Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing.
Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing.
复制标题
DOI：
10.1093/nar/gky442
复制
发表时间：
2018-07-27
影响因子：
14.9
通讯作者：
Larionov V
中科院分区：
文献类型：
--
作者：
Kim JH;Dilthey AT;Nagaraja R;Lee HS;Koren S;Dudekula D;Wood Iii WH;Piao Y;Ogurtsov AY;Utani K;Noskov VN;Shabalina SA;Schlessinger D;Phillippy AM;Larionov V
尽管人类核糖体在蛋白质生物合成中起着关键作用，但人们对核糖体DNA（rDNA）或其前rRNA和rRNA产物的序列变异程度知之甚少。我们恢复核糖体DNA片段从一个单一的人类21号染色体转化相关重组（TAR）克隆在酵母中。覆盖21号染色体rDNA互补序列的13个分离株的精确长读段测序显示串联重复rDNA拷贝之间存在实质性变化，几个回文结构和先前参考序列中的潜在错误。这些克隆揭示了45 S转录单位中的101个变异位点和基因间间隔区序列中的235个变异位点。大约60%的45 S变体在独立的全基因组或RNA-seq数据中得到证实，其中47个在成熟的18 S/28 S rRNA序列中进一步观察到。TAR克隆和长读段测序能够准确重建多个rDNA单元和一个新的高质量的44 838 bp rDNA参考序列，我们已经用从单个个体的21号染色体上检测到的变体对其进行了注释。观察到的大量变异揭示了人类rDNA的异质性，从而打开了核糖体动力学相应变异的可能性。
Despite the key role of the human ribosome in protein biosynthesis, little is known about the extent of sequence variation in ribosomal DNA (rDNA) or its pre-rRNA and rRNA products. We recovered ribosomal DNA segments from a single human chromosome 21 using transformation-associated recombination (TAR) cloning in yeast. Accurate long-read sequencing of 13 isolates covering ∼0.82 Mb of the chromosome 21 rDNA complement revealed substantial variation among tandem repeat rDNA copies, several palindromic structures and potential errors in the previous reference sequence. These clones revealed 101 variant positions in the 45S transcription unit and 235 in the intergenic spacer sequence. Approximately 60% of the 45S variants were confirmed in independent whole-genome or RNA-seq data, with 47 of these further observed in mature 18S/28S rRNA sequences. TAR cloning and long-read sequencing enabled the accurate reconstruction of multiple rDNA units and a new, high-quality 44 838 bp rDNA reference sequence, which we have annotated with variants detected from chromosome 21 of a single individual. The large number of variants observed reveal heterogeneity in human rDNA, opening up the possibility of corresponding variations in ribosome dynamics.
登录
查看更多内容
影响因子：
46.9
作者：
Jain M;Olsen HE;Turner DJ;Stoddart D;Bulazel KV;Paten B;Haussler D;Willard HF;Akeson M;Miga KH
通讯作者：
Miga KH
影响因子：
7
作者：
Harrow J;Frankish A;Gonzalez JM;Tapanari E;Diekhans M;Kokocinski F;Aken BL;Barrell D;Zadissa A;Searle S;Barnes I;Bignell A;Boychenko V;Hunt T;Kay M;Mukherjee G;Rajan J;Despacio-Reyes G;Saunders G;Steward C;Harte R;Lin M;Howald C;Tanzer A;Derrien T;Chrast J;Walters N;Balasubramanian S;Pei B;Tress M;Rodriguez JM;Ezkurdia I;van Baren J;Brent M;Haussler D;Kellis M;Valencia A;Reymond A;Gerstein M;Guigó R;Hubbard TJ
通讯作者：
Hubbard TJ
影响因子：
7
作者：
Floutsakou I;Agrawal S;Nguyen TT;Seoighe C;Ganley AR;McStay B
通讯作者：
McStay B
影响因子：
7
作者：
Eberle, Michael A.;Fritzilas, Epameinondas;Bentley, David R.
通讯作者：
Bentley, David R.
影响因子：
3.2
作者：
Héliot, L;Mongelard, F;Usson, Y
通讯作者：
Usson, Y