The compact macronuclear genome of the ciliate halteria grandinella: A transcriptome-like genome with 23,000 nanochromosomes

Weibo Zheng, Chundi Wang, Michael Lynch, Shan Gao

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

How to achieve protein diversity by genome and transcriptome processing is essential for organismal complexity and adaptation. The present work identifies that the macronuclear genome of Halteria grandinella, a cosmopolitan unicellu-lar eukaryote, is composed almost entirely of gene-sized nanochromosomes with extremely short nongenic regions. This challenges our usual understanding of chromosomal structure and suggests the possibility of novel mechvanisms in transcriptional regulation. Comprehensive analysis of multiple data sets reveals that Halteria transcription dynamics are influenced by: (i) nonuniform nanochromosome copy numbers correlated with gene-expression level; (ii) dynamic alterations at both the DNA and RNA levels, including alternative internal eliminated sequence (IES) deletions during macronucleus formation and large-scale alternative splicing in transcript maturation; and (iii) extremely short 59 and 39 untranslated regions (UTRs) and uni-versal TATA box-like motifs in the compact 59 subtelomeric regions of most chromo-somes. This study broadens the view of ciliate biology and the evolution of unicellu-lar eukaryotes, and identifies Halteria as one of the most compact known eukaryotic genomes, indicating that complex cell structure does not require complex gene architecture.

Original languageEnglish (US)
Article numbere01964-20
Pages (from-to)1-16
Number of pages16
JournalmBio
Volume12
Issue number1
DOIs
StatePublished - Jan 1 2021

Keywords

  • Alternative DNA splicing
  • Ciliate
  • Halteria grandinella
  • Nanochromosomes
  • Transcriptional initiation

ASJC Scopus subject areas

  • Microbiology
  • Virology

Fingerprint Dive into the research topics of 'The compact macronuclear genome of the ciliate halteria grandinella: A transcriptome-like genome with 23,000 nanochromosomes'. Together they form a unique fingerprint.

Cite this