Recently there have been expanding cases of non-Mendelian inheritance termed homology-dependent, i.e. sequence-dependent. Like in many other eukaryotes, sequence-dependent silencing of a gene can occur during vegetative growth; in addition, these mechanisms can participate in the programming of genome rearrangements during development. One particular distinguishing feature in ciliates is the decoupling of germline and somatic functions by two distinct nuclei, the diploid micronucleus (MIC) and a DNA-rich macronucleus (MAC). Micronuclear meiosis initiates sexual events and after haploid nuclei exchange, new micro- and macronuclei develop from the zygotic nucleus; the old MAC is eventually lost and replaced by the new one.
Advances in ciliate molecular biology have shown that very similar developmental alternatives can be determined by programmed genome rearrangements. Indeed, the development of a new macronucleus involves extensive rearrangements of the germline genome, including elimination of transposons and other repeated sequences and the precise excision of numerous single-copy Internal Eliminated Sequences (IESs) from coding and non-coding sequences. Genome-wide rearrangements discard nearly all non-genic DNA, resulting in streamlined gene-rich genomes. In Paramecium,
for instance, ~40,000 genes occupy only 72 Mb [13
]. In some cases, for example in the ciliate Oxytricha
, reordering, or "unscrambling", of the remaining DNA segments (Macronucleus Destined Segments, or MDSs) also occurs by translocation or inversion.
The amazingly high degree of specificity and reproducibility suggests a general mechanism for programming rearrangements. The parental ciliate cell must provide sufficient amount of information in order to produce a fully functional new macronucleus. Details of the mechanism that allows the cell to perfectly recognize hundreds of thousands of DNA sequences for elimination or rearrangement remain largely unknown. However, the discovery of homology-dependent maternal effects that can modify rearrangements patterns has shed some light on this process. In Paramecium
, both types of developmentally-regulated genome rearrangements—precise excision of IESs and imprecise DNA elimination—can be controlled by homology-dependent maternal effects that score the presence or absence of a gene in the macronucleus [14
]. Microinjection of a specific DNA sequence into the parental macronucleus can prevent that sequence from being eliminated from the progeny’s somatic genome. This appears to be general for a subset (approximately one third) of Paramecium
] termed maternally controlled IESs, or mcIESs. These observations imply trans-nuclear genome comparison during development.
The earliest model for epigenetic programming of DNA rearrangements, proposed by Paramecium
researchers, assumed that the whole genome of the parental MAC is transcribed, and that transcripts are exported to the developing MAC, where they regulate rearrangements in a homology-dependent manner. Two possibilities for regulating IES excision were proposed: either the maternal transcripts simply inhibit excision of homologous sequences or they provide homologous templates for repair after constitutive elimination [19
]. The latter hypothesis was rejected after demonstrating that mutations engineered in the sequence injected into the old MAC were not copied in the IES maintained in the new MAC; this was recently confirmed by showing that cleavage does not occur in engineered cell lines containing the IES permanently present in the MAC [21
]. On the other hand, there has been recent evidence in support of a protective
role of parental MAC transcripts in Paramecium
: use of RNAi to degrade specific transcripts results in elimination of homologous DNA sequences in the new MAC for both genes [22
] and IESs [23
]. However, a template role for maternal transcripts remains an attractive model to explain the specificity of rearrangements in other ciliates, including Oxytricha
, which is likely over one billion years distant from Paramecium
and requires more complex DNA rearrangements via descrambling
, in addition to removal of hundreds of thousands of intervening IESs, to construct functional, transcriptionally-active genes in the macronucleus. In this case, the maternal transcripts would provide templates for cleavage and repair during the DNA descrambling process.