Agriculture Reference
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astonishing connection that strongly implies that there has been an
evolutionary transition from an invasive TE DNA removal system to
an invasive gene silencing system and that both use nucleotide pairing to
convey information speci
city (Matzke and Scheid 2007).
The transition of DNA elimination to DNA expression silencing may
also be represented by the incredible conservation of the cross-species
homologous function of the chromodomain containing archetypal pro-
tein Heterochromatin Protein 1 (HP1) that controls heterochromatin
spreading (James and Elgin 1986). The DNA elimination proteins, Pro-
grammed DNA Degredation-1 (Pdd-1) and Pdd-3 in ciliates, also contain
chromodomain modules and bind to chromatin. Chromodomain-depen-
dent chromatin modi
cation was found to be both required for DNA
elimination and to be involved in the RNA interference (RNAi)-mediated
chromatin silencing system (Garnier et al. 2004; Nowaki et al. 2005). The
ciliate surveillance system appears to have both intriguingly similar and
different features with respect to its relationship with RNA-mediated
gene silencing in multicellular systems. Ciliate and multicellular DNA
surveillance occurs by RNA/RNA, not RNA/DNA pairing, indicating
that the genomic DNA must be transcribed to be surveilled. Remarkably,
in RNA-directed chromatin silencing, the target locus also must be
transcribed and the recognition occurs through RNA/RNA pairing.
Also, paired sequences are blocked from targeted dysfunction by elim-
ination. Elimination is therefore the default pathway, whereas in
dsRNA-mediated silencing in complex species, gene function is the
default pathway (Mochizuki and Gorovsky 2004). This disparity may
re
c locus targeting
dsRNA versus a whole genome surveillance process (Yao and Chao
2005). Homologous nucleotide pairing in sexual reproduction became
extraordinarily accurate and ef
ect the different error rate tolerances of speci
cient by the coevolution of the elaborate
protein machinery involved. This machinery may participate in infor-
mation storage and transfer such as in dsRNA-mediated silencing. The
possible structural or functional relationships of pairing factors such as
Dmc1 and Rad51, in RNA or DNA pairing-mediated gene silencing
remain largely unexplored.
The
fingerprints of the introduction of repetitive DNA sequences into
genomes by TE invasion are also found in epigenetic mechanisms in
many other species, such as in the germ line identity and function that
occurs in female gametophyte formation in
Arabidopsis
, involving
AGO9 (Olmedo-Mon
l et al. 2010), with the PiWi and Aubergine class
ARGONAUTE proteins in
Drosophila
, with Zebra
sh P element-medi-
ated silencing (Kavi et al. 2005; Girard et al. 2006; Irvine et al. 2006;
Megosh et al. 2006; Klattenhoff and Theurkauf 2008) and activity of
