PgmNr C40: Transiently maintained somatic chromosomes of Tetrahymena contain development-specific genes.

Authors:
Y. Liu 1 ; L. Feng 1 ; E. Hamilton 2 ; J. Xiong 3 ; G. Wang 3 ; W. Dui 1 ; L. Khadr 1 ; W. Miao 3 ; E. Orias 2


Institutes
1) Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; 2) Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; 3) Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.


Abstract:

In the ciliate Tetrahymena, programmed genome rearrangement events accompany the differentiation of the somatic macronucleus (MAC) from the germline micronucleus (MIC). Internal eliminated sequences (IES), most of which are likely derived from transposable elements, are excised by an RNAi-dependent pathway. Furthermore, the 5 MIC chromosomes are fragmented into ~200 MAC chromosomes at highly conserved chromosome breakage sequences (CBS), followed by de novo telomere addition. Intriguingly, some MAC chromosomes are lost soon after MAC differentiation, thereafter referred to as non-maintained macronuclear chromosomes (NMC).

Systematic comparison between the MIC and MAC genome sequences reveals several large NMC. In contrast to IES, NMC are still present in developing MAC during late conjugation. More importantly, these NMC generate high levels of mRNA, but very low levels of small RNA.  Many NMC-contained genes encode conserved proteins, potentially involved in development-specific events. Here we focus on NMC-3 (~12 kb), which contains TPB3, a putative PiggyBac transposase with potential roles in IES excision. NMC-3 is quickly lost in mature MAC during asexual propagation, attributable to lack of efficient replication origins. Deleting either the left or right flanking CBS effectively prevents its loss. TPB3 is expressed late in conjugation, during developing MAC formation of the progeny. Deleting NMC-3 from the germline MIC of parental cells—and consequently developing MAC of the progeny—abolishes TPB3 expression.  Conjugation progress delay and progeny growth defects are also observed. Sequencing developing and mature MAC genomes from these progeny reveals that a small subset of IES is affected. We conclude that these NMC contain development-related genes, providing a novel mechanism for achieving a highly specific gene expression pattern.