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Multi-omics of Circular RNAs and Their Responses to Hormones in Moso Bamboo (Phyllostachys edulis). 毛竹环状rna的多组学研究及其对激素的响应。
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-08-01 Epub Date: 2023-02-16 DOI: 10.1016/j.gpb.2023.01.007
Yongsheng Wang, Huihui Wang, Huiyuan Wang, Ruifan Zhou, Ji Wu, Zekun Zhang, Yandong Jin, Tao Li, Markus V Kohnen, Xuqing Liu, Wentao Wei, Kai Chen, Yubang Gao, Jiazhi Ding, Hangxiao Zhang, Bo Liu, Chentao Lin, Lianfeng Gu

Circular RNAs (circRNAs) are endogenous non-coding RNAs with covalently closed structures, which have important functions in plants. However, their biogenesis, degradation, and function upon treatment with gibberellins (GAs) and auxins (1-naphthaleneacetic acid, NAA) remain unknown. Here, we systematically identified and characterized the expression patterns, evolutionary conservation, genomic features, and internal structures of circRNAs using RNase R-treated libraries from moso bamboo (Phyllostachys edulis) seedlings. Moreover, we investigated the biogenesis of circRNAs dependent on both cis- and trans-regulation. We explored the function of circRNAs, including their roles in regulating microRNA (miRNA)-related genes and modulating the alternative splicing of their linear counterparts. Importantly, we developed a customized degradome sequencing approach to detect miRNA-mediated cleavage of circRNAs. Finally, we presented a comprehensive view of the participation of circRNAs in the regulation of hormone metabolism upon treatment of bamboo seedlings with GA and NAA. Collectively, our study provides insights into the biogenesis, function, and miRNA-mediated degradation of circRNAs in moso bamboo.

环状rna (circRNAs)是一种具有共价封闭结构的内源性非编码rna,在植物中具有重要的功能。然而,它们的生物发生、降解和在赤霉素(GAs)和生长素(1-萘乙酸,NAA)处理下的功能仍然未知。本研究利用RNase r处理的毛竹幼苗文库,系统地鉴定和表征了环状rna的表达模式、进化保守性、基因组特征和内部结构。此外,我们还研究了依赖于顺式和反式调控的环状rna的生物发生。我们探索了环状rna的功能,包括它们在调节microRNA (miRNA)相关基因和调节其线性对应物的选择性剪接中的作用。重要的是,我们开发了一种定制的降解组测序方法来检测mirna介导的环状rna切割。最后,我们全面介绍了在GA和NAA处理竹幼苗后,circrna参与调节激素代谢的情况。总的来说,我们的研究深入了解了毛竹中环状rna的生物发生、功能和mirna介导的降解。
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引用次数: 0
Transcriptome-wide Dynamics of m6A mRNA Methylation During Porcine Spermatogenesis. 猪精子发生过程中 m6A mRNA 甲基化在整个转录组的动态变化
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-08-01 Epub Date: 2021-09-17 DOI: 10.1016/j.gpb.2021.08.006
Zidong Liu, Xiaoxu Chen, Pengfei Zhang, Fuyuan Li, Lingkai Zhang, Xueliang Li, Tao Huang, Yi Zheng, Taiyong Yu, Tao Zhang, Wenxian Zeng, Hongzhao Lu, Yinghua Lv

Spermatogenesis is a continual process that occurs in the testes, in which diploid spermatogonial stem cells (SSCs) differentiate and generate haploid spermatozoa. This highly efficient and intricate process is orchestrated at multiple levels. N6-methyladenosine (m6A), an epigenetic modification prevalent in mRNAs, is implicated in the transcriptional regulation during spermatogenesis. However, the dynamics of m6A modification in non-rodent mammalian species remains unclear. Here, we systematically investigated the profile and role of m6A during spermatogenesis in pigs. By analyzing the transcriptomic distribution of m6A in spermatogonia, spermatocytes, and round spermatids, we identified a globally conserved m6A pattern between porcine and murine genes with spermatogenic function. We found that m6A was enriched in a group of genes that specifically encode the metabolic enzymes and regulators. In addition, transcriptomes in porcine male germ cells could be subjected to the m6A modification. Our data show that m6A plays the regulatory roles during spermatogenesis in pigs, which is similar to that in mice. Illustrations of this point are three genes (SETDB1, FOXO1, and FOXO3) that are crucial to the determination of the fate of SSCs. To the best of our knowledge, this study for the first time uncovers the expression profile and role of m6A during spermatogenesis in large animals and provides insights into the intricate transcriptional regulation underlying the lifelong male fertility in non-rodent mammalian species.

