Article Online - Genomics, Proteomics & Bioinformatics

Tomas Lindahl completed his medical studies at Karolinska Institute in 1970. Yet, his work has always been dedicated to unraveling fundamental mechanisms of DNA decay and DNA repair. His research is characterized with groundbreaking discoveries on the instability of our genome, the identification of novel DNA repair activities, the characterization of DNA repair pathways, and the association to diseases, throughout his 40 years of scientific career.

2015年10月7日，Tomas Lindahl博士因其在基因修复领域的突出贡献，和Aziz Sancar博士、Paul Modrich博士共同获得了2015年诺贝尔化学奖。Tomas于1970年在卡罗林斯卡学院完成了他的医学学业。在接下来40余年的科研生涯中，他主要从事基因组不稳定性、DNA修复机制、DNA修复通路以及疾病相关研究，获得了许多突破性的重大发现。至今为止，他的研究成果一直被用于揭示DNA降解和修复的表观遗传学调控基本机制。本文就Tomas的科学成就进行简要概述，以帮助大家更好地了解整个基因修复领域的发展情况。

DNA double-strand breaks (DSBs), which arise following exposure to a number of endogenous and exogenous agents, can be repaired by either the homologous recombination (HR) or non-homologous end-joining (NHEJ) pathways in eukaryotic cells. A vital step in HR repair is DNA end resection, which generates a long 3′ single-stranded DNA (ssDNA) tail that can invade the homologous DNA strand. The generation of 3′ ssDNA is not only essential for HR repair, but also promotes activation of the ataxia telangiectasia and Rad3-related protein (ATR). Multiple factors, including the MRN/X complex, C-terminal-binding protein interacting protein (CtIP)/Sae2, exonuclease 1 (EXO1), Bloom syndrome protein (BLM)/Sgs1, DNA2 nuclease/helicase, and several chromatin remodelers, cooperate to complete the process of end resection. Here we review the basic machinery involved in DNA end resection in eukaryotic cells.

Protein poly ADP-ribosylation (PARylation) is a widespread post-translational modification at DNA lesions, which is catalyzed by poly(ADP-ribose) polymerases (PARPs). This modification regulates a number of biological processes including chromatin reorganization, DNA damage response (DDR), transcriptional regulation, apoptosis, and mitosis. PARP1, functioning as a DNA damage sensor, can be activated by DNA lesions, forming PAR chains that serve as a docking platform for DNA repair factors with high biochemical complexity. Here, we highlight molecular insights into PARylation recognition, the expanding role of PARylation in DDR pathways, and the functional interaction between PARylation and ubiquitination, which will offer us a better understanding of the biological roles of this unique post-translational modification.

DNA发生损伤时，在DNA损伤位点蛋白的多聚ADP核糖基化（PARylation）是一种常见的修饰方式，此修饰是由ADP核糖多聚酶（PARRs）介导的。PARylation参与调控生物体多项活动，包括染色质重塑，DNA损伤修复，转录调控，凋亡和有丝分裂。PARP1作为DNA损伤的感受因子，可以被DNA损伤所激活，合成PAR链，PAR链可以为参与DNA修复的蛋白提供停泊位点。作为一种蛋白修饰，PAR链的合成与降解修饰被严格的控制。PARPs家族的几个成员参与了PAR链的合成，而PARG等参与了大部分PAR链的降解。越是深入地了解PAR修饰的过程，对此开发出新药的可能性就越大。目前，美国FDA已批准olaparib（一种PARP的抑制剂）用于治疗BRCA基因缺陷相关的卵巢癌患者，并取得了较好的临床效果。本文我们重点阐述PAR链的识别，PAR修饰在DNA损伤修复途径的作用，和泛素化与PAR修饰之间的联系，对这些问题的阐述将有利于我们对PAR，这种独特的翻译后修饰有更进一步的认识。

Ubiquitin-fold modifier 1 (UFM1) is one of the newly-identified ubiquitin-like proteins. Similar to ubiquitin, UFM1 is conjugated to its target proteins by a three-step enzymatic reaction. The UFM1-activating enzyme, ubiquitin-like modifier-activating enzyme 5 (UBA5), serves as the E1 to activate UFM1; UFM1-conjugating enzyme 1 (UFC1) acts as the E2 to transfer the activated UFM1 to the active site of the E2; and the UFM1-specific ligase 1 (UFL1) acts as the E3 to recognize its substrate, transfer, and ligate the UFM1 from E2 to the substrate. This process is called ufmylation. UFM1 chains can be cleaved from its target proteins by UFM1-specific proteases (UfSPs), suggesting that the ufmylation modification is reversible. UFM1 cascade is conserved among nearly all of the eukaryotic organisms, but not in yeast, and associated with several cellular activities including the endoplasmic reticulum stress response and hematopoiesis. Furthermore, the UFM1 cascade is closely related to a series of human diseases. In this review, we summarize the molecular details of this reversible modification process, the recent progress of its functional studies, as well as its implication in tumorigenesis and potential therapeutic targets for cancer.

