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人类蛋白质N-糖基化的十二年全基因组关联研究 Review
Anna Timoshchuk, Sodbo Sharapov, Yurii S. Aulchenko
《工程（英文）》 2023年 第26卷 第7期 页码 17-31 doi: 10.1016/j.eng.2023.03.013
Most human-secreted and membrane-bound proteins have covalently attached oligosaccharide chains, or glycans. Glycosylation influences the physical and chemical properties of proteins, as well as their biological functions. Unsurprisingly, alterations in protein glycosylation have been implicated in a growing number of human diseases, and glycans are increasingly being considered as potential therapeutic targets, an essential part of therapeutics, and biomarkers. Although glycosylation pathways are biochemically well-studied, little is known about the networks of genes that guide the cell- and tissue-specific regulation of these biochemical reactions in humans in vivo. The lack of a detailed understanding of the mechanisms regulating glycome variation and linking the glycome to human health and disease is slowing progress in clinical applications of human glycobiology. Two of the tools that can provide much sought-after knowledge of human in vivo glycobiology are human genetics and genomics, which offer a powerful data-driven agnostic approach for dissecting the biology of complex traits. This review summarizes the current state of human populational glycogenomics. In Section 1, we provide a brief overview of the N-glycan's structural organization, and in Section 2, we give a description of the major blood plasma glycoproteins. Next, in Section 3, we summarize, systemize, and generalize the results from current N-glycosylation genome-wide association studies (GWASs) that provide novel knowledge of the genetic regulation of the populational variation of glycosylation. Until now, such studies have been limited to an analysis of the human blood plasma N-glycome and the N-glycosylation of immunoglobulin G and transferrin. While these three glycomes make up a rather limited set compared with the enormous multitude of glycomes of different tissues and glycoproteins, the study of these three does allow for powerful analysis and generalization. Finally, in Section 4, we turn to genes in the established loci, paying particular attention to genes with strong support in Section 5. At the end of the review, in Sections 6 and 7, we describe special cases of interest in light of new discoveries, focusing on possible mechanisms of action and biological targets of genetic variation that have been implicated in human protein N-glycosylation.
夏家辉
《中国工程科学》 2000年 第2卷 第11期 页码 1-11
介绍了中国医学遗传学国家重点实验室在遗传病家系收集、疾病基因定位、疾病基因克隆和疾病基因功能研究方面的研究工作。用细胞遗传学G显带技术于1975年发现了一条与鼻咽癌相关的标记染色体t（1；3）（q44；p11）；1981年将睾丸决定基因（TDF）定位于Yp11.32带；1991年以来收集遗传病家系345种共590个；1996年用显微切割、PCR、微克隆技术克隆了EXT2基因；1998年用基因家族-候选疾病基因克隆方法克隆了遗传性神经性耳聋基因GJB3；1999年用连锁分析和全基因组扫描将一种遗传性弥漫性浅表性光敏性汗孔角化症定位于12q23.2带，并在基因功能研究中发现了一个新的细胞内转运蛋白。
关键词： 遗传病家系 基因定位和克隆 基因家族-候选疾病基因克隆 基因组扫描 基因功能研究
代谢组扩展生物学的“旁中心法则”——对理解基因组学-糖组学-代谢组学-表观基因组学互作的意义
Albert Stuart Reece
《工程（英文）》 2023年 第26卷 第7期 页码 16-16 doi: 10.1016/j.eng.2022.07.011
The central dogma of biology holds that the transcription of DNA into RNA and the translation of RNA into proteins forms the primary axis of biological activity [1]. Following major advances in the description of the complex glycan and lipid chains that are added onto these basic building blocks, the glycome and lipidome have recently been added to this doctrine as an exciting new extension named the ‘‘paracentral dogma” [2]. However, it has been pointed out that biological systems can include many layers, which are described in modern omics technology platforms relating to both cell-intrinsic and cell-extrinsic layers of control, including metabolomic, microbiomic, immunological, epigenomic, epitranscriptomic, proteomic and phosphoproteomic layers [3].
