Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation

Kevin Van Bortle,Michael P Snyder,Douglas H Phanstiel

doi:10.1186/s13059-017-1310-3

Kevin Van Bortle, Michael P Snyder + Show 1 more

Open Access

https://doi.org/10.1186/s13059-017-1310-3

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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.

Highlights

The human genome is hierarchically organized into local and long-range structures that help shape cell-type-specific transcription patterns
For tDNA transcription profiling, we chose to map nascent RNA reads to the entire human genome space to avoid false positives arising from sequence reads that are unrelated to Transfer RNA (tRNA) [50]
Downregulation of tRNA genes coincides with enhanced MAF1 occupancy We find that the expression of transcription factor (TF) involved in RNA polymerase III initiation and transcription elongation moderately decreases after differentiation of THP-1 monocytes (Fig. 5a)

Summary

Introduction

The human genome is hierarchically organized into local and long-range structures that help shape cell-type-specific transcription patterns. Mapping of RNA polymerase III, represents an imperfect measure of tRNA gene activity that does not directly assay the level of nascently transcribed RNA To this end, biotin-capture based genomic run-on experiments, such as BioGRO and precision nuclear run-on sequencing (PRO-seq), allow quantitative transcriptional profiling and mapping of RNA polymerases [18,19,20,21]. Biotin-capture based genomic run-on experiments, such as BioGRO and precision nuclear run-on sequencing (PRO-seq), allow quantitative transcriptional profiling and mapping of RNA polymerases [18,19,20,21] Leveraging both RNA polymerase III occupancy with biotin-capture of nascent, demethylated tRNAs may provide a more accurate measure of tRNA gene expression in growing cells

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