Recombination-independent homologous pairing: its existence and implications
In many organisms, homologous (or repetitive) chromosomal regions can engage in pairing or/and undergo
concerted epigenetic changes in the apparent absence of DNA breakage and recombination [1]. A large
number of such homology-dependent phenomena has been described in animals [1,2]. For example, during
mammalian development, selected allelic loci are known to pair transiently, presumably to establish appro-
priate patterns of gene expression [3]. The association of X chromosomes prior to random X-chromosome
inactivation in mammalian females provides a paradigmatic example of such a process [4]. Moreover, mam-
malian genomes contain large amounts of repetitive DNA normally silenced in the form of constitutive hete-
rochromatin [5]. The initiation of such silencing can occur on newly introduced exogenous tandem repeat
arrays and does not require RNA interference [6,7], whereas its pathological misregulation has been impli-
cated in several types of cancer [8] and other disease, such as Type I Facioscapulohumeral muscular dys-
trophy [9]. The mechanistic basis of homology (or repeat) recognition in all these situations remains
unknown.
The classical example of recombination-independent pairing was described in Drosophila melanogaster and
other Diptera insects [10]. In these animals, homologous chromosomes remain associated in the majority of
cell types during development and later in the adult life. The paired state is dynamic [11] and plays a critical
role in regulating transvection, a phenomenon in which two alleles comprise one expression unit due to their
close physical proximity [10]. Recent studies using haplotype-resolved HiC [12,13] and super-resolution
microscopy [14] yielded two important insights. First, it became apparent that the degree of pairing fluctu-
ates substantially along the chromosome lengths, where tightly-paired regions are interrupted by loosely-
paired regions. Second, within the tightly-paired regions, homologous segments could not be distinguished
even at the highest resolution, hinting at a possibility that such pairing was established at distances corre-
sponding to direct DNA-DNA contacts.
The widespread occurrence of recombination-independent homology-directed phenomena contrasts with the
limited understanding of their basis for at least two reasons. First, such processes normally involve large and
functionally important genomic regions, which are hard to manipulate and analyze experimentally. Second,
the only currently accepted general mechanism of homology recognition between double-stranded DNA
(dsDNA) is the Watson-Crick base pairing in cross-hybridization of complementary single strands, which
occurs normally after strand breaking and base-pair opening by enzymes involved in recombination. Thus,
elucidating mechanistic aspects of recombination-independent pairing requires both better model systems
and better understanding of the biophysical properties of DNA.
Meiosis as a dedicated pairing stage
Homologous pairing is most apparent in meiosis, a specialized cell division that halves the number of chro -
mosomes to generate gametes [15]. Observable meiotic pairing commences in early prophase I, normally
after chromosomes begin to compact and individualize [16]. By late prophase I, homologous chromosomes
become closely aligned in a configuration known as synapsis.
Canonically, the synapsis of homologous chromosomes requires the break-generating function of Spo11 [17].
This program is documented in mammals and also in some popular model organisms such as S. cerevisiae
[18]. Alternatively, homologous chromosomes can pair and fully synapse in the absence of Spo11 [18]. Such
pairing takes place in D. melanogaster and the roundworm Caenorhabditis elegans [18]. It is called recombi-
nation-independent because it occurs normally in the absence of Spo11-mediated double-strand breaks [16].
Several hypotheses were put forward to explain the phenomenon of recombination-independent pairing. For
example, the pairing was proposed to occur directly at the DNA level via G-quadruplexes [19], other four-
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