精子发生是睾丸中发生的一个持续过程,在这个过程中,二倍体精原干细胞(SSC)分化并生成单倍体精子。这一高效而复杂的过程在多个层面上进行协调。N6-甲基腺苷(m6A)是mRNA中普遍存在的一种表观遗传修饰,与精子发生过程中的转录调控有关。然而,m6A修饰在非啮齿类哺乳动物物种中的动态变化仍不清楚。在这里,我们系统地研究了猪精子发生过程中m6A的概况和作用。通过分析 m6A 在精原细胞、精母细胞和圆形精子中的转录组分布,我们发现了猪和鼠具有生精功能的基因之间全球保守的 m6A 模式。我们发现,m6A 富集在一组专门编码代谢酶和调节因子的基因中。此外,猪雄性生殖细胞的转录组也可能受到 m6A 的修饰。我们的数据表明,m6A 在猪的精子发生过程中起着调控作用,这与小鼠的情况类似。三个基因(SETDB1、FOXO1 和 FOXO3)对决定造精细胞的命运至关重要,它们就是这方面的例证。据我们所知,这项研究首次揭示了m6A在大型动物精子发生过程中的表达谱和作用,为我们深入了解非啮齿类哺乳动物物种中雄性终生生育能力背后错综复杂的转录调控提供了线索。
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引用次数: 0
Specific Regulation of m6A by SRSF7 Promotes the Progression of Glioblastoma. SRSF7对m6A的特异性调控促进了胶质母细胞瘤的进展
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-08-01 Epub Date: 2021-12-23 DOI: 10.1016/j.gpb.2021.11.001
Yixian Cun, Sanqi An, Haiqing Zheng, Jing Lan, Wenfang Chen, Wanjun Luo, Chengguo Yao, Xincheng Li, Xiang Huang, Xiang Sun, Zehong Wu, Yameng Hu, Ziwen Li, Shuxia Zhang, Geyan Wu, Meisongzhu Yang, Miaoling Tang, Ruyuan Yu, Xinyi Liao, Guicheng Gao, Wei Zhao, Jinkai Wang, Jun Li

Serine/arginine-rich splicing factor 7 (SRSF7), a known splicing factor, has been revealed to play oncogenic roles in multiple cancers. However, the mechanisms underlying its oncogenic roles have not been well addressed. Here, based on N6-methyladenosine (m6A) co-methylation network analysis across diverse cell lines, we find that the gene expression of SRSF7 is positively correlated with glioblastoma (GBM) cell-specific m6A methylation. We then indicate that SRSF7 is a novel m6A regulator, which specifically facilitates the m6A methylation near its binding sites on the mRNAs involved in cell proliferation and migration, through recruiting the methyltransferase complex. Moreover, SRSF7 promotes the proliferation and migration of GBM cells largely dependent on the presence of the m6A methyltransferase. The two m6A sites on the mRNA for PDZ-binding kinase (PBK) are regulated by SRSF7 and partially mediate the effects of SRSF7 in GBM cells through recognition by insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2). Together, our discovery reveals a novel role of SRSF7 in regulating m6A and validates the presence and functional importance of temporal- and spatial-specific regulation of m6A mediated by RNA-binding proteins (RBPs).