泛素折叠修饰因子1（UFM1）是最近新发现的一种小的类泛素蛋白。像泛素一样，UFM1也可通过三步酶促反应连接到其靶蛋白上。E1，UFM1激活酶 UBA5，在ATP的帮助下，激活UFM1，露出其C端保守的甘氨酸；随后，激活的UFM1被转移到E2，UFM1结合酶UFC1上；E3，UFM1连接酶UFL1可结合UFC1，并识别特异性UFM1化修饰的底物，从而将UFM1 转移并连接到底物上；这一过程被叫做Ufmylation。同时，UFM1特异性蛋白酶UFSPs可将底物上的UFM1剪切下来，从而实现UFM1的循环利用，也说明了Ufmylation是一种可逆性修饰。UFM1 修饰系统在除酵母以外的几乎所有的真核生物中高度保守，并且与内质网胁迫响应，造血作用，以及多种人类疾病相关。本文中，我们详细总结了可逆UFM1修饰的分子机制，以及UFM1化修饰的研究进展，并且说明了UFM1修饰在肿瘤发生中的可能作用，以及可作为潜在的抗癌药物靶点。

Maintenance of tissue-specific stem cells is vital for organ homeostasis and organismal longevity. Hematopoietic stem cells (HSCs) are the most primitive cell type in the hematopoietic system. They divide asymmetrically and give rise to daughter cells with HSC identity (self-renewal) and progenitor progenies (differentiation), which further proliferate and differentiate into full hematopoietic lineages. Mammalian ageing process is accompanied with abnormalities in the HSC self-renewal and differentiation. Transcriptional changes and epigenetic modulations have been implicated as the key regulators in HSC ageing process. The DNA damage response (DDR) in the cells involves an orchestrated signaling pathway, consisting of cell cycle regulation, cell death and senescence, transcriptional regulation, as well as chromatin remodeling. Recent studies employing DNA repair-deficient mouse models indicate that DDR could intrinsically and extrinsically regulate HSC maintenance and play important roles in tissue homeostasis of the hematopoietic system. In this review, we summarize the current understanding of how the DDR determines the HSC fates and finally contributes to organismal ageing.

组织特异性干细胞的维持对生物体组织器官的动态平衡和生物体寿命至关重要。造血干细胞（HSC）是造血系统中在系统发育等级上最为原始的一类细胞。在正常生理条件下，哺乳动物成体造血干细胞通过不对称分裂的方式产生具有造血干细胞特性的子代细胞（HSC自我更新）；同时HSC亦可通过分裂，产生分化的造血祖细胞（HSC分化）。造血祖细胞的进一步分裂和分化可建立整个造血系统。哺乳动物衰老过程伴随着HSC的自我更新和分化能力的缺陷。研究表明，转录水平调控和表观遗传修饰均与造血干细胞的功能衰退和生物体衰老相关。DNA损伤反应是生物体在细胞和整体层面应对DNA损伤所采取的一种系统性分子应对事件。它包括DNA损伤的识别、关键蛋白催化活力的激活（如蛋白激酶的活化等）、DNA损伤修复机器的启动和修复后细胞动态变化等，涉及到转录调控、染色质重构、细胞周期调控与细胞死亡和衰老等分子细胞生物学事件。DNA损伤修复缺陷小鼠模型研究表明，小鼠HSC中DNA损伤的累计和DNA损伤反应的激活可以通过直接改变HSC的细胞命运（如细胞死亡、衰老和分化等）和调节HSC所处微环境（HSC干细胞龛）与系统大环境（血液中细胞因子改变等）来影响HSC自我更新和分化能力，进而控制HSC和生物体的衰老。在本综述中，作者将从HSC衰老的内因和外因两个层面，详细探讨DNA损伤反应在HSC衰老中的作用机制。

The DNA damage response (DDR) is a complex biological system activated by different types of DNA damage. Mutations in certain components of the DDR machinery can lead to genomic instability disorders that culminate in tissue degeneration, premature aging, and various types of cancers. Intriguingly, malfunctioning DDR plays a role in the etiology of late onset brain degenerative disorders such as Parkinson’s, Alzheimer’s, and Huntington’s diseases. For many years, brain degenerative disorders were thought to result from aberrant neural death. Here we discuss the evidence that supports our novel hypothesis that brain degenerative diseases involve dysfunction of glial cells (astrocytes, microglia, and oligodendrocytes). Impairment in the functionality of glial cells results in pathological neuro-glial interactions that, in turn, generate a “hostile” environment that impairs the functionality of neuronal cells. These events can lead to systematic neural demise on a scale that appears to be proportional to the severity of the neurological deficit.

