ArticleScience (New York, N.Y.)2022
Transcriptional neighborhoods regulate transcript isoform lengths and expression levels.
Article in Science (New York, N.Y.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Synthetic Chromosomes in Yeast: A Platform for Understanding and Programming Eukaryotic Life.Microbial biotechnology · 2026Review
- Assembly and delivery of large DNA via chromosome elimination in yeast.Nature protocols · 2025Review
- Unraveling the regulatory dynamics of bidirectional promoters for modulating gene co-expression and metabolic flux in Saccharomyces cerevisiae.Nucleic acids research · 2025Article
- Transcriptional stochasticity reveals multiple mechanisms of long non-coding RNA regulation at the Xist-Tsix locus.Nature communications · 2025Article
- Multi-Omics Analysis Reveals Impacts of LincRNA Deletion on Yeast Protein Synthesis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Synthetic Genetic Elements Enable Rapid Characterization of Inorganic Carbon Uptake Systems inACS synthetic biology · 2025Article
- YeastFab Cloning of Toxic Genes and Protein Expression Optimization in Yeast.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Towards the first synthetic eukaryotic cell.Biosafety and health · 2024Review
- The rise and future of CRISPR-based approaches for high-throughput genomics.FEMS microbiology reviews · 2024Review
- Methodological advances enabled by the construction of a synthetic yeast genome.Cell reports methods · 2024Article
- Size fractionated NET-Seq reveals a conserved architecture of transcription units around yeast genes.Yeast (Chichester, England) · 2024Article
- A designer synthetic chromosome fragment functions in moss.Nature plants · 2024Article
- Building synthetic chromosomes from natural DNA.Nature communications · 2023Article
- Building a eukaryotic chromosome arm by de novo design and synthesis.Nature communications · 2023Article
- Consequences of a telomerase-related fitness defect and chromosome substitution technology in yeastCell genomics · 2023Article
- Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1.Heliyon · 2023Article
- Advancing Desulfurization in the Model BiocatalystApplied and environmental microbiology · 2023Article
- Investigation of Genome Biology by Synthetic Genome Engineering.Bioengineering (Basel, Switzerland) · 2023Review
- 3' Untranslated Regions Are Modular Entities That Determine Polyadenylation Profiles.Molecular and cellular biology · 2022Article
- Neighbourly modulation of transcript isoforms.Nature reviews. Genetics · 2022Article
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6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Sequence features of genes and their flanking regulatory regions are determinants of RNA transcript isoform expression and have been used as context-independent plug-and-play modules in synthetic biology. However, genetic context-including the adjacent transcriptional environment-also influences transcript isoform expression levels and boundaries. We used synthetic yeast strains with stochastically repositioned genes to systematically disentangle the effects of sequence and context. Profiling 120 million full-length transcript molecules across 612 genomic perturbations, we observed sequence-independent alterations to gene expression levels and transcript isoform boundaries that were influenced by neighboring transcription. We identified features of transcriptional context that could predict these alterations and used these features to engineer a synthetic circuit where transcript length was controlled by neighboring transcription. This demonstrates how positional context can be leveraged in synthetic genome engineering.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.