丝氨酸/精氨酸丰富的剪接因子7(SRSF7)是一种已知的剪接因子,已被发现在多种癌症中发挥致癌作用。然而,其致癌作用的机制尚未得到很好的研究。在这里,基于对不同细胞系的 N6-甲基腺苷(m6A)共甲基化网络分析,我们发现 SRSF7 的基因表达与胶质母细胞瘤(GBM)细胞特异性 m6A 甲基化呈正相关。我们随后指出,SRSF7 是一种新型 m6A 调节因子,它通过招募甲基转移酶复合物,特异性地促进其结合位点附近参与细胞增殖和迁移的 mRNA 上的 m6A 甲基化。此外,SRSF7 促进 GBM 细胞的增殖和迁移主要依赖于 m6A 甲基转移酶的存在。PDZ结合激酶(PBK)mRNA上的两个m6A位点受SRSF7调控,并通过胰岛素样生长因子2 mRNA结合蛋白2(IGF2BP2)的识别,部分介导SRSF7在GBM细胞中的作用。总之,我们的发现揭示了 SRSF7 在调控 m6A 中的新作用,并验证了 RNA 结合蛋白(RBPs)介导的 m6A 时空特异性调控的存在及其功能重要性。
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引用次数: 0
RNA Methylome Reveals the m6A-mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-withering. RNA甲基组揭示m6a介导的日光萎蔫下茶叶风味代谢物调控
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-08-01 Epub Date: 2023-02-14 DOI: 10.1016/j.gpb.2023.02.003
Chen Zhu, Shuting Zhang, Chengzhe Zhou, Caiyun Tian, Biying Shi, Kai Xu, Linjie Huang, Yun Sun, Yuling Lin, Zhongxiong Lai, Yuqiong Guo

The epitranscriptomic mark N6-methyladenosine (m6A), which is the predominant internal modification in RNA, is important for plant responses to diverse stresses. Multiple environmental stresses caused by the tea-withering process can greatly influence the accumulation of specialized metabolites and the formation of tea flavor. However, the effects of the m6A-mediated regulatory mechanism on flavor-related metabolic pathways in tea leaves remain relatively uncharacterized. We performed an integrated RNA methylome and transcriptome analysis to explore the m6A-mediated regulatory mechanism and its effects on flavonoid and terpenoid metabolism in tea (Camellia sinensis) leaves under solar-withering conditions. Dynamic changes in global m6A level in tea leaves were mainly controlled by two m6A erasers (CsALKBH4A and CsALKBH4B) during solar-withering treatments. Differentially methylated peak-associated genes following solar-withering treatments with different shading rates were assigned to terpenoid biosynthesis and spliceosome pathways. Further analyses indicated that CsALKBH4-driven RNA demethylation can directly affect the accumulation of volatile terpenoids by mediating the stability and abundance of terpenoid biosynthesis-related transcripts and also indirectly influence the flavonoid, catechin, and theaflavin contents by triggering alternative splicing-mediated regulation. Our findings revealed a novel layer of epitranscriptomic gene regulation in tea flavor-related metabolic pathways and established a link between the m6A-mediated regulatory mechanism and the formation of tea flavor under solar-withering conditions.

外转录组标记n6 -甲基腺苷(n6 - methylladenosine, m6A)是RNA中主要的内部修饰,在植物对各种逆境的响应中起着重要作用。茶叶萎凋过程中产生的多种环境胁迫对茶叶特殊代谢物的积累和茶叶风味的形成有很大的影响。然而,m6a介导的调节机制对茶叶风味相关代谢途径的影响尚不明确。我们通过RNA甲基组和转录组分析,探讨了m6a介导的调控机制及其对太阳萎蔫条件下茶(Camellia sinensis)叶片黄酮和萜类代谢的影响。日光枯萎处理期间,全球茶叶中m6A水平的动态变化主要受CsALKBH4A和CsALKBH4B两种m6A擦除剂控制。在不同遮光率的日光枯萎处理下,不同甲基化的峰相关基因与萜类生物合成和剪接体途径有关。进一步分析表明,csalkbh4驱动的RNA去甲基化可以通过介导萜类生物合成相关转录物的稳定性和丰度直接影响挥发性萜类的积累,也可以通过触发选择性剪接介导的调节间接影响类黄酮、儿茶素和茶黄素的含量。我们的研究结果揭示了一层新的表观转录组基因调控茶叶风味相关代谢途径,并建立了m6a介导的调控机制与日光萎凋条件下茶叶风味形成之间的联系。
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引用次数: 0
m6A Profile Dynamics Indicates Regulation of Oyster Development by m6A-RNA Epitranscriptomes. m6A基因谱动态表明m6A- rna表转录组对牡蛎发育的调控。
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-08-01 Epub Date: 2022-12-07 DOI: 10.1016/j.gpb.2022.12.002
Lorane Le Franc, Bruno Petton, Pascal Favrel, Guillaume Rivière

