I've been trying to retrieve the complete human rDNA sequence (non-spacers and spacers), which should be about 43-kb in length using Biomart, NCBI, and rnacentral, but I have only been able to find the 13-kb non-spacer sequence. Are the spacer regions not yet sequenced due to difficulty in sequencing a repetitive region? Thanks for your help.
3 Answers
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In 1.1 version of (since that version) "Complete genome" assembly of homo sapiens (never achieved before) compared to 1.0 (previous version) 5 last gaps (all somehow in the rDNA) were fixed and now it all is there! https://genome.ucsc.edu/cgi-bin/hgTracks?genome=t2t-chm13-v1.1&hubUrl=http://t2t.gi.ucsc.edu/chm13/hub/hub.txt
https://www.ncbi.nlm.nih.gov/assembly/GCA_009914755.3
Delta from 1.0 version is there https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/changes/v1.0_to_v1.1/v1.0_to_v1.1.chain and delta from patch 13 of GRCh38 is here: https://t2t.gi.ucsc.edu/chm13/hub/t2t-chm13-v1.0/hg38Lastz/t2t-chm13-v1.0.hg38.over.chain.gz
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Managed to find the complete sequence of the repeating unit:
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To the best of my knowledge, of the estimated 500 copies of rDNA repeats in the human genome only 1 and half repeats has been sequenced and published. Mammalian rDNA repeats are hard to clone and appear unstable in yeast and e coli.
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$\begingroup$ Great, that's useful to know. I assume that there must be mutations in at least some of the noncoding regions that would enable positional information for certain sequences. $\endgroup$– matkCommented Jun 8, 2018 at 10:31
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$\begingroup$ Yes, there must be sequence variability in the non-coding region. However as rDNA arrays are rather unstable and recombine within a yeast or ecoli host. Hence isolating rDNA repeat array and making a rough map of rDNA repeat arrays is next to impossible. $\endgroup$– JayCkatCommented Jun 8, 2018 at 14:12
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$\begingroup$ Reference in support of this assertion please. I thought methodological developments in sequencing meant that this situation could be dealt with. $\endgroup$– DavidCommented Jun 8, 2018 at 19:05
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$\begingroup$ Welcome to the "gaps" in human genome. Parts of the genome of eukaryote that are very difficult to explore must less experiment with. Here is a reference but it does quite cover recombinational instability of repeat arrays that prevent other methods to study them. ncbi.nlm.nih.gov/pmc/articles/PMC5098217 $\endgroup$– JayCkatCommented Jun 9, 2018 at 1:19