Tandemly repeated DNA families in the mouse genome.
Tandemly repeated DNA families in the mouse genome.
复制标题
DOI：
10.1186/1471-2164-12-531
复制
发表时间：
2011-10-28
期刊：
影响因子：
4.4
通讯作者：
Podgornaya OI
中科院分区：
文献类型：
--
作者：
Komissarov AS;Gavrilova EV;Demin SJ;Ishov AM;Podgornaya OI
串联DNA重复序列的功能和形态学研究，结合了大多数基因组的大部分，大多是有限的，由于这些基因组元件的不完整的表征。我们在这里报告了在小鼠基因组组装中发现的大串联重复序列（TR）的全基因组分析。利用生物信息学方法，我们在两个小鼠全基因组霰弹枪（WGS）序列中发现了阵列大小超过3kb的大TR。根据序列相似性、染色体位置、单体长度、阵列变异性和GC含量对大TR进行分类；我们确定了4个超家族、8个家族和62个亚家族，其中包括60个以前没有描述过的亚家族。1)着丝粒小卫星超家族仅存在于参考基因组的未组装部分。2)中心周围主卫星是最丰富的超家族，具有高阶重复结构。3)转座因子相关超族包含两个家族。4)非均质串联重复序列的超家族包括4个家族。一个家族仅在WGS中发现，而两个家族代表单位点或多位点的串联重复。尽管TRPC-21A-MM具有多位点位置，但由于其丰富，严格的中心点周围位置以及与大型人类卫星的相似性，它被放置在一个分离的家族中。为了证实我们的数据，我们接下来对来自不同家族的三个重复序列进行原位杂交。TRPC-21A-MM探针与3号和17号染色体杂交，多位点TR-22A-MM探针与10条染色体杂交，单位点TR-54B-MM探针与染色体末端出现的长环杂交。除了在原位分析中预测的几个外染色体TR阳性外，可能表明异色基因组区域的基因组组装不准确。染色体特异性TR已被预测为小鼠，但没有可靠的细胞遗传学探针。我们报告了新的分析，在硅鉴定和原位3/17染色体特异性探针TRPC-21-MM确认。因此，新的分类已被证明是继续基因组研究的有用工具，而带注释的TR可以成为染色体识别的细胞遗传学探针的宝贵来源。
Functional and morphological studies of tandem DNA repeats, that combine high portion of most genomes, are mostly limited due to the incomplete characterization of these genome elements. We report here a genome wide analysis of the large tandem repeats (TR) found in the mouse genome assemblies. Using a bioinformatics approach, we identified large TR with array size more than 3 kb in two mouse whole genome shotgun (WGS) assemblies. Large TR were classified based on sequence similarity, chromosome position, monomer length, array variability, and GC content; we identified four superfamilies, eight families, and 62 subfamilies - including 60 not previously described. 1) The superfamily of centromeric minor satellite is only found in the unassembled part of the reference genome. 2) The pericentromeric major satellite is the most abundant superfamily and reveals high order repeat structure. 3) Transposable elements related superfamily contains two families. 4) The superfamily of heterogeneous tandem repeats includes four families. One family is found only in the WGS, while two families represent tandem repeats with either single or multi locus location. Despite multi locus location, TRPC-21A-MM is placed into a separated family due to its abundance, strictly pericentromeric location, and resemblance to big human satellites. To confirm our data, we next performed in situ hybridization with three repeats from distinct families. TRPC-21A-MM probe hybridized to chromosomes 3 and 17, multi locus TR-22A-MM probe hybridized to ten chromosomes, and single locus TR-54B-MM probe hybridized with the long loops that emerge from chromosome ends. In addition to in silico predicted several extra-chromosomes were positive for TR by in situ analysis, potentially indicating inaccurate genome assembly of the heterochromatic genome regions. Chromosome-specific TR had been predicted for mouse but no reliable cytogenetic probes were available before. We report new analysis that identified in silico and confirmed in situ 3/17 chromosome-specific probe TRPC-21-MM. Thus, the new classification had proven to be useful tool for continuation of genome study, while annotated TR can be the valuable source of cytogenetic probes for chromosome recognition.
登录
查看更多内容
影响因子：
4.3
作者：
Giordano J;Ge Y;Gelfand Y;Abrusán G;Benson G;Warburton PE
通讯作者：
Warburton PE
影响因子：
64.8
作者：
COOKE, HJ;BROWN, WAR;RAPPOLD, GA
通讯作者：
RAPPOLD, GA
影响因子：
14.9
作者：
Blake JA;Bult CJ;Eppig JT;Kadin JA;Richardson JE;Mouse Genome Database Group
通讯作者：
Mouse Genome Database Group
影响因子：
64.8
作者：
通讯作者：
--
DOI：
10.1159/000132989
发表时间：
1990-01-01
期刊：
CYTOGENETICS AND CELL GENETICS
影响因子：
--
作者：
BROCCOLI, D;MILLER, OJ;MILLER, DA
通讯作者：
MILLER, DA