The N6-methylation of RNA adenosines (N6-methyladenosine, m6A) is an important regulator of gene expression with critical implications in vertebrate and insect development. However, the developmental significance of epitranscriptomes in lophotrochozoan organisms remains unknown. Using methylated RNA immunoprecipitation sequencing (MeRIP-seq), we generated transcriptome-wide m6A-RNA methylomes covering the entire development of the oyster from oocytes to juveniles. Oyster RNA classes display specific m6A signatures, with messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) exhibiting distinct profiles and being highly methylated compared to transposable element (TE) transcripts. Epitranscriptomes are dynamic and correspond to the chronological steps of development (cleavage, gastrulation, organogenesis, and metamorphosis), with minimal mRNA and lncRNA methylation at the morula stage followed by a global increase. mRNA m6A levels are correlated with transcript levels, and shifts in methylation profiles correspond to expression kinetics. Differentially methylated transcripts cluster according to embryo-larval stages and bear the corresponding developmental functions (cell division, signal transduction, morphogenesis, and cell differentiation). The m6A level of TE transcripts is also regulated and peaks during the gastrulation. We demonstrate that m6A-RNA methylomes are dynamic and associated with gene expression regulation during oyster development. The putative epitranscriptome implication in the cleavage, maternal-to-zygotic transition, and cell differentiation in a lophotrochozoan model brings new insights into the control and evolution of developmental processes.

RNA腺苷的n6甲基化(n6 - methylladenosine, m6A)是一个重要的基因表达调控因子,在脊椎动物和昆虫的发育中具有重要意义。然而,表转录组在光藻生物中的发育意义尚不清楚。使用甲基化RNA免疫沉淀测序(MeRIP-seq),我们生成了转录组范围内的m6A-RNA甲基组,涵盖了牡蛎从卵母细胞到幼体的整个发育过程。牡蛎RNA类显示出特定的m6A特征,信使RNA (mrna)和长链非编码RNA (lncRNAs)表现出不同的特征,与转座因子(TE)转录物相比,它们被高度甲基化。表观转录组是动态的,与发育的时间顺序步骤(卵裂、原肠胚形成、器官发生和变态)相对应,在桑葚胚阶段mRNA和lncRNA甲基化最小,随后全球增加。mRNA m6A水平与转录物水平相关,甲基化谱的变化对应于表达动力学。差异甲基化转录物根据胚胎-幼虫阶段聚集,并承担相应的发育功能(细胞分裂、信号转导、形态发生和细胞分化)。TE转录本的m6A水平也受到调控,并在原肠胚形成期间达到峰值。我们证明了m6A-RNA甲基组是动态的,并与牡蛎发育过程中的基因表达调控有关。在光合动物模型中,表观转录组在卵裂、母系到合子的转变和细胞分化中的潜在意义为发育过程的控制和进化提供了新的见解。
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引用次数: 0
The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers. 人类癌症中功能性A-to-I RNA编辑事件的综合研究。
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-06-01 Epub Date: 2023-01-25 DOI: 10.1016/j.gpb.2022.12.010
Sijia Wu, Zhiwei Fan, Pora Kim, Liyu Huang, Xiaobo Zhou

Adenosine-to-inosine (A-to-I) RNA editing, constituting nearly 90% of all RNA editing events in humans, has been reported to contribute to the tumorigenesis in diverse cancers. However, the comprehensive map for functional A-to-I RNA editing events in cancers is still insufficient. To fill this gap, we systematically and intensively analyzed multiple tumorigenic mechanisms of A-to-I RNA editing events in samples across 33 cancer types from The Cancer Genome Atlas. For individual candidate among ∼ 1,500,000 quantified RNA editing events, we performed diverse types of downstream functional annotations. Finally, we identified 24,236 potentially functional A-to-I RNA editing events, including the cases in APOL1, IGFBP3, GRIA2, BLCAP, and miR-589-3p. These events might play crucial roles in the scenarios of tumorigenesis, due to their tumor-related editing frequencies or probable effects on altered expression profiles, protein functions, splicing patterns, and microRNA regulations of tumor genes. Our functional A-to-I RNA editing events (https://ccsm.uth.edu/CAeditome/) will help better understand the cancer pathology from the A-to-I RNA editing aspect.