DNA损伤应答（DNA damage response, DDR）是一种由不同种类DNA损伤激活的复杂生物学系统。DDR系统某一组件的突变可引起基因组的紊乱，进而会导致组织变性、过早老化及多种癌症。有趣的是，非正常的DDR系统在一些晚发型脑退行性疾病中发挥作用，例如帕金森、阿尔茨海默氏症和亨廷顿病。多年来，脑退行性疾病被认为是异常神经死亡的结果。本文讨论了支持我们新假设的证据。我们认为脑退行性疾病包含了神经胶质细胞（星形胶质细胞，小胶质细胞和少突胶质细胞）的功能障碍。神经胶质细胞功能受损导致病理性神经胶质细胞相互作用，形成一个“敌对”的环境，损害神经细胞的功能。这可导致一定程度上神经系统的死亡，且与神经功能缺损的严重程度成正比。

Mammalian topoisomerase 1 (TOP1) is an essential enzyme for normal development. TOP1 relaxes supercoiled DNA to remove helical constraints that can otherwise hinder DNA replication and transcription and thus block cell growth. Unfortunately, this exact activity can covalently trap TOP1 on the DNA that could lead to cell death or mutagenesis, a precursor for tumorigenesis. It is therefore important for cells to find a proper balance between the utilization of the TOP1 catalytic activity to maintain DNA topology and the risk of accumulating the toxic DNA damages due to TOP1 trapping that prevents normal cell growth. In an apparent contradiction to the negative attribute of the TOP1 activity to genome stability, the detrimental effect of the TOP1-induced DNA lesions on cell survival has made this enzyme a prime target for cancer therapies to kill fast-growing cancer cells. In addition, cumulative evidence supports a direct role of TOP1 in promoting transcriptional progression independent of its topoisomerase activity. The involvement of TOP1 in transcriptional regulation has recently become a focus in developing potential new treatments for a subtype of autism spectrum disorders. Clearly, the impact of TOP1 on human health is multifold. In this review, we will summarize our current understandings on how TOP1 contributes to human diseases and how its activity is targeted for disease treatments.

哺乳动物的DNA拓扑异构酶 I (Topoisomerase I，TOP I)是细胞内关键的核酶。DNA的超螺旋结构会妨碍DNA的复制以及转录等过程，拓扑异构酶I可以通过两个连续的转酯化反应释放DNA的超螺旋结构来参与重要的DNA代谢和细胞生长过程。但是在解螺旋过程中形成的短暂的DNA－TOP I共价中间物可能会导致DNA损失，诱导细胞凋亡或基因突变，后者可能诱发肿瘤。因此对于正常细胞至关重要的是如何在利用TOP I来维持DNA的拓扑结构的同时，减少由于DNA－TOP I共价中间物的累积而引起的DNA损伤以及细胞异常之间保持平衡。另一方面因为累积具有细胞毒性的共价中间物可以诱导细胞凋亡，所以使得TOP I成为一个重要的化疗药物设计靶点，针对杀伤那些快速增长的肿瘤细胞。另外，有实验表明TOP I具有不依赖于其拓扑酶酶活而促进DNA的转录的能力。近来TOP I在调节转录过程中的重要作用使得它成为研发新的治疗自闭症方案的焦点。总而言之，TOP I影响着人类健康的很多方面。该文主要总结了近年来TOP I与人类疾病的研究工作，以及以它做为靶点治疗疾病的进展。

近期，杨运桂研究组发表在Mol Cell的文章揭示了N6-甲基腺嘌呤结合蛋白YTHDC1具有对含有m6A修饰的pre-mRNA进行选择性剪接的调控功能，另外两篇由何川研究组、伊成器研究组分别发表在Nature和Nat Chem Biol上的文章首次报道了全转录组上N1-甲基腺嘌呤的高分辨率图谱，推测N1-甲基腺嘌呤对mRNA翻译具有潜在调控作用。本文介绍了上述三篇文章的研究结果、测序手段以及揭示的重要生物学意义，并对RNA修饰领域的未来研究热点做出展望。

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