It is well known that stem and progenitor cells have a metabolism that is based on glycolysis and glutaminolysis [4]. Although this provides less energy to the cell than oxidative phosphorylation, it suffices for these cells’ needs, since such cells are generally relatively quiescent and normally suppress energy-intensive processes such as genome duplication and transcription. Moreover, it has been shown that the high intracellular lactate levels involved in such states not only inhibits the key gatekeeper enzymes of oxidative phosphorylation (i.e., pyruvate dehydrogenase and carnitine palmitoyl acyltransferase) but also actually covalently modifies them by lactylation in order to maintain this inhibited metabolic–epigenomic state [5]. In addition, intermediate metabolism and nutrients are the source of the very extensive library of post-translational modifications to DNA, RNA, and proteins, as well as supplying cellular energy for many of the required reactions. Hence, the metabolic state locks in and reinforces the epigenomic state, and the metabolome and epigenome thereby play mutually reinforcing roles. This self-reinforcing coordination explains why it is so difficult to generate induced pluripotent cells and is a contributory explanation for why the described protocols typically have such low cellular yields.
These concepts become even more important when it is considered that cancer cells are de-differentiated, similarly rely on glycolysis and glutaminolysis, and are similarly metabolically–epigenomically–genomically synchronized. The disruption of this metabolic system is a key focus of mechanistic cancer research.
These important considerations imply that the descriptive and predictive power of the newly described ‘‘paracentral dogma” of biology may be usefully and meaningfully extended by including the metabolome, along with the genome, transcriptome, proteome, glycome, and lipidome, to describe cell-intrinsic regulation—not only in terms of another omics analytical layer but also as a fully predictive and interactive partner in the symphonic-like multilayer coordination that evidently comprises cellular regulatory layering.
深古菌门的核心代谢功能和热环境起源 Article
冯晓远, 王寅炤, Rahul Zubi, 王风平
《工程（英文）》 2019年 第5卷 第3期 页码 498-504 doi: 10.1016/j.eng.2019.01.011
宿主微生物组内的基因组突变——适应性进化或净化选择 Review
张家超, Rob Knight
《工程（英文）》 2023年 第20卷 第1期 页码 96-102 doi: 10.1016/j.eng.2021.11.018
二代测序技术转变了人们评估宿主相关微生物区系和微生物组的分类组成功能的能力。未来10 年将会开展更多的人类微生物组研究，特别是那些探索微生物组内基因组突变的研究。本文聚焦于微生物组内菌株之间的共同进化，塑造了宿主肠道微生物种内和种间的菌株水平多样性。还探讨了微生物基因组突变与常见代谢疾病之间的关联，以及病原体和益生菌在入侵和定植过程中的适应性进化。最后，讨论了注释和分析微生物基因组突变方法和算法的研究进展。
陈松林,徐文腾,陈张帆
《中国工程科学》 2019年 第21卷 第6期 页码 39-47 doi: 10.15302/J-SSCAE-2019.06.007
本文主要从基因组和转录组层面分析了极地动物基因资源的研究现状，梳理了本领域研究中存在的问题，并提出了未来发展战略。极地动物基因组测序起步较晚，迄今只完成了 13种极地动物的全基因组测序。在转录组研究方面，人们对极地的 31个物种进行了转录组测序，并在以下四个方向重点开展了研究：环境适应性研究；污染物应激反应的分子机制研究；不同发育阶段或不同组织中的转录组分析；功能基因挖掘。本领域研究由于起步晚，研究广度和深度都有待加强，但极地动物的基因资源研究具有战略意义。建议国家设立“极地动物基因资源发掘与应用”重点研发计划专项，围绕极地渔业动物特殊性状遗传解析、特有基因功能分析和基因工程产品研发等开展研究。
关键词： 极地动物 基因组，转录组，基因资源
刘红,杨帆,张笑冰,张继瑜,杨国威,董杰,薛颖,侯云德,袁正宏,闻玉梅,徐建国,陈洪松,马大龙,王宇,杨剑,沈岩,强伯勤,吴洪涛,贺秉坤,吕渭川,金奇
《中国工程科学》 2002年 第4卷 第10期 页码 40-47
关键词： 福氏2a志贺菌301株 全基因组序列测定 痢疾岛 毒力岛
牙鲆50K SNP芯片的研制及其在抗病性状基因组选择中的应用 Article
周茜, 陈亚东, 卢昇, 刘洋, 徐文腾, 李仰真, 王磊, 王娜, 杨英明, 陈松林
《工程（英文）》 2021年 第7卷 第3期 页码 406-411 doi: 10.1016/j.eng.2020.06.017
标题 作者 时间 类型 操作
分子标记的开发和系统发育基因组学实操班
2019年06月27日
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中国遗传学会基因组编辑分会第二次会员代表大会暨全国学术年会
2019年11月22日
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第七届国际昆虫生理生化与分子生物学论坛及第四届国际昆虫基因组学大会
2019年07月02日
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全国小麦基因组学及分子育种大会
2019年08月26日
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