腺苷到肌苷(A-to-I)RNA编辑占人类所有RNA编辑事件的近90%,据报道有助于多种癌症的肿瘤发生。然而,癌症中功能性A-to-I RNA编辑事件的全面图谱仍然不足。为了填补这一空白,我们系统深入地分析了癌症基因组图谱中33种癌症类型样本中A-To-I RNA编辑事件的多种致瘤机制。对于约1500000个定量RNA编辑事件中的单个候选者,我们进行了不同类型的下游功能注释。最后,我们确定了24236个潜在的功能性A-to-I RNA编辑事件,包括APOL1、IGFBP3、GRIA2、BLCAP和miR-589-3p中的病例。这些事件可能在肿瘤发生的场景中发挥关键作用,因为它们与肿瘤相关的编辑频率或可能对肿瘤基因的表达谱、蛋白质功能、剪接模式和微小RNA调节的改变产生影响。我们的功能性A-to-I RNA编辑活动(https://ccsm.uth.edu/CAeditome/)将有助于从A-to-I RNA编辑方面更好地理解癌症病理学。
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引用次数: 0
CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network. CNEReg通过发育基因调控网络解释反刍动物特有的保守非编码元件。
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-06-01 Epub Date: 2022-12-07 DOI: 10.1016/j.gpb.2022.11.007
Xiangyu Pan, Zhaoxia Ma, Xinqi Sun, Hui Li, Tingting Zhang, Chen Zhao, Nini Wang, Rasmus Heller, Wing Hung Wong, Wen Wang, Yu Jiang, Yong Wang

The genetic information coded in DNA leads to trait innovation via a gene regulatory network (GRN) in development. Here, we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network (CNEReg) to investigate the ruminant multi-chambered stomach innovation. We generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep, and revealed 1601 active ruminant-specific conserved non-coding elements (active-RSCNEs). To interpret the function of these active-RSCNEs, we defined toolkit transcription factors (TTFs) and modeled their regulation on rumen-specific genes via batteries of active-RSCNEs during development. Our developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional modules. Notably, 6 TTFs (OTX1, SOX21, HOXC8, SOX2, TP63, and PPARG), as well as 16 active-RSCNEs, functionally distinguished the rumen from the esophagus. Our study provides a systematic approach to understanding how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data.

DNA编码的遗传信息在发育过程中通过基因调控网络(GRN)引导性状创新。在此,我们开发了一种保守的非编码元件解释方法,将多组学数据整合到基因调控网络(gene regulatory network, CNEReg)中,以研究反刍动物多室胃创新。我们生成了绵羊瘤胃和食道发育过程中的配对表达和染色质可及性数据,并揭示了1601个活跃的反刍动物特异性保守非编码元件(active- rscnes)。为了解释这些活性- rscnes的功能,我们定义了工具包转录因子(ttf),并在发育过程中通过活性- rscnes细胞模拟了它们对瘤胃特异性基因的调控。我们的发育GRN发现18个ttf和313个活性rscnes调节7个瘤胃功能模块。值得注意的是,6个ttf (OTX1、SOX21、HOXC8、SOX2、TP63和PPARG)以及16个活性rscnes在功能上区分了瘤胃和食管。我们的研究提供了一种系统的方法来理解基因调控是如何进化和塑造复杂性状的,通过将进化-发展概念与发育多组学数据相结合。
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引用次数: 0
The First Crested Duck Genome Reveals Clues to Genetic Compensation and Crest Cushion Formation. 第一个鸭冠基因组揭示了遗传补偿和冠垫形成的线索。
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-06-01 Epub Date: 2023-08-29 DOI: 10.1016/j.gpb.2023.08.002
Guobin Chang, Xiaoya Yuan, Qixin Guo, Hao Bai, Xiaofang Cao, Meng Liu, Zhixiu Wang, Bichun Li, Shasha Wang, Yong Jiang, Zhiquan Wang, Yang Zhang, Qi Xu, Qianqian Song, Rui Pan, Lingling Qiu, Tiantian Gu, Xinsheng Wu, Yulin Bi, Zhengfeng Cao, Yu Zhang, Yang Chen, Hong Li, Jianfeng Liu, Wangcheng Dai, Guohong Chen

