ArticleGenome biology2017
Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed, 46 citations in OpenAlex.
- Multilevel genomic constraints shape nuclear tRNA gene organization in plants.The Plant journal : for cell and molecular biology · 2026Article
- Regulation of tRNA expression during the social cycle of the amoeba Dictyostelium discoideum.BMC molecular and cell biology · 2026Article
- Targeting tRNA-Arg-TCT-4-1 suppresses cancer cell growth and tumorigenesis.bioRxiv : the preprint server for biology · 2026Article
- Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations.Nature communications · 2025Article
- An RNA polymerase III tissue and tumor atlas uncovers context-specific activities linked to 3D epigenome regulatory mechanisms.bioRxiv : the preprint server for biology · 2025Article
- Aspergillus fumigatus dsRNA virus promotes fungal fitness and pathogenicity in the mammalian host.Nature microbiology · 2025Article
- A tRNA gene potential to activate interferon signaling involves selective termination and is suppressible by La protein/SSB.Nucleic acids research · 2025Article
- Neuron-Specific Glycine Metabolism Links Transfer RNA Epitranscriptomic Regulation to Complex Behaviors.Biological psychiatry global open science · 2025Article
- Inter-chromosomal transcription hubs shape the 3D genome architecture of African trypanosomes.Nature communications · 2024Article
- Evidence of RNA polymerase III recruitment and transcription at protein-coding gene promoters.Molecular cell · 2024Article
- Selective gene expression maintains human tRNA anticodon pools during differentiation.Nature cell biology · 2024Article
- Selection of tRNA Genes in Human Breast Tumours Varies Substantially between Individuals.Cancers · 2023Article
- tRNA dysregulation and disease.Nature reviews. Genetics · 2022Review
- A cancer-associated RNA polymerase III identity drives robust transcription and expression of snaR-A noncoding RNA.Nature communications · 2022Article
- Widespread association of ERα with RMRP and tRNA genes in MCF-7 cells and breast cancers.Gene · 2022Article
- RNA polymerase III transcription and cancer: A tale of two RPC7 subunits.Frontiers in molecular biosciences · 2022Review
- The nuclear and cytoplasmic activities of RNA polymerase III, and an evolving transcriptome for surveillance.Nucleic acids research · 2021Article
- The genomic loci of specific human tRNA genes exhibit ageing-related DNA hypermethylation.Nature communications · 2021Article
- Extensive profiling of the expressions of tRNAs and tRNA-derived fragments (tRFs) reveals the complexities of tRNA and tRF populations in plants.Science China. Life sciences · 2021Article
- RNA Polymerase III, Ageing and Longevity.Frontiers in genetics · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundThe human genome is hierarchically organized into local and long-range structures that help shape cell-type-specific transcription patterns. Transfer RNA (tRNA) genes (tDNAs), which are transcribed by RNA polymerase III (RNAPIII) and encode RNA molecules responsible for translation, are dispersed throughout the genome and, in many cases, linearly organized into genomic clusters with other tDNAs. Whether the location and three-dimensional organization of tDNAs contribute to the activity of these genes has remained difficult to address, due in part to unique challenges related to tRNA sequencing. We therefore devised integrated tDNA expression profiling, a method that combines RNAPIII mapping with biotin-capture of nascent tRNAs. We apply this method to the study of dynamic tRNA gene regulation during macrophage development and further integrate these data with high-resolution maps of 3D chromatin structure.
resultsIntegrated tDNA expression profiling reveals domain-level and loop-based organization of tRNA gene transcription during cellular differentiation. tRNA genes connected by DNA loops, which are proximal to CTCF binding sites and expressed at elevated levels compared to non-loop tDNAs, change coordinately with tDNAs and protein-coding genes at distal ends of interactions mapped by in situ Hi-C. We find that downregulated tRNA genes are specifically marked by enhanced promoter-proximal binding of MAF1, a transcriptional repressor of RNAPIII activity, altogether revealing multiple levels of tDNA regulation during cellular differentiation.
conclusionsWe present evidence of both local and coordinated long-range regulation of human tDNA expression, suggesting the location and organization of tRNA genes contribute to dynamic tDNA activity during macrophage development.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.