TRNA Genes Affect Chromosome Structure and Function via Local Effects.

Omar Hamdani,Josefina Ocampo,Josh Lawrimore,Oliver J Rando,David J Clark,Rohinton T Kamakaka,Kenneth Y Wu,Tetsuya J Kobayashi,Namrita Dhillon,Kerry Bloom,Tsung-Han S Hsieh,Răzvan V Chereji,Masaya Oki,Brandon Friedman,Jacob G Kirkland,Derek Fulton,Takahiro Fujita

doi:10.1128/mcb.00432-18

Abstract

The genome is packaged and organized in an ordered, nonrandom manner, and specific chromatin segments contact nuclear substructures to mediate this organization. tRNA genes (tDNAs) are binding sites for transcription factors and architectural proteins and are thought to play an important role in the organization of the genome. In this study, we investigate the roles of tDNAs in genomic organization and chromosome function by editing a chromosome so that it lacked any tDNAs. Surprisingly our analyses of this tDNA-less chromosome show that loss of tDNAs does not grossly affect chromatin architecture or chromosome tethering and mobility. However, loss of tDNAs affects local nucleosome positioning and the binding of SMC proteins at these loci. The absence of tDNAs also leads to changes in centromere clustering and a reduction in the frequency of long-range HML-HMR heterochromatin clustering with concomitant effects on gene silencing. We propose that the tDNAs primarily affect local chromatin structure, which results in effects on long-range chromosome architecture.

Highlights

The genome is packaged and organized in an ordered, nonrandom manner, and specific chromatin segments contact nuclear substructures to mediate this organization. tRNA genes are binding sites for transcription factors and architectural proteins and are thought to play an important role in the organization of the genome
TRNA genes are a class of active genes found on all chromosomes and are bound by transcription factors TFIIIB and TFIIIC and RNA polymerase (Pol) III. tDNAs are short, highly transcribed DNA sequences [21] that are usually nucleosome free with strongly positioned flanking nucleosomes [22,23,24,25]
TFIIIC helps recruit TFIIIB to AT-rich sequences upstream of the tDNA. tDNA-bound transcription factors function via interactions with cofactors. tRNA genes are sites of binding for numerous chromatin proteins, including the architectural SMC proteins, nuclear pore proteins, chromatin remodelers, and histone modifiers

Summary

Introduction

The genome is packaged and organized in an ordered, nonrandom manner, and specific chromatin segments contact nuclear substructures to mediate this organization. tRNA genes (tDNAs) are binding sites for transcription factors and architectural proteins and are thought to play an important role in the organization of the genome. TRNA genes (tDNAs) are binding sites for transcription factors and architectural proteins and are thought to play an important role in the organization of the genome. Attachment of centromeres to the spindle pole and attachment of telomeres to the nuclear membrane depending upon chromosome arm length help organize the nucleus [8]. Besides DNA sequence elements, numerous proteins play a role in nuclear organization via networks of interactions between nuclear-membrane and chromatin-bound proteins. While individual tRNA genes turn over rapidly as a result of mutational inactivation and gene loss [36,37,38], a subset of tDNAs are syntenic with respect to neighboring sequences [39, 40], and data suggest that these conserved tDNAs possess chromosome position-specific functions in gene regulation (reviewed in references 41 and 42). The presence of a tDNA in close proximity to an RNA Pol II-transcribed gene promoter antagonizes transcription from the Pol II-transcribed gene in a phenomenon referred to as tRNA gene-mediated (tgm) silencing [30, 51, 52]

Methods

Results

Conclusion