Transcription-Austin最新文献

{"title":"Characterization of physical interactions between the <i>Drosophila</i> insulator binding protein BEAF and transcription-associated proteins.","authors":"Sunday Negedu, Elizabeth J Vidrine, Karissa L Chen, Cassidy L Magnon, Jamuna Tandukar, Khai B Lejeune, Oluwatobi T Ojemakinde, J Keller McKowen, Craig M Hart","doi":"10.1080/21541264.2026.2727737","DOIUrl":"https://doi.org/10.1080/21541264.2026.2727737","url":null,"abstract":"<p><p>Originally identified as a chromatin domain insulator binding protein, <i>Drosophila melanogaster</i> BEAF (Boundary Element-Associated Factor of 32 kDa) is predominantly associated with transcription start sites (TSSs) of housekeeping genes. It was previously shown that BEAF directly interacts with the transcription factor Serendipity-δ (Sry-δ). TSS-proximal BEAF can interact with distantly bound Sry-δ to activate a reporter gene. However, it is unknown if the ability of BEAF to communicate with transcription-associated factors from a distance is a common property. Here, we use yeast 2-hybrid assays to show that BEAF directly interacts with a variety of transcription-associated factors: both FACT subunits (Dre4 and SSRP), DREF, Rib, ROW, Map60, Apt, Wds, Cdk1, GFZF, and weakly with Adf1 and Kdm5. We further explored the interaction of BEAF with the histone chaperone FACT and transcription factors DREF, Rib, and ROW, including interrogating communication from a distance with a reporter gene assay and by analysis of S2 cell high-throughput chromosome conformation capture (Hi-C) data. When tagged with a VP16 activation domain, all five proteins activated <i>RpS12</i> and <i>yellow</i> promoters cooperatively with adjacent, promoter-proximal BEAF. Only ROW and the FACT subunit SSRP communicated with BEAF from a distance, and only ROW exhibited long-range interaction with BEAF in Hi-C data. Our results provide evidence for three mechanisms by which promoter-proximal BEAF might facilitate gene activation. First, it might affect promoter chromatin accessibility by recruiting chromatin proteins like FACT. Second, consistent with the model of housekeeping gene regulation by promoter-proximal elements, BEAF might cooperate with adjacent interacting transcription factors for promoter activation. Third, a subset of interacting transcription factors, including ROW and Sry-δ, might interact with BEAF from a distance, modifying the traditional paradigm of local regulation of housekeeping genes.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"1-25"},"PeriodicalIF":3.8,"publicationDate":"2026-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148945952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Statement of Retraction: Orphan nuclear receptor transcription factors as drug targets.","authors":"","doi":"10.1080/21541264.2026.2714669","DOIUrl":"https://doi.org/10.1080/21541264.2026.2714669","url":null,"abstract":"","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"1"},"PeriodicalIF":3.8,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148799592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MicroRNA expression and functions in viral infections.","authors":"Rebecca L Skalsky","doi":"10.1080/21541264.2026.2690822","DOIUrl":"https://doi.org/10.1080/21541264.2026.2690822","url":null,"abstract":"<p><p>MicroRNAs (miRNAs) are small, noncoding RNAs that have emerged as powerful players in the post-transcriptional regulation of gene expression. In the context of viral infections, cellular miRNAs play significant roles in modulating the complex host responses to pathogens and have essential roles in shaping viral replication. Moreover, several virus families encode viral miRNAs that manipulate the host environment and can tap into miRNA-regulated gene networks. Viral antigen expression itself can be directly miRNA regulated, and infection outcomes are substantially shaped by the miRNA activities that influence host anti-viral defense mechanisms. This review discusses common themes for both human and viral miRNAs in viral infection processes, highlighting their dual functions in both suppressing and promoting viral life cycles.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"1-13"},"PeriodicalIF":3.8,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148370504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RNA polymerase II removal: transcription quality control and gene regulation.","authors":"Benjamin Haworth, Pegah Abyaneh, Ana Tufegdžić Vidaković","doi":"10.1080/21541264.2026.2698182","DOIUrl":"10.1080/21541264.2026.2698182","url":null,"abstract":"<p><p>At the heart of the central dogma is the synthesis of RNA from a DNA template. In eukaryotes, this process is carried out by three RNA Polymerases - Pol I, II and III. While Pol I and Pol III are dedicated to producing rRNAs and tRNAs, it is Pol II that drives the complexity of eukaryotic life, transcribing all protein-coding genes and thousands of non-coding RNA loci in a context-specific manner. As such, Pol II faces specific challenges: it must traverse tens to thousands of kilobases of DNA, overcome any obstacles along the way and associate with the correct regulatory factors at the correct time and place. What happens if any of this goes wrong? Over the last couple of years, we learned that Pol II molecules unable to overcome these challenges are removed from genes. Moreover, cells also use eviction and destruction of the Pol II apparatus to regulate gene expression. Strikingly, some studies estimate the fate of at least 80% of Pol II molecules is to be removed from genes rather than to complete transcription. This Review will summarize recent discoveries of pathways that clear Pol II at different stages of the transcription cycle.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"17 2","pages":"129-162"},"PeriodicalIF":3.