Functional atlas of vertebrate viral RNA elements that stabilize RNA and enhance translation.

Host transcriptional corepressor TLE1 is commonly exploited by RNA viruses for replication.

Viral genomes encode transcriptional regulators that alter the expression of host genes to facilitate virus replication, and the comprehensive regulatory network they form is largely elusive. Utilizing influenza A virus (IAV) as a model, we demonstrate that the viral nucleoprotein (NP) harnesses the host transcriptional corepressor TLE1 to enhance viral polymerase activity while suppressing the cellular innate response. NP-TLE1 recognition was realized via a conserved basic helix-loop-helix (bHLH)-like motif across IAV subtypes, which subsequently recruited another transcription factor, Kruppel-like factor 4 (KLF4), to suppress antiviral signaling. Blockage of the NP-TLE1 interaction by a peptide AH49A provided antiviral protection in vitro and in vivo. Moreover, the NP-TLE1-KLF4 axis was widely observed across various RNA viruses, as evidenced by the presence of a bHLH-like motif in the SARS-CoV-2 nucleocapsid protein. Loss-of-function substitutions in the bHLH-like motif attenuated the replication of both IAV and SARS-CoV-2. Our study reveals how RNA viruses exploit the components of the host transcription machinery to facilitate virus replication.

Introns encode a vast class of Kink-loop RNAs that autoregulate pre-mRNA splicing

Introns occupy nearly one-third of the human genome, yet whether they encode widespread regulatory functions remains unclear. Here, we identify a pervasive class of intron-derived Kink-loop RNAs (klRNAs) that locally control pre-mRNA processing. Using complementary enrichment strategies, we uncovered approximately 15,200 and 3,500 previously unannotated klRNAs in humans and mice, respectively. Bound by the conserved RNA-binding protein 15.5K, klRNAs constitute a distinct family of structured RNAs that arise predominantly from introns, lack the canonical stems of Kink-turn motifs, and do not exhibit antisense complementarity to known non-coding RNAs. Depletion of 15.5K disrupts klRNA biogenesis and leads to their global loss. Transcriptome-wide analyses reveal that klRNAs function predominantly in cis to suppress excision of their host introns in a kink-loop structure-dependent manner, thereby enabling introns to regulate their own processing. Together, our findings establish RNA structure-encoded autoregulation as a pervasive mechanism controlling intron fate and reveal that introns are active sources of regulatory RNAs. One Sentence Summary A huge class of orphan backward K-loop RNAs

Cross-genus analysis reveals architecturally programmed sgRNA synthesis patterns in coronaviruses.

Coronaviruses employ discontinuous transcription to produce canonical subgenomic RNAs (sgRNAs) essential for gene expression. Although TRS-dependent template switching mechanism has been proposed, its structural basis remains poorly defined, and the functional significance of abundant non-canonical sgRNAs persists as a critical gap since the discovery of discontinuous RNA synthesis. Here, we help bridge this gap through the first cross-genus integrated analysis of coronavirus transcriptomes and RNA interactomes. We show that canonical sgRNA formation is associated with same-direction RNA-RNA interactions. In contrast, non-canonical sgRNAs form through distinct architectural mechanisms: short-range junctions mediated by stem-loop structures overlapping genomic deletion hotspots, and conserved long-range ORF1a-N interactions generating sgRNAs encoding immune-modulatory ORFs - a function not previously attributed to non-canonical transcription. These findings suggest architecturally programmed discontinuous RNA synthesis and highlight a potential link between non-canonical sgRNAs, genomic plasticity, and immune modulation, which may have implications for coronavirus adaptation.

Canonically minimal RNA-guided insertion sequences expand into large elements that disseminate antimicrobial resistance

Using high-throughput junction mapping together with large-scale comparative genomics, this work redefined the in vivo structural boundaries, growth, and mobilization of IS110 elements and uncovered a previously unrecognized size continuum extending to ∼100 kb, driven by progressive additions.

A small RNA guides a post-transcriptional regulatory protein to its target

Sense-Antisense RNA duplexes mediate stress-responsive translational control in Plasmodium falciparum.

Plasmodium falciparum, the primary cause of human malaria, relies on tightly coordinated gene-expression programs to adapt to host-derived stress despite possessing a limited repertoire of canonical transcription factors. Antisense long noncoding RNAs have emerged as important regulators of parasite biology, including virulence gene regulation and sexual commitment; however, their prevalence, origin, and broader functional significance remain poorly understood. Here, we demonstrate that antisense transcription is a widespread, reproducible, and regulated feature of the P. falciparum transcriptome rather than a byproduct of pervasive euchromatic transcription. Environmental stress, including febrile temperature exposure and artemisinin treatment, extensively remodelled antisense transcription, particularly at loci associated with virulence and stress adaptation, promoting widespread sense-antisense RNA duplex formation. Functional analyses of two stress-responsive chromatin regulators, PfGCN5 and PfHDAC1, identified as antisense-expressing loci, revealed that increased antisense expression elevated steady-state mRNA abundance while reducing cognate protein levels. Mechanistically, sense-antisense RNA duplex formation stabilized complementary transcripts but suppressed translation. Integrated transcriptomic, RNA-RNA duplex profiling, ribosome sequencing, and proteomic analyses further showed that duplex-enriched transcripts exhibit reduced ribosome occupancy and reduced protein abundance, accompanied by localized antisense enrichment near transcription end sites and altered ribosome distribution consistent with impaired translational engagement. Collectively, our findings identify an antisense RNA-ribosome regulatory axis that couples RNA duplex formation to adaptive translational control, providing a previously unrecognized mechanism underlying stress adaptation and post-transcriptional gene regulation in P. falciparum.