Construction of gene co-expression networks in cultured silkworm cells and identification of previously uncharacterized lepidopteran-specific genes required for chromosome dynamics
Construction of gene co-expression networks in cultured silkworm cells and identification of previously uncharacterized lepidopteran-specific genes required for chromosome dynamics
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DOI：
10.1016/j.ibmb.2022.103875
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发表时间：
2022-11-25
影响因子：
3.8
通讯作者：
Kusakabe，Takahiro
中科院分区：
文献类型：
--
作者：
Mon，Hiroaki;Sato，Masanao;Kusakabe，Takahiro
测序技术和生物信息学的进步加速了许多物种的基因发现和基于同源性的功能注释，大量的靶向基因研究极大地扩展了对基因功能的理解。尽管如此，仍然有许多基因与其他进化谱系中的基因缺乏同源性，并且被留下为功能未知的基因。我们从家蚕卵巢来源的细胞系 BmN4 构建了基因共表达网络，并尝试根据功能已知和未知基因之间的相关性来推断未表征基因的生物学作用。在这个网络中，我们重点关注涉及染色体结构、动力学和完整性的共表达模块，并选择未表征的基因进行后续基于 RNAi 的表型筛选。这种方法能够鉴定出 5 个基因，这些基因的敲低会导致染色体动力学和有丝分裂中纺锤体形态的异常。其中之一是最近鉴定的基因 BmCenp-T，它在构建蚕全着丝粒染色体上的动粒蛋白复合物中发挥着核心作用。在本研究中，我们提出了一种构建基因共表达网络并选择候选基因进行小规模 RNAi 筛选的方法。这种方法是对基于同源性注释的补充，并且可能有助于分析谱系特异性的未表征基因，例如孤儿基因。
Advances in sequencing technology and bioinformatics have accelerated gene discovery and homology-based functional annotation in many species, and numerous targeted gene studies have greatly expanded the understanding of gene functions. Nevertheless, there are still many genes that lack homology with genes in other evolutionary lineages and are left as genes with unknown functions. We constructed a gene co-expression network from theBombyx moriovary-derived cell line, BmN4, and attempted to infer the biological roles of uncharacterized genes based on the correlation between the function-known and unknown genes. Within this network, we focused on the co-expression modules involved in chromosome architecture, dynamics, and integrity, and selected the uncharacterized genes for subsequent RNAi-based phenotypic screening. This approach enabled the identification of 5 genes whose knockdown led to abnormalities in chromosome dynamics and spindle morphology in mitosis. One of them was a recently characterized gene, BmCenp-T, which plays a central role in building the kinetochore protein complex on the silkworm holocentric chromosomes. In this study, we suggest a method for constructing the gene co-expression network and selecting candidate genes for small-scale RNAi screening. This approach is complementary to homology-based annotation and may be useful for the analysis of lineage-specific uncharacterized genes such as orphan genes.