The Chinese crested (CC) duck is a unique indigenous waterfowl breed, which has a crest cushion that affects its survival rate. Therefore, the CC duck is an ideal model to investigate the genetic compensation response to maintain genetic stability. In the present study, we first generated a chromosome-level genome of CC ducks. Comparative genomics revealed that genes related to tissue repair, immune function, and tumors were under strong positive selection, indicating that these adaptive changes might enhance cancer resistance and immune response to maintain the genetic stability of CC ducks. We also assembled a Chinese spot-billed (Csp-b) duck genome, and detected the structural variations (SVs) in the genome assemblies of three ducks (i.e., CC duck, Csp-b duck, and Peking duck). Functional analysis revealed that several SVs were related to the immune system of CC ducks, further strongly suggesting that genetic compensation in the anti-tumor and immune systems supports the survival of CC ducks. Moreover, we confirmed that the CC duck originated from the mallard ducks. Finally, we revealed the physiological and genetic basis of crest traits and identified a causative mutation in TAS2R40 that leads to crest formation. Overall, the findings of this study provide new insights into the role of genetic compensation in adaptive evolution.

中华凤头鸭是一种独特的本土水禽品种,其羽冠垫影响其成活率。因此,CC鸭是研究遗传补偿反应以保持遗传稳定性的理想模型。在本研究中,我们首先生成了CC鸭的染色体水平基因组。比较基因组学显示,与组织修复、免疫功能和肿瘤相关的基因处于强阳性选择下,表明这些适应性变化可能增强癌症抵抗力和免疫反应,以维持CC鸭的遗传稳定性。我们还组装了中国斑嘴鸭(Csp-b)基因组,并检测了三种鸭(即CC鸭、Csp-b鸭和北京鸭)基因组组装中的结构变异。功能分析表明,几种SV与CC鸭的免疫系统有关,这进一步有力地表明,抗肿瘤和免疫系统中的基因补偿支持CC鸭的生存。此外,我们确认CC鸭源自绿头鸭。最后,我们揭示了嵴性状的生理和遗传基础,并在TAS2R40中鉴定了一个导致嵴形成的致病突变。总的来说,这项研究的发现为遗传补偿在适应性进化中的作用提供了新的见解。
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引用次数: 0
stAPAminer: Mining Spatial Patterns of Alternative Polyadenylation for Spatially Resolved Transcriptomic Studies. stAPAminer:为空间解析转录组学研究挖掘选择性聚腺苷化的空间模式。
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-06-01 Epub Date: 2023-01-18 DOI: 10.1016/j.gpb.2023.01.003
Guoli Ji, Qi Tang, Sheng Zhu, Junyi Zhu, Pengchao Ye, Shuting Xia, Xiaohui Wu

Alternative polyadenylation (APA) contributes to transcriptome complexity and gene expression regulation and has been implicated in various cellular processes and diseases. Single-cell RNA sequencing (scRNA-seq) has enabled the profiling of APA at the single-cell level; however, the spatial information of cells is not preserved in scRNA-seq. Alternatively, spatial transcriptomics (ST) technologies provide opportunities to decipher the spatial context of the transcriptomic landscape. Pioneering studies have revealed potential spatially variable genes and/or splice isoforms; however, the pattern of APA usage in spatial contexts remains unappreciated. In this study, we developed a toolkit called stAPAminer for mining spatial patterns of APA from spatially barcoded ST data. APA sites were identified and quantified from the ST data. In particular, an imputation model based on the k-nearest neighbors algorithm was designed to recover APA signals, and then APA genes with spatial patterns of APA usage variation were identified. By analyzing well-established ST data of the mouse olfactory bulb (MOB), we presented a detailed view of spatial APA usage across morphological layers of the MOB. We compiled a comprehensive list of genes with spatial APA dynamics and obtained several major spatial expression patterns that represent spatial APA dynamics in different morphological layers. By extending this analysis to two additional replicates of the MOB ST data, we observed that the spatial APA patterns of several genes were reproducible among replicates. stAPAminer employs the power of ST to explore the transcriptional atlas of spatial APA patterns with spatial resolution. This toolkit is available at https://github.com/BMILAB/stAPAminer and https://ngdc.cncb.ac.cn/biocode/tools/BT007320.