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13501999/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148809307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Goldilocks state of transcriptional readthrough for chimeric splicing.","authors":"Guillaume F Chanfreau","doi":"10.1080/21541264.2026.2642485","DOIUrl":"10.1080/21541264.2026.2642485","url":null,"abstract":"<p><p>Proper transcription termination coupled to pre-mRNA cleavage and polyadenylation is an important step in gene expression as it generates the 3'UTR of mRNAs and defines transcription units. Defective termination (transcriptional readthrough) can suppress transcription of downstream genes by transcriptional interference but can also promote the production of chimeric transcripts, which contain the exons of upstream genes spliced to exons of downstream genes. This review will summarize current findings of chimeric splicing between exons of adjacent genes generated by transcriptional readthrough and the conditions that promote these events. Chimeric splicing can be facilitated by inactivation of factors that promote transcription termination or of specific splicing factors, particularly those involved in 3'-splice site recognition. This effect is due to the tight coupling between recognition of the terminal intron 3'-splice site and of the downstream polyadenylation sites, and its impact on transcriptional termination. Production of chimeric transcripts is also increased in cellular conditions that perturb transcription termination, such as cellular stress, treatment with the chemotherapeutic agent Imatinib or viral infections. However, not all conditions that promote transcriptional readthrough result in chimeric splicing, suggesting that the production of chimeric mRNAs requires a \"Goldilocks\" state of alteration of the transcriptional machinery that allows for transcriptional readthrough without a general reduction of splicing efficiency.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"87-99"},"PeriodicalIF":3.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13501980/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147655180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isoform-resolved transcriptomics reveals stage-specific isoform switching and protein domain remodeling in <i>Helicoverpa armigera</i>.","authors":"Himalshi K Wickramage, Jack W Royle, Pawel Sadowski, Kevin J Dudley","doi":"10.1080/21541264.2026.2708591","DOIUrl":"10.1080/21541264.2026.2708591","url":null,"abstract":"<p><p>Insects exhibit pronounced developmental plasticity, driven by complex regulation of gene expression, including isoform-level modulation across developmental stages. However, the role of isoform-level regulation in the developmental transitions of <i>Helicoverpa armigera</i> remains underexplored. Here, we performed transcriptome analysis to characterize gene isoform-specific expression changes between the pupa and adult stages of <i>H. armigera</i>. Differential gene-isoform expression analysis revealed that many multi-isoform genes displayed distinct stage-biased regulation that was undetectable at the gene level, uncovering hidden layers of transcriptional complexity. Functional enrichment analyses of differentially expressed multi-isoform genes highlighted MAPK, Hippo, Wnt and apoptosis pathways, consistent with major cellular remodeling processes during the pupa to adult transition. Isoform switching analysis further identified isoform usage shifts between stages, particularly among genes associated with signaling and metabolic regulation. Protein domain and structural modeling revealed that several isoform pairs differed in domain composition, sequence identity, and predicted fold conformation, indicating potential functional divergence in isoform switched genes. Together, these findings suggest that isoform-level modulation may contribute to stage-specific diversification in <i>H. armigera</i>. This work establishes a foundation for understanding isoform‑driven developmental plasticity in insects and underscores the importance of isoform-level resolution for elucidating mechanisms of developmental gene regulation.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"163-180"},"PeriodicalIF":3.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13502018/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148594061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Promoter contacts by TFB and TFEα during archaeal transcription initiation.","authors":"Michael Micorescu, Kimberly Sheffield, Vlad Geshka, Hannah Tierney, Michael S Bartlett","doi":"10.1080/21541264.2026.2698170","DOIUrl":"10.1080/21541264.2026.2698170","url":null,"abstract":"<p><p>Transcription initiation by archaeal RNA polymerase (RNAP) is assisted by transcription factors, TBP, TFB, and TFEα, which show sequence, structural and functional homology to eukaryotic TBP, TFIIB, and TFIIEα. Previous low-resolution cross-linking studies of transcription complexes from the hyperthermophile archaeon <i>Pyrococcus furiosus</i> showed that the transcription bubble DNA makes extensive contacts with TFB and TFEα. Here, contacts between TFB and TFEα surfaces and promoter DNA are mapped with amino acid-to-base precision, using a high-resolution cross-link mapping method. The non-canonical amino acid <i>p</i>-benzoyl phenylalanine (Bpa) was incorporated into TFB1 or TFEα at several positions, transcription complexes were formed and cross-links induced, and the positions of cross-links were mapped by primer extension. In transcription pre-initiation complexes forming a transcription bubble (PICs), the TFB1 B-reader helix and loop conserved sequences interact with the DNA transcribed (T) strand near the upstream side of the transcription bubble, while the B-linker strand conserved sequence interacts with both the transcribed and the non-transcribed (NT) strands. In a 5 nucleotide initially transcribing complex (ITC), cross-links to TFB1 changed for the B-reader but not the B-linker, suggesting scrunching of part of the T strand in the RNAP main channel. The TFEα winged helix cross-linked the NT strand at the upstream edge of the transcription bubble in the PIC. In the ITC, the NT strand changed position dramatically relative to the TFEα wing tip, indicating that the DNA NT strand can bulge out of the main channel as transcription begins and downstream DNA is pulled in. The cross-linking data were compared with structural models of the archaeal PIC and ITC, and indicate that interactions between TFB conserved motifs and DNA are conserved from archaea to humans, while archaeal TFEα contacts to DNA are apparently dissimilar from what is seen in human RNAP II initiation complexes.