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HNRNPD regulates the biogenesis of circRNAs and the ratio of mRNAs to circRNAs for a set of genes. HNRNPD 可调节 circRNA 的生物生成以及一组基因的 mRNA 与 circRNA 的比例。
IF 3.6 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-01-01 Epub Date: 2024-08-24 DOI: 10.1080/15476286.2024.2386500
Shuhui Chang, Yucong Wang, Xiaolin Wang, Hanyuan Liu, Tao Zhang, Yangge Zheng, Xueren Wang, Ge Shan, Liang Chen

Exonic circular RNAs (ecircRNAs) in animal cells are generated by backsplicing, and the biogenesis of ecircRNAs is regulated by an array of RNA binding proteins (RBPs). HNRNPD is a heterogeneous nuclear ribonucleoprotein family member with both cytoplasmic and nuclear roles, and whether HNRNPD regulates the biogenesis of circRNAs remains unknown. In this study, we examine the role of HNRNPD in the biogenesis of ecircRNAs. The levels of ecircRNAs are primarily increased upon depletion of HNRNPD. HNRNPD preferentially binds to motifs enriched with A and U nucleotides, and the flanking introns of ecircRNAs tend to have more numbers and higher intensity of HNRNPD binding sites. The levels of mRNAs are generally not significantly altered in HNRNPD knockout cells. For a small set of genes, the circRNA:mRNA ratio is substantially affected, and the mRNA levels of some of these genes demonstrate a significant decrease in HNRNPD knockout cells. CDK1 is identified as a key gene modulated by HNRNPD in the context of circRNA biogenesis. HNRNPD suppresses the biogenesis of circCDK1 and favours the generation of CDK1 mRNA, and the CDK1 protein is a critical regulator of the cell cycle and apoptosis. HNRNPD can participate in cellular physiology, including the cell cycle and apoptosis, and plays roles in clear cell renal cell carcinoma (ccRCC) by modulating circRNA biogenesis and the mRNA levels of key genes, such as CDK1.

动物细胞中的外显子环状RNA(ecircRNAs)是通过反拼接产生的,而ecircRNAs的生物发生受一系列RNA结合蛋白(RBPs)的调控。 HNRNPD是一种异质性核核糖核蛋白家族成员,具有细胞质和细胞核的双重作用,而HNRNPD是否调控circRNAs的生物发生仍是未知数。本研究探讨了 HNRNPD 在 ecircRNAs 生物发生过程中的作用。消耗 HNRNPD 后,ecircRNAs 的水平主要会增加。HNRNPD 优先与富含 A 和 U 核苷酸的基团结合,ecircRNA 的内含子侧翼往往有更多和更高强度的 HNRNPD 结合位点。在 HNRNPD 基因敲除的细胞中,mRNA 的水平一般不会发生显著变化。对于一小部分基因,circRNA:mRNA 的比例会受到很大影响,其中一些基因的 mRNA 水平在 HNRNPD 基因敲除细胞中会显著下降。CDK1 被确定为在 circRNA 生物发生过程中受 HNRNPD 调节的关键基因。HNRNPD 抑制了 circCDK1 的生物发生,有利于 CDK1 mRNA 的生成,而 CDK1 蛋白是细胞周期和细胞凋亡的关键调节因子。HNRNPD 可参与细胞生理,包括细胞周期和细胞凋亡,并通过调节 circRNA 的生物生成和 CDK1 等关键基因的 mRNA 水平,在透明细胞肾细胞癌(ccRCC)中发挥作用。
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引用次数: 0
Regulation of magnesium ion transport in Escherichia coli: insights into the role of the 5' upstream region in corA expression. 大肠杆菌镁离子转运的调控:5' 上游区域在 corA 表达中的作用。
IF 3.6 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-01-01 Epub Date: 2024-11-08 DOI: 10.1080/15476286.2024.2421665
A-S Vézina Bédard, A Michaud, F Quenette, N Singh, F de Lemos Martins, J T Wade, M Guillier, D A Lafontaine