选择性多腺苷酸化(APA)有助于转录组的复杂性和基因表达调控,并与各种细胞过程和疾病有关。单细胞RNA测序(scRNA-seq)使APA能够在单细胞水平上进行分析;然而,细胞的空间信息并没有保存在scRNA-seq中。或者,空间转录组学(ST)技术提供了破译转录组学景观的空间背景的机会。开拓性研究揭示了潜在的空间可变基因和/或剪接异构体;然而,APA在空间语境中的使用模式仍然没有得到重视。在这项研究中,我们开发了一个名为stAPAminer的工具包,用于从空间条形码ST数据中挖掘APA的空间模式。APA位点从ST数据中进行鉴定和定量。特别是,设计了一个基于k近邻算法的插补模型来恢复APA信号,然后识别出具有APA使用变异空间模式的APA基因。通过分析小鼠嗅球(MOB)的成熟ST数据,我们提供了跨MOB形态层的空间APA使用的详细视图。我们编制了一份具有空间APA动力学的基因的综合列表,并获得了几个主要的空间表达模式,这些模式代表了不同形态层中的空间APA动态。通过将该分析扩展到MOB ST数据的另外两个重复,我们观察到几个基因的空间APA模式在重复中是可重复的。stAPAminer利用ST的力量以空间分辨率探索空间APA模式的转录图谱。此工具包位于https://github.com/BMILAB/stAPAminer和https://ngdc.cncb.ac.cn/biocode/tools/BT007320.
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引用次数: 0
Recent Advances in Assembly of Complex Plant Genomes. 植物复杂基因组组装的最新进展。
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-06-01 Epub Date: 2023-04-25 DOI: 10.1016/j.gpb.2023.04.004
Weilong Kong, Yibin Wang, Shengcheng Zhang, Jiaxin Yu, Xingtan Zhang

Over the past 20 years, tremendous advances in sequencing technologies and computational algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already, ranging from those of nonvascular plants to those of flowering plants. However, complex plant genome assembly is still challenging and remains difficult to fully resolve with conventional sequencing and assembly methods due to high heterozygosity, highly repetitive sequences, or high ploidy characteristics of complex genomes. Herein, we summarize the challenges of and advances in complex plant genome assembly, including feasible experimental strategies, upgrades to sequencing technology, existing assembly methods, and different phasing algorithms. Moreover, we list actual cases of complex genome projects for readers to refer to and draw upon to solve future problems related to complex genomes. Finally, we expect that the accurate, gapless, telomere-to-telomere, and fully phased assembly of complex plant genomes could soon become routine.

在过去的20年里,测序技术和计算算法的巨大进步促使植物基因组研究进入了一个繁荣的时代,已经解码了数百个基因组,从无血管植物的基因组到开花植物的基因组。然而,由于复杂基因组的高杂合性、高重复序列或高倍性特征,植物复合体基因组组装仍然具有挑战性,并且仍然难以用传统的测序和组装方法完全解决。在此,我们总结了复杂植物基因组组装的挑战和进展,包括可行的实验策略、测序技术的升级、现有的组装方法和不同的阶段算法。此外,我们列出了复杂基因组项目的实际案例,供读者参考和借鉴,以解决未来与复杂基因组相关的问题。最后,我们预计,复杂植物基因组的准确、无缺口、端粒到端粒的全阶段组装可能很快成为常规。
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引用次数: 0
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Genomics, Proteomics & Bioinformatics
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