Robust Genetic Analysis of the X-Linked Anophthalmic (Ie) Mouse.
Robust Genetic Analysis of the X-Linked Anophthalmic (Ie) Mouse.
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DOI：
10.3390/genes13101797
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发表时间：
2022-10-05
期刊：
影响因子：
3.5
通讯作者：
Rainger, Joe
中科院分区：
文献类型：
--
作者：
Hernandez-Moran, Brianda A.;Papanastasiou, Andrew S.;Parry, David;Meynert, Alison;Gautier, Philippe;Grimes, Graeme;Adams, Ian R.;Trejo-Reveles, Violeta;Bengani, Hemant;Keighren, Margaret;Jackson, Ian J.;Adams, David J.;FitzPatrick, David R.;Rainger, Joe
关键词：
无眼症（眼睛缺失）描述了早期胚胎眼睛发育的失败。75%的双侧无眼症病例是由一组相对较小的基因突变引起的，但目前仍有25%的家庭没有得到分子诊断。在这里，我们报告了我们的实验工作，旨在揭示发育和遗传基础的无眼症的特点，X连锁的Ie（眼耳减少）X射线诱导的等位基因在小鼠中，是在1947年首次确定。胚胎表型的组织学分析显示，在视泡阶段后，正常的眼睛发育失败，腹侧视网膜特别严重畸形。连锁分析将该突变定位于X染色体上的~6 Mb区域。受影响和未受影响的雄性同窝仔的短和长读全基因组测序（WGS）证实了Ie连锁，但未发现合理的致病变体或结构重排。这些分析确实减少了关键的候选间隔，并揭示了祖先DNA中存在多个变体的证据，尽管没有发现改变编码序列或Ie独特的变体。为了在遗传水平上研究早期胚胎事件，我们然后产生了来自雄性Ie胚胎和野生型同窝仔的小鼠ES细胞。从培养的视泡类器官产生的RNA-seq和可访问的染色质测序（ATAC-seq）数据没有揭示Ie和野生型之间的基因表达或推定的顺式调控元件的可访问性的任何大的差异。然而，一个公正的TF足迹分析可访问的染色质区域确实提供了证据，在全基因组范围内减少与腹侧眼的发展，在IE中的转录因子的结合，并增加Zic家族的转录因子，包括Zic 3，这是位于IE细化的关键区间内的结合的证据。我们得出结论，在chrX：56，145，000 - 58，385，000处的改进的Ie关键区域包含可能与改变的顺式调节相关的多个遗传变体，但不包含令人信服的致病突变。关键转录因子与染色质结合的变化导致发育过程中基因表达的改变，可能是通过Zic 3的微妙错误调节，这为在Ie中观察到的无眼表型提供了一个合理的原因，但需要进一步的工作来确定精确的致病等位基因及其遗传机制。
Anophthalmia (missing eye) describes a failure of early embryonic ocular development. Mutations in a relatively small set of genes account for 75% of bilateral anophthalmia cases, yet 25% of families currently are left without a molecular diagnosis. Here, we report our experimental work that aimed to uncover the developmental and genetic basis of the anophthalmia characterising the X-linked Ie (eye-ear reduction) X-ray-induced allele in mouse that was first identified in 1947. Histological analysis of the embryonic phenotype showed failure of normal eye development after the optic vesicle stage with particularly severe malformation of the ventral retina. Linkage analysis mapped this mutation to a ~6 Mb region on the X chromosome. Short- and long-read whole-genome sequencing (WGS) of affected and unaffected male littermates confirmed the Ie linkage but identified no plausible causative variants or structural rearrangements. These analyses did reduce the critical candidate interval and revealed evidence of multiple variants within the ancestral DNA, although none were found that altered coding sequences or that were unique to Ie. To investigate early embryonic events at a genetic level, we then generated mouse ES cells derived from male Ie embryos and wild type littermates. RNA-seq and accessible chromatin sequencing (ATAC-seq) data generated from cultured optic vesicle organoids did not reveal any large differences in gene expression or accessibility of putative cis-regulatory elements between Ie and wild type. However, an unbiased TF-footprinting analysis of accessible chromatin regions did provide evidence of a genome-wide reduction in binding of transcription factors associated with ventral eye development in Ie, and evidence of an increase in binding of the Zic-family of transcription factors, including Zic3, which is located within the Ie-refined critical interval. We conclude that the refined Ie critical region at chrX: 56,145,000–58,385,000 contains multiple genetic variants that may be linked to altered cis regulation but does not contain a convincing causative mutation. Changes in the binding of key transcription factors to chromatin causing altered gene expression during development, possibly through a subtle mis-regulation of Zic3, presents a plausible cause for the anophthalmia phenotype observed in Ie, but further work is required to determine the precise causative allele and its genetic mechanism.
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影响因子：
12.3
作者：
McLaren W;Gil L;Hunt SE;Riat HS;Ritchie GR;Thormann A;Flicek P;Cunningham F
通讯作者：
Cunningham F
影响因子：
16.6
作者：
Adewoye, Adeolu B.;Lindsay, Sarah J.;Dubrova, Yuri E.;Hurles, Matthew E.
通讯作者：
Hurles, Matthew E.
影响因子：
2.1
作者：
Inoue, Masashi;Kamachi, Yusuke;Kondoh, Hisato
通讯作者：
Kondoh, Hisato
影响因子：
14.9
作者：
McCarthy DJ;Chen Y;Smyth GK
通讯作者：
Smyth GK
影响因子：
64.8
作者：
Dickinson ME;Flenniken AM;Ji X;Teboul L;Wong MD;White JK;Meehan TF;Weninger WJ;Westerberg H;Adissu H;Baker CN;Bower L;Brown JM;Caddle LB;Chiani F;Clary D;Cleak J;Daly MJ;Denegre JM;Doe B;Dolan ME;Edie SM;Fuchs H;Gailus-Durner V;Galli A;Gambadoro A;Gallegos J;Guo S;Horner NR;Hsu CW;Johnson SJ;Kalaga S;Keith LC;Lanoue L;Lawson TN;Lek M;Mark M;Marschall S;Mason J;McElwee ML;Newbigging S;Nutter LM;Peterson KA;Ramirez-Solis R;Rowland DJ;Ryder E;Samocha KE;Seavitt JR;Selloum M;Szoke-Kovacs Z;Tamura M;Trainor AG;Tudose I;Wakana S;Warren J;Wendling O;West DB;Wong L;Yoshiki A;International Mouse Phenotyping Consortium;Jackson Laboratory;Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS);Charles River Laboratories;MRC Harwell;Toronto Centre for Phenogenomics;Wellcome Trust Sanger Institute;RIKEN BioResource Center;MacArthur DG;Tocchini-Valentini GP;Gao X;Flicek P;Bradley A;Skarnes WC;Justice MJ;Parkinson HE;Moore M;Wells S;Braun RE;Svenson KL;de Angelis MH;Herault Y;Mohun T;Mallon AM;Henkelman RM;Brown SD;Adams DJ;Lloyd KC;McKerlie C;Beaudet AL;Bućan M;Murray SA
通讯作者：
Murray SA