In Escherichia coli, transport of magnesium ions across the cellular membrane relies on MgtA and CorA transporters. While the expression of mgtA is controlled by the two-component system PhoQ/PhoP and 5' upstream region elements, corA expression is considered to be constitutive and not to depend on cellular factors. Importantly, the 5' upstream region of corA is predicted to fold into structures highly similar to the magnesium-sensing mgtA 5' upstream region. Here using biochemical and genetic assays, we show that the intracellular concentration of magnesium ions affects corA expression. Similarly to mgtA, we find that the effect of magnesium ions on corA expression is mediated by the 5' upstream region. We demonstrate that the RNA structure is important for regulation and that the Rho transcription factor is involved in the modulation of transcription termination. Consistent with previous studies, we find that translation of corL, a short ORF located within the 5' upstream region, is important for corA regulation. Our data indicate that the efficiency of corL translation is inversely proportional to corA expression, similar to what has been described for mgtA and corA in Salmonella enterica. Using a novel assay to control the import of magnesium ions, we show that while the expression of mgtA is regulated by both extra- and intracellular magnesium ions, corA is regulated by variations in intracellular magnesium ions. Our results support a model in which the expression of corA is regulated by the 5' upstream region that senses variations of intracellular magnesium ions.

在大肠杆菌中,镁离子跨细胞膜的转运依赖于 MgtA 和 CorA 转运体。mgtA 的表达受双组分系统 PhoQ/PhoP 和 5' 上游区域元件的控制,而 corA 的表达被认为是组成性的,不依赖于细胞因素。重要的是,据预测,corA 的 5'上游区域折叠成的结构与镁传感 mgtA 的 5'上游区域高度相似。在这里,我们利用生化和遗传实验证明,细胞内的镁离子浓度会影响 corA 的表达。与 mgtA 相似,我们发现镁离子对 corA 表达的影响是由 5' 上游区域介导的。我们证明了 RNA 结构对调控的重要性,以及 Rho 转录因子参与了转录终止的调控。与之前的研究一致,我们发现位于 5' 上游区域的短 ORF(corL)的翻译对 corA 的调控非常重要。我们的数据表明,corL 的翻译效率与 corA 的表达成反比,这与肠炎沙门氏菌中 mgtA 和 corA 的情况类似。利用一种控制镁离子输入的新型检测方法,我们发现 mgtA 的表达受细胞外和细胞内镁离子的调节,而 corA 则受细胞内镁离子变化的调节。我们的研究结果支持这样一个模型,即 corA 的表达受感知细胞内镁离子变化的 5' 上游区域的调控。
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引用次数: 0
Low dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis 低剂量核糖体 DNA P 环突变影响拟南芥的生长发育并强化自噬作用
IF 4.1 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2023-12-29 DOI: 10.1080/15476286.2023.2298532
Thiruvenkadam Shanmugam, Palak Chaturvedi, Deniz Streit, Arindam Ghatak, Thorsten Bergelt, Stefan Simm, Wolfram Weckwerth, Enrico Schleiff
Arabidopsis contains hundreds of ribosomal DNA copies organized within the nucleolar organizing regions (NORs) in chromosomes 2 and 4. There are four major types of variants of rDNA, VAR1–4, based ...
拟南芥含有数百个核糖体DNA拷贝,这些拷贝组织在第2和第4号染色体的核极组织区(NORs)中。rDNA 有四种主要变体,即 VAR1-4,基于...
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引用次数: 0
Structural and computational studies of HIV-1 RNA HIV-1 RNA 的结构和计算研究
IF 4.1 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2023-12-15 DOI: 10.1080/15476286.2023.2289709
Lev Levintov, Harish Vashisth
Viruses remain a global threat to animals, plants, and humans. The type 1 human immunodeficiency virus (HIV-1) is a member of the retrovirus family and carries an RNA genome, which is reverse trans...
病毒仍然是对动物、植物和人类的全球性威胁。1 型人类免疫缺陷病毒(HIV-1)是逆转录病毒家族的一员,它携带 RNA 基因组,并通过逆转录技术将 RNA 转录成病毒。
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引用次数: 0
mRNA nuclear export: how mRNA identity features distinguish functional RNAs from junk transcripts mRNA 核输出:mRNA 身份特征如何区分功能 RNA 与垃圾转录本
IF 4.1 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2023-12-13 DOI: 10.1080/15476286.2023.2293339
Alexander F. Palazzo, Yi Qiu, Yoon Mo Kang
The division of the cellular space into nucleoplasm and cytoplasm promotes quality control mechanisms that prevent misprocessed mRNAs and junk RNAs from gaining access to the translational machiner...
将细胞空间划分为核质和细胞质可促进质量控制机制,防止处理不当的 mRNA 和垃圾 RNA 进入翻译机器。
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引用次数: 0
Therapeutic potential of natural antisense transcripts and various mechanisms involved for clinical applications and disease prevention 天然反义转录本的治疗潜力以及临床应用和疾病预防所涉及的各种机制
IF 4.1 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2023-12-13 DOI: 10.1080/15476286.2023.2293335
Ashiq Ali, Aisha Khatoon, Chenran Shao, Bilal Murtaza, Qaisar Tanveer, Zhongjing Su
Antisense transcription, a prevalent occurrence in mammalian genomes, gives rise to natural antisense transcripts (NATs) as RNA molecules. These NATs serve as agents of diverse transcriptional and ...
反义转录是哺乳动物基因组中的一种普遍现象,它产生了作为 RNA 分子的天然反义转录本(NATs)。这些反义转录本是多种转录和...
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引用次数: 0
Unraveling C-to-U RNA editing events from direct RNA sequencing 通过直接 RNA 测序揭示 C 到 U RNA 编辑事件
IF 4.1 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2023-12-13 DOI: 10.1080/15476286.2023.2290843
Adriano Fonzino, Caterina Manzari, Paola Spadavecchia, Uday Munagala, Serena Torrini, Silvestro Conticello, Graziano Pesole, Ernesto Picardi
In mammals, RNA editing events involve the conversion of adenosine (A) in inosine (I) by ADAR enzymes or the hydrolytic deamination of cytosine (C) in uracil (U) by the APOBEC family of enzymes, mo...
在哺乳动物中,RNA 编辑事件包括 ADAR 酶将腺苷 (A) 转化为肌苷 (I),或 APOBEC 酶家族将胞嘧啶 (C) 水解脱氨为尿嘧啶 (U)。
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引用次数: 0
Correction. 校正
IF 4.1 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2023-09-30 DOI: 10.1080/15476286.2023.2264666
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引用次数: 0
Presentation of Ocular Syphilis with Bilateral Optic Neuropathy. 眼部梅毒并发双侧视神经病变。
IF 0.8 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2023-07-05 eCollection Date: 2023-01-01 DOI: 10.1080/01658107.2023.2222800
Mustafa Kayabaşı, Seher Köksaldı, Ali Osman Saatci, Meltem Söylev Bajin