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"113-128"},"PeriodicalIF":3.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13502027/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148438411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Endogenous eukaryotic CHO-K1 cell promoters as tools to improve the production of a difficult-to-express recombinant protein.","authors":"María Belén Ardusso, Agustina Gugliotta, Victoria Gastaldi, Claudio Prieto","doi":"10.1080/21541264.2026.2690790","DOIUrl":"10.1080/21541264.2026.2690790","url":null,"abstract":"<p><p>Recombinant proteins with applications in human and veterinary medicine are mainly produced in mammalian expression systems, particularly Chinese hamster ovary (CHO) cells. Although these cells enable proper folding and post-translational modifications, they often exhibit low specific productivity, which represents a critical limitation in large-scale biopharmaceutical manufacturing. Strong viral promoters, including CMV and its enhancer-enriched variant CMV+E, are commonly used to drive transgene expression. However, they are susceptible to epigenetic silencing and progressive loss of activity during prolonged culture, which can compromise yield stability. Endogenous host-cell promoters constitute a promising alternative, as they can maintain transgene expression in alignment with physiological and bioprocess regulatory mechanisms. Here, we assessed the activity of endogenous eukaryotic promoters previously identified in our laboratory from highly expressed CHO-K1 genes. The receptor-binding domain (RBD) of SARS-CoV-2 was selected as a model of a complex secretory glycoprotein domain. Our results demonstrate that the Hspa5 and Vim promoters enable sustained and high-level expression of recombinant RBD protein in CHO-K1 cells, achieving performance comparable to the enhancer-containing viral promoter CMV+E. Notably, Hspa5 and Vim are unoptimized genomic sequences lacking classical enhancers; nevertheless, their intrinsic stability and reduced susceptibility to silencing make them attractive regulatory elements for recombinant protein production. These findings highlight their potential for next-generation promoter engineering and for the development of long-term, high-yield mammalian expression systems for complex therapeutic proteins.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"100-112"},"PeriodicalIF":3.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13502045/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148333616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"miRNA dynamics in development: orchestrators of gene expression and cell fate.","authors":"Vaishnav Vasudevan, Mathieu W Segonds, Martin J Simard","doi":"10.1080/21541264.2026.2643027","DOIUrl":"10.1080/21541264.2026.2643027","url":null,"abstract":"<p><p>MicroRNAs (miRNAs) are central regulators of gene expression, shaping cell fate, tissue identity, and organismal physiology. From the earliest stages of development through later processes of tissue differentiation, miRNAs operate within dynamic, context-dependent networks. Although the predominant role of miRNAs is to guide Argonaute-containing complexes to repress target mRNAs, the downstream consequences and mechanisms of action vary widely across developmental stages and tissue types. In this review, we examine the diverse roles of microRNAs in animal development across species and highlight emerging perspectives that are progressively refining our understanding of their function.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"67-86"},"PeriodicalIF":3.8,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13134402/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147475852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic and structural insights into TATA-Binding protein from cestodes.","authors":"Abraham Landa, Elisa Heredia-Gómez, Cristina González-Kulikova, Laura A Velázquez-Villegas, Oscar Rodríguez-Lima","doi":"10.1080/21541264.2026.2633940","DOIUrl":"10.1080/21541264.2026.2633940","url":null,"abstract":"<p><p>The TATA-binding protein (TBP) is an essential component of the eukaryotic transcriptional machinery, yet little is known about the structure, evolution, and functional divergence of TBP paralogs in parasitic flatworms. Here, we performed a comprehensive comparative analysis of TBP1 and TBP2 across cestode species of medical and veterinary relevance. Using genomic annotation, multiple sequence alignment, homology modeling, phylogenetics, electrostatic potential mapping, and protein - DNA docking complemented with molecular dynamics (MD) simulations, we reveal that both paralogs maintain a highly conserved genomic organization and the canonical TBP α/β saddle architecture. TBP1 exhibits moderate variability in sequence and electrostatic in peripheral regions, whereas TBP2 is more conserved, suggesting distinct evolutionary constraints. Despite paralog divergence, all cestode TBPs retain the key aromatic and basic residues required for minor-groove recognition of the TATA box and interaction with general transcription factors. Docking and MD simulations confirm a conserved pattern of TATA-binding across species, with TBP2 displaying exceptionally uniform interaction networks. Together, these findings provide genomic and structural data for TBPs in cestodes, suggesting the existence of paralog-specific regulatory roles and offering new insights into transcriptional control in parasitic flatworms.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"12-27"},"PeriodicalIF":3.8,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13134418/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147311209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}