Volume: 22, Issue: 1

Commentary

On the Responsible Use of Chatbots in Bioinformatics

Gangqing Hu, Li Liu, Dong Xu

no abstract

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Review Article

Microbiome in Female Reproductive Health: Implications for Fertility and Assisted Reproductive Technologies

Liwen Xiao, Zhenqiang Zuo, Fangqing Zhao

The microbiome plays a critical role in the process of conception and the outcomes of pregnancy. Disruptions in microbiome homeostasis in women of reproductive age can lead to various pregnancy complications, which significantly impact maternal and fetal health. Recent studies have associated the microbiome in the female reproductive tract (FRT) with assisted reproductive technology (ART) outcomes, and restoring microbiome balance has been shown to improve fertility in infertile couples. This review provides an overview of the role of the microbiome in female reproductive health, including its implications for pregnancy outcomes and ARTs. Additionally, recent advances in the use of microbial biomarkers as indicators of pregnancy disorders are summarized. A comprehensive understanding of the characteristics of the microbiome before and during pregnancy and its impact on reproductive health will greatly promote maternal and fetal health. Such knowledge can also contribute to the development of ARTs and microbiome-based interventions.

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Review Article

RNase P: Beyond Precursor tRNA Processing

Peipei Wang, Juntao Lin, Xiangyang Zheng, Xingzhi Xu

Ribonuclease P (RNase P) was first described in the 1970’s as an endoribonuclease acting in the maturation of precursor transfer RNAs (tRNAs). More recent studies, however, have uncovered non-canonical roles for RNase P and its components. Here, we review the recent progress of its involvement in chromatin assembly, DNA damage response, and maintenance of genome stability with implications in tumorigenesis. The possibility of RNase P as a therapeutic target in cancer is also discussed.

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Review Article

Substrate and Functional Diversity of Protein Lysine Post-translational Modifications

Bingbing Hao, Kaifeng Chen, Linhui Zhai, Muyin Liu, Bin Liu, Minjia Tan

Lysine post-translational modifications (PTMs) are widespread and versatile protein PTMs that are involved in diverse biological processes by regulating the fundamental functions of histone and non-histone proteins. Dysregulation of lysine PTMs is implicated in many diseases, and targeting lysine PTM regulatory factors, including writers, erasers, and readers, has become an effective strategy for disease therapy. The continuing development of mass spectrometry (MS) technologies coupled with antibody-based affinity enrichment technologies greatly promotes the discovery and decoding of PTMs. The global characterization of lysine PTMs is crucial for deciphering the regulatory networks, molecular functions, and mechanisms of action of lysine PTMs. In this review, we focus on lysine PTMs, and provide a summary of the regulatory enzymes of diverse lysine PTMs and the proteomics advances in lysine PTMs by MS technologies. We also discuss the types and biological functions of lysine PTM crosstalks on histone and non-histone proteins and current druggable targets of lysine PTM regulatory factors for disease therapy.
赖氨酸翻译后修饰（Lysine PTMs）是广泛存在于蛋白质赖氨酸残基上的翻译后修饰类型，其通过调节组蛋白和非组蛋白的基本功能参与细胞内多种生物过程。赖氨酸修饰的失调与许多疾病有关，目前靶向赖氨酸修饰调节因子已成为疾病治疗的有效策略。生物质谱技术与基于抗体的亲和富集技术的不断发展极大地促进了蛋白质翻译后修饰的发现和功能解析。赖氨酸修饰的全局表征对于破译赖氨酸修饰的调节网络、分子功能和作用机制至关重要。在这篇综述中，我们总结了赖氨酸修饰的相应调控酶以及基于生物质谱技术的赖氨酸修饰蛋白质组学进展。此外，我们还讨论了组蛋白和非组蛋白上赖氨酸修饰间交互作用的类型和生物学功能，以及目前可用于疾病治疗的赖氨酸修饰调节因子药物靶点。

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Original Research

Whole-genome Sequencing Reveals Autooctoploidy in Chinese Sturgeon and Its Evolutionary Trajectories

Binzhong Wang, Bin Wu, Xueqing Liu, Yacheng Hu, Yao Ming, Mingzhou Bai, Juanjuan Liu, Kan Xiao, Qingkai Zeng, Jing Yang, Hongqi Wang, Baifu Guo, Chun Tan, Zixuan Hu, Xun Zhao, Yanhong Li, Zhen Yue, Junpu Mei, Wei Jiang, Yuanjin Yang, Zhiyuan Li, Yong Gao, Lei Chen, Jianbo Jian, Hejun Du

The order Acipenseriformes, which includes sturgeons and paddlefishes, represents “living fossils” with complex genomes that are good models for understanding whole-genome duplication (WGD) and ploidy evolution in fishes. Here, we sequenced and assembled the first high-quality chromosome-level genome for the complex octoploid Acipenser sinensis (Chinese sturgeon), a critically endangered species that also represents a poorly understood ploidy group in Acipenseriformes. Our results show that A. sinensis is a complex autooctoploid species containing four kinds of octovalents (8n), a hexavalent (6n), two tetravalents (4n), and a divalent (2n). An analysis taking into account delayed rediploidization reveals that the octoploid genome composition of Chinese sturgeon results from two rounds of homologous WGDs, and further provides insights into the timing of its ploidy evolution. This study provides the first octoploid genome resource of Acipenseriformes for understanding ploidy compositions and evolutionary trajectories of polyploid fishes.
研究问题 如何构建高质量的中华鲟单倍型参考基因组序列？基于该参考基因组解析鲟鱼研究领域内，针对现存鲟形目物种倍性进化的世纪争论：以中华鲟为代表的类群是四倍体还是八倍体、鲟形目多倍体来源于同源还是异源全基因组加倍（WGD）、WGD和鲟形目物种分化的时序关系、鲟形目分化时间？ 研究方法 利用人工诱导方法制备的中华鲟雌核发育个体，基于PacBio测序数据，采用多种基因组组装方法，对各高质量的组装结果进行融合。利用二代Illumina测序数据进行矫正，采用Hi-C完成基因组的染色体挂载。对中华鲟正常发育个体进行重测序，开展k-mer、SSR、SNP及TE分析判断中华鲟倍性和同源性。分离谱系特异性全基因组加倍基因（lineage-specific ohnologue resolution, LORe）和祖先全基因组加倍基因（ancestral ohnologue resolution, AORe），利用AORe的分化判定鲟科和匙吻鲟科/白鲟科的物种形成和WGD过程。 主要结果 1、首次实现中华鲟全基因组组装和信息的解析。完成66条（2个单倍型，2 monoploids）参考基因组染色体序列的组装，BUSCO的完整度评估结果达95.6%，并进行了基因功能注释。这也是目前解析的首个八倍体动物的基因组，为中华鲟等濒危鲟鱼保护研究和经济类鲟鱼育种提供了重要参考数据。 2、解析了中华鲟的倍性组分，表明其为复杂倍性组成的八倍体物种，推测其存在的延迟二倍化现象和两次同源WGD造成了目前复杂倍性状态。为多倍体物种研究和脊椎动物进化提供了重要参考数据。 3、推测鲟鱼类和匙吻鲟类的共同祖先在约210百万年前经历了鲟形目特异的第一次WGD（As3R），在约150百万年前两类鲟鱼发生分化，约35百万前中华鲟祖先发生了第二次谱系特异性的WGD。该结果为鲟形目鱼类进化提供了重要参考。

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