrate its efficacy in Caenorhabditis elegans. We use genetic code expans…

Rolling circle amplification (RCA) is a powerful isothermal nucleic acid amplification technique prized for its robustness and simplicity. However, conventional RCA-based detection is fundamentally limited by the stoichiometry of padlock probe ligation, wherein each target molecule ideally yields only one circular template. Existing strategies to improve ligation efficiency often sacrifice key be…

Upstream open reading frames (uORFs) are critical regulators of messenger RNA translation, yet their evolutionary dynamics remain poorly understood. Here, we analyze uORF evolution across Drosophila species and uncover pervasive birth-death turnover. This process is characterized by a persistent excess of upstream start codon (uATG) gains over losses, shaped by the interplay of mutational input a…

Current one-pot clustered regularly interspaced short palindromic repeats diagnostics are limited by the cis-cleavage activity of Cas nucleases, which leads to amplicon degradation during amplification. Here, we report a streamlined strategy that overcomes this limitation. By integrating a bipartite split-crRNA into Cas12a (SCas12a), we separate target recognition from PAM dependency and complete…

Segmented virus genomes, such as those of influenza A viruses (IAVs), consist of multiple segments. This structure enables the generation of novel strains through reassortment, where segments from different strains combine, greatly increasing the genetic diversity of segmented viruses. Reassortment can confer new biological properties to viruses, such as increased transmission rates, as evidenced…

Changes in RNA splicing over the course of evolution have profoundly diversified the functional landscape of the human genome. Emerging evidence suggests that inverted pairs of intronic Alu elements can promote exon skipping by forming RNA stem-loop structures. However, their prevalence and influence throughout evolution remain unknown. Here, we present a systematic analysis of inverted Alu pairs…

During pre-mRNA splicing, the branch helix forms when U2 snRNP engages with introns to initiate spliceosome assembly. The branch helix is mutually exclusive with the U2 snRNA branchpoint-interacting stem loop (BSL). In yeast, BSL alteration affects branchpoint recognition, but its role in human cells, where branchpoint usage is more flexible, is unknown. To examine the impact of perturbing BSL ba…

Cellular RNA folds into complex helical structures that are attractive targets for controlling biological activity and treating diseases using RNA-binding ligands. Peptide nucleic acid (PNA) is a neutral DNA analog uniquely suited for triple-helical recognition of RNA. However, the applications of triplex-forming PNAs have been limited by sequence restrictions, as stable base triples are formed o…

Type I toxin-antitoxin systems (T1TAs) rely on tight posttranscriptional control to prevent inadvertent toxin synthesis, yet the molecular mechanisms underlying this control are highly diverse. Here, we uncover an RNA-based mechanism that controls translation initiation in the enterobacterial timPR system. Unlike most T1TAs, which typically rely on ribonucleolytic messenger RNA (mRNA) processing …

SUMOylation regulates chromatin states and transcriptional programs that preserve cellular identity, yet how perturbation of the SUMOylation pathway impacts adipocyte plasticity remains unclear. Here, we show that brief pharmacologic inhibition of SUMOylation in human pre-adipocytes using TAK-981 primes stable de novo beige differentiation in the presence of the PPARG agonist rosiglitazone. Trans…

Enzymatic toxins targeting nucleic acids are a widespread strategy for resolving biological conflicts. Ubiquitous HEPN domain-containing proteins harbor a conserved RNase motif and are found in both prokaryotes and eukaryotes. In prokaryotes, HEPN domain toxins frequently pair with adjacent MNT domain antitoxins to form the prevalent type VII HepT/MntA toxin-antitoxin (TA) system. Here, we identi…

The Yes-associated protein YAP belongs to the TEAD (TEA/ATTS domain) transcriptional co-activators that shuttle between the cytoplasm and the nuclear compartment. YAP and its paralog TAZ (transcriptional co-activator with PDZ-binding motif) play essential roles in the Hippo pathway to control tissue and organ size. In addition, YAP is critically involved in numerous cellular processes such as dif…

Site-specific non-long terminal repeat (non-LTR) retrotransposon-mediated gene therapy has the potential to revolutionize medicine by allowing insertion of large gene cargos at specific sites in a genome. Despite decades of effort, the reaction sequence of these elements remains to be fully elucidated, limiting the ability to engineer improved activity for gene insertion. One major question conce…

Bacteria of class Bacteroidia lack Shine-Dalgarno (SD) sequences and instead rely on other messenger RNA (mRNA) features, including upstream adenines, for start codon selection. Bacteroidia ribosomes contain the anti-SD (ASD) sequence of 16S ribosomal RNA (rRNA) but are "blind" to SD sequences. This occurs due to the sequestration of the ASD through interactions with bS21, bS18, and bS6 on the 30…

Bacteroidia ribosomes are "blind" to Shine-Dalgarno (SD) sequences because the anti-SD (ASD) of 16S rRNA is sequestered by bS21, bS18, and bS6 on the 30S platform. In Flavobacterium johnsoniae, one gene contains a strong SD sequence-rpsU, which encodes bS21. Flavobacterium johnsoniae ribosomes lacking bS21 translate rpsU at a higher rate, which establishes an autoregulatory cycle. Here, we target…