Microhomology-mediated mechanisms underlie non-recurrent disease-causing microdeletions of the FOXL2 gene or its regulatory domain.
Microhomology-mediated mechanisms underlie non-recurrent disease-causing microdeletions of the FOXL2 gene or its regulatory domain.
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DOI：
10.1371/journal.pgen.1003358
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发表时间：
2013
期刊：
影响因子：
4.5
通讯作者：
De Baere E
中科院分区：
文献类型：
--
作者：
Verdin H;D'haene B;Beysen D;Novikova Y;Menten B;Sante T;Lapunzina P;Nevado J;Carvalho CM;Lupski JR;De Baere E
基因组疾病通常是由反复发生的拷贝数变异(CNV)引起的，其潜在机制是非等位基因同源重组(Nahr)。近年来，微同源介导的修复机制，如微同源介导的末端连接(MMEJ)、分叉停滞和模板切换(FoSTeS)、微同源介导的断裂诱导复制(MMBIR)、串联复制滑移(SRS)和断裂诱导的SRS(BISRS)在人类疾病中被描述为非复发CNV的病因学。此外，它们的形成可能受到基因组结构特征的刺激。然而，这些机制在多大程度上有助于罕见的、位点特异性的致病CNV，在很大程度上还没有被探索。在这里，包含FOXL2(32个)或其调控结构域(10个)的42个FOXL2基因座微缺失的精细图谱，可作为与遗传病有关的罕见的、特定于基因座的CNV的模型。这些缺失会导致眼睑畸形综合症(BPES)，这是一种影响眼皮和卵巢的发育状况。对于断点定位，我们使用了基于靶向阵列的比较基因组杂交(ACGH)、定量聚合酶链式反应(QPCR)、长程聚合酶链式反应(Long-Range PCR)和连接产物的Sanger测序。在24个特征性断点连接中，91.7%发现了微同源性，范围在1到66个碱基对之间，与随机对照样本相比显著丰富。我们的结果表明，至少50%的微缺失是由微同源基因介导的修复机制造成的。此外，基因组结构特征，如序列基序、非B DNA构象和重复元件，在所有断点区都被发现。综上所述，这些微缺失中的大多数是由微同源介导的机制如MMEJ、FoSTeS、MMBIR、SRS或BISRS引起的。此外，我们假设基因组结构可能通过增加DNA断裂的易感性或促进复制分叉停滞来驱动它们的形成。最后，我们以基因座为中心的研究，阐明了涉及单基因疾病的大量罕见微缺失的病因学，可以作为遗传病中其他聚集性、非复发性微缺失的模型。基因组紊乱是描述由导致一个或多个基因拷贝数变化的基因组异常引起的疾病的一个通用术语。具有相同长度和聚集性断裂点的一组患者的相同长度的拷贝数变化称为反复重排。这些主要来自一个研究得很好的机制，即非等位基因同源重组(Nahr)。相比之下，非经常性重排的大小各不相同，断点分散，可能源于几种不同的机制，但这些机制尚未完全了解。在这里，我们试图进一步了解这些机制在多大程度上有助于非重复性重排，以及周围基因组结构的可能作用。为此，我们调查了一组独特的患者，他们的FOXL2区域的非复发性缺失导致了眼睑畸形综合征。我们观察到，这些缺失中的大多数可能是由微同源性介导的几种机制造成的。此外，我们的数据表明，罕见的致病性微缺失不是随机发生的基因组序列，而可能是由周围的基因组结构引导的。最后，我们的研究阐明了与遗传病有关的一组独特的位点特异性微缺失的病因学，可以作为其他遗传疾病中基因组异常形成的模型。
Genomic disorders are often caused by recurrent copy number variations (CNVs), with nonallelic homologous recombination (NAHR) as the underlying mechanism. Recently, several microhomology-mediated repair mechanisms—such as microhomology-mediated end-joining (MMEJ), fork stalling and template switching (FoSTeS), microhomology-mediated break-induced replication (MMBIR), serial replication slippage (SRS), and break-induced SRS (BISRS)—were described in the etiology of non-recurrent CNVs in human disease. In addition, their formation may be stimulated by genomic architectural features. It is, however, largely unexplored to what extent these mechanisms contribute to rare, locus-specific pathogenic CNVs. Here, fine-mapping of 42 microdeletions of the FOXL2 locus, encompassing FOXL2 (32) or its regulatory domain (10), serves as a model for rare, locus-specific CNVs implicated in genetic disease. These deletions lead to blepharophimosis syndrome (BPES), a developmental condition affecting the eyelids and the ovary. For breakpoint mapping we used targeted array-based comparative genomic hybridization (aCGH), quantitative PCR (qPCR), long-range PCR, and Sanger sequencing of the junction products. Microhomology, ranging from 1 bp to 66 bp, was found in 91.7% of 24 characterized breakpoint junctions, being significantly enriched in comparison with a random control sample. Our results show that microhomology-mediated repair mechanisms underlie at least 50% of these microdeletions. Moreover, genomic architectural features, like sequence motifs, non-B DNA conformations, and repetitive elements, were found in all breakpoint regions. In conclusion, the majority of these microdeletions result from microhomology-mediated mechanisms like MMEJ, FoSTeS, MMBIR, SRS, or BISRS. Moreover, we hypothesize that the genomic architecture might drive their formation by increasing the susceptibility for DNA breakage or promote replication fork stalling. Finally, our locus-centered study, elucidating the etiology of a large set of rare microdeletions involved in a monogenic disorder, can serve as a model for other clustered, non-recurrent microdeletions in genetic disease. Genomic disorder is a general term describing conditions caused by genomic aberrations leading to a copy number change of one or more genes. Copy number changes with the same length and clustered breakpoints for a group of patients with the same disorder are named recurrent rearrangements. These originate mostly from a well-studied mechanism, namely nonallelic homologous recombination (NAHR). In contrast, non-recurrent rearrangements vary in size, have scattered breakpoints, and can originate from several different mechanisms that are not fully understood. Here we tried to gain further insight into the extent to which these mechanisms contribute to non-recurrent rearrangements and into the possible role of the surrounding genomic architecture. To this end, we investigated a unique group of patients with non-recurrent deletions of the FOXL2 region causing blepharophimosis syndrome. We observed that the majority of these deletions can result from several mechanisms mediated by microhomology. Furthermore, our data suggest that rare pathogenic microdeletions do not occur at random genome sequences, but are possibly guided by the surrounding genomic architecture. Finally, our study, elucidating the etiology of a unique cohort of locus-specific microdeletions implicated in genetic disease, can serve as a model for the formation of genomic aberrations in other genetic disorders.
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影响因子：
30.8
作者：
Iafrate, AJ;Feuk, L;Lee, C
通讯作者：
Lee, C
影响因子：
30.8
作者：
Cooper, Gregory M.;Zerr, Troy;Kidd, Jeffrey M.;Eichler, Evan E.;Nickerson, Deborah A.
通讯作者：
Nickerson, Deborah A.
DOI：
10.1186/1755-8417-1-4
发表时间：
2008-11-03
期刊：
PathoGenetics
影响因子：
--
作者：
Gu W;Zhang F;Lupski JR
通讯作者：
Lupski JR
DOI：
10.1073/pnas.0914454107
发表时间：
2010-07-20
影响因子：
11.1
作者：
De, Subhajyoti;Babu, M. Madan
通讯作者：
Babu, M. Madan
影响因子：
30.8
作者：
Crisponi, L;Deiana, M;Pilia, G
通讯作者：
Pilia, G