The distribution of alternating AT sequences in eukaryotic genomes suggests a role in homologous chromosome recognition in meiosis

Abstract

There are general features of chromosome dynamics, such as homologue recognition in early meiosis, which are expected to involve related sequence motifs in non-coding DNA, with a similar distribution in different species. A search for such motifs is presented here. It has been carried out with the CONREPP program. It has been found that short alternating AT sequences (10-20 bases) have a similar distribution in most eukaryotic organisms, with some exceptions related to unique meiotic features. All other microsatellite and repeat sequences vary significantly in different organisms. It is concluded that the unique structural features and uniform distribution of alternating AT sequences indicate that they may facilitate homologous chromosome pairing in the early preleptotene stage of meiosis. They may also play a role in the compaction of DNA in mitotic chromosomes.

Sequence analysis of wheat subtelomeres reveals a high polymorphism among homoeologous chromosomes

“…We chose these proteins because of their putative role in these processes and because of the availability of identified DNA‐binding sites. Distal subtelomere sequences were analyzed for the distribution of predicted DNA‐binding sites of putative wheat proteins homologous to human SMC1β meiosis‐specific cohesion (Revenkova, Eijpe, Heyting, Gross, & Jessberger, 2001), Ying Yang 1 protein (Beagan et al., 2017) and high mobility group proteins HMG (Subirana & Messeguer, 2011). Sequences were identified and plotted using MAST (MEME Suite 5.0.5).…”

“…Proteins were selected based on their putative role in initial meiotic events described previously in the bibliography, and the availability of identified DNA‐binding sites. Distal subtelomeric sequences were analyzed for the distribution of predicted DNA‐binding sites of putative wheat proteins homologous to human SMC1β meiosis‐specific cohesin (Revenkova et al., 2001), Ying Yang 1 protein (Beagan et al., 2017) and HMG proteins (Subirana & Messeguer, 2011). Besides their role in sister chromatid cohesion, cohesins are very important for various meiosis‐specific events including chromosomal axis formation, synaptonemal complex formation and reciprocal recombination (Ding et al., 2016; Ishiguro, Kim, Fujiyama‐Nakamura, Shigeaki Kato, & Watanabe, 2011).…”

“…Ying Yang 1 is an architectural protein with a critical role in connecting higher‐order chromatin folding in animals (Beagan et al., 2017) and in Arabidopsis (Wu et al., 2012). HMG proteins have been suggested to be involved in initial interactions between homologues, prior to proper pairing, through their potential interaction with AT‐rich sites (Subirana & Messeguer, 2011). Our results revealed that the distribution of putative binding sites for the proteins investigated was chromosome‐specific, with evident differences in density and distribution of these putative binding sites among homoeologues, in agreement with their putative role in specific homologous chromosome pairing.…”

“…Although CTCF has not been found in plants (Ong & Corces, 2014), other orthologous plant protein(s) might be playing a similar function. Other proteins such as the high mobility group proteins HMG were also suggested as meiotic actors in initial steps of homologous chromosome pairing through their presumed interaction at AT‐rich sites (Subirana & Messeguer, 2011). Thus, it seems realistic to study the presence and distribution of the putative binding sites of these proteins in wheat subtelomeric regions.…”

Structure of the DNA Duplex d(ATTAAT)2 with Hoogsteen Hydrogen Bonds

“…It is also likely that some regions of the genome may have this conformation “in vivo” under appropriate conditions, since the transition between both forms has a very low energetic cost. The tendency to accommodate extra-helical bases in the minor groove [ 7 – 9 ] may help to form DNA crosslinks during meiosis [ 21 ] or in the compact territories of gene-poor chromosomes in the nucleus [ 22 ]. Furthermore the formation of continuous helices ( Fig.…”