A 60-year-old otherwise healthy male presented with a 1 year history of bilateral progressive visual loss. His best-corrected visual acuity was counting fingers at 2 m with his right eye and counting fingers at 0.5 m with his left eye. Visual field testing revealed bilateral near-total loss of visual fields. Slit-lamp examination was unremarkable, apart from bilateral grade two nuclear sclerotic cataracts. Both optic discs were pale-looking with some retinal pigment epithelial alterations at the left papillomacular region. Enhanced depth imaging optical coherence tomography depicted punctate hyperreflective dots at the inner choroidal level corresponding to the retinal pigment epithelial changes in the left eye. Fundus autofluorescence imaging revealed patchy hyper-autofluorescent and hypo-autofluorescent areas, and there was mild staining in the early and late phases of the fluorescein angiogram at the papillomacular region in the left eye. A diagnosis of bilateral optic neuropathy was made. A full systemic work-up was carried out, and serological tests pointed out the presence of syphilis with normal cranial magnetic resonance imaging. He was treated accordingly. Our case clearly demonstrates the importance of a high clinical suspicion for syphilis in cases of optic neuropathy.

一名 60 岁、身体健康的男性患者出现双侧进行性视力下降,病史已有 1 年。他的最佳矫正视力为右眼在 2 米处数手指,左眼在 0.5 米处数手指。视野测试显示双侧视野接近完全丧失。裂隙灯检查除了双侧二级核硬化性白内障外,没有其他异常。双侧视盘外观苍白,左侧乳头状区有一些视网膜色素上皮改变。增强深度成像光学相干断层扫描显示,左眼视网膜色素上皮病变对应的脉络膜内层有点状高反射点。眼底自发荧光成像显示斑片状高自发荧光区和低自发荧光区,左眼乳头黄斑区荧光素血管造影早期和晚期有轻度染色。诊断结果为双侧视神经病变。对他进行了全面的全身检查,血清学检测显示存在梅毒,头颅磁共振成像正常。他接受了相应的治疗。我们的病例清楚地表明,临床上高度怀疑梅毒对视神经病变的重要性。
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引用次数: 0
RNA therapeutics. RNA 疗法。
IF 4.1 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2023-01-11 DOI: 10.1080/15476286.2022.2161704
Tony Gutschner
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RNA Biology
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