Molecular hallmarks of long non-coding RNAs in aging and its significant effect on aging-associated diseases

Aging is linked to the deterioration of many physical and cognitive abilities and is the leading risk factor for Alzheimer’s disease. The growing aging population is a significant healthcare problem globally that researchers must investigate to better understand the underlying aging processes. Advances in microarrays and sequencing techniques have resulted in deeper analyses of diverse essential genomes(e.g., mouse, human, and rat) and their corresponding cell types, their organ-specific transcriptomes, and the tissue involved in aging. Traditional gene controllers such as DNA-and RNA-binding proteins significantly influence such programs, causing the need to sort out long non-coding RNAs, a new class of powerful gene regulatory elements. However, their functional significance in the aging process and senescence has yet to be investigated and identified. Several recent researchers have associated the initiation and development of senescence and aging in mammals with several well-reported and novel long non-coding RNAs. In this review article, we identified and analyzed the evolving functions of long non-coding RNAs in cellular processes, including cellular senescence, aging, and age-related pathogenesis, which are the major hallmarks of long non-coding RNAs in aging.

Single-cell transcriptome sequencing reveals the mechanism regulating rice plumule development

Seed plumules comprise multiple developing tissues and are key sites for above-ground plant organ morphogenesis.Here,the spatial expression of genes in developing rice seed plumules was characterized by single-cell transcriptome sequencing in Zhongjiazao 17,a popular Chinese indica rice cultivar.Of 15 cell clusters,13 were assigned to cell types using marker genes and cluster-specific genes.Marker genes of multiple cell types were expressed in several clusters,suggesting a complex developmental system.Some genes for signaling by phytohormones such as abscisic acid were highly expressed in specific clusters.Various cis-elements in the promoters of genes specifically expressed in cell clusters were calculated,and some key hormone-related motifs were frequent in certain clusters.Spatial expression patterns of genes involved in rapid seed germination,seedling growth,and development were identified.These findings enhanced our understanding of cellular diversity and specialization within plumules of rice,a monocotyledonous model crop.

Regulatory mechanisms of long non-coding RNAs

Long non-coding RNAs(lncRNAs) belong to a large and complex family of RNAs, which play many important roles in regulating gene expression. However, the mechanism underlying the dynamic expression of lncRNAs is still not very clear. In order to identify lncRNAs and clarify the mechanisms involved, we collected basic information and highlighted the mechanisms underlying lncRNA expression and regulation. Overall, lncRNAs are regulated by several similar transcription factors and protein-coding genes. Epigenetic modification(DNA methylation and histone modification) can also downregulate lncRNA levels in tissues and cells. Moreover, lncRNAs may be degraded or cleaved via interaction with miRNAs and miRNAassociated protein complexes. Furthermore, alternative RNA splicing(AS) may play a significant role in the post-transcriptional regulation of lncRNAs.

Auto-selection order of Markov chain for background sequences with chi-square test

Modeling non coding background sequences appropriately is important for the detection of regulatory elements from DNA sequences. Based on the chi square statistic test, some explanations about why to choose higher order Markov chain model and how to automatically select the proper order are given in this paper. The chi square test is first run on synthetic data sets to show that it can efficiently find the proper order of Markov chain. Using chi square test, distinct higher order context dependences inherent in ten sets of sequences of yeast S.cerevisiae from other literature have been found. So the Markov chain with higher order would be more suitable for modeling the non coding background sequences than an independent model.

Long non-coding RNAs era in liver cancer

Hepatocellular carcinoma(HCC) is one of the most common malignancies leading to high mortality rates in the general population and the sixth most common cancer worldwide. HCC is characterized by deregulation of multiple genes and signalling pathways. These genetic effects can involve both protein coding genes as well as non-coding RNA genes. Long noncoding RNAs(lnc RNAs) are transcripts longer than 200 nt, constituting a subpopulation of nc RNAs. Their biological effects are not well understood comparedto small non-coding RNA(micro RNAs), but they have been recently recognized to exert a crucial role in the regulation of gene expression and modulation of signalling pathways. Notably, several studies indicated that lnc RNAs contribute to the pathogenesis and progression of HCC. Investigating the molecular mechanisms underlying lnc RNAs expression opens potential applications in diagnosis and treatment of liver disease. This editorial provides three examples(MALAT-1 metastasis associated lung adenocarcinoma transcript, HULC highly upregulated in liver cancer and HOTAIR HOX transcript antisense intergenic RNA) of well-known lnc RNAs upregulated in HCC, whose mechanisms of action are known, and for which therapeutic applications are delineated. Targeting of lnc RNAs using several approaches(siR NA-mediated silencing or changing their secondary structure) offers new possibility to treat HCC.

Expression of long non-coding RNAs in complete transection spinal cord injury: a transcriptomic analysis

Long non-coding RNAs(lncRNAs)are abundantly expressed in the central nervous system and exert a critical role in gene regulation via multiple biological processes.To uncover the functional significance and molecular mechanisms of lncRNAs in spinal cord injury(SCI),the expression signatures of lncRNAs were profiled using RNA sequencing(RNA-seq)technology in a Sprague-Dawley rat model of the 10th thoracic vertebra complete transection SCI.Results showed that 116 of 14,802 detected lncRNAs were differentially expressed,among which 16—including eight up-regulated(H19,Vof16,Hmox2-ps1,LOC100910973,Ybx1-ps3,Nnat,Gcgr,LOC680254)and eight down-regulated(Rmrp,Terc,Ngrn,Ppp2r2b,Cox6a2,Rpl37a-ps1,LOC360231,Rpph1)—demonstrated fold changes>2 in response to transection SCI.A subset of these RNA-seq results was validated by quantitative real-time PCR.The levels of 821 mRNAs were also significantly altered post-SCI;592 mRNAs were up-regulated and 229 mRNAs were down-regulated by more than 2-fold.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)analyses showed that differentially expressed mRNAs were related to GO biological processes and molecular functions such as injury and inflammation response,wound repair,and apoptosis,and were significantly enriched in 15 KEGG pathways,including cell phagocytosis,tumor necrosis factor alpha pathway,and leukocyte migration.Our results reveal the expression profiles of lncRNAs and mRNAs in the rat spinal cord of a complete transection model,and these differentially expressed lncRNAs and mRNAs represent potential novel targets for SCI treatment.We suggest that lncRNAs may play an important role in the early immuno-inflammatory response after spinal cord injury.This study was approved by the Administration Committee of Experimental Animals,Guangdong Province,China.

Prediction of candidate small non-coding RNAs inAgrobacterium by computational analysis

Small non-coding RNAs with important regulatory roles are not confined to eukaryotes. Recent work has uncovered a growing number of bacterial small RNAs （sRNAs）, some of which have been shown to regulate critical cellular processes. Computational approaches, in combination with molecular experiments, have played an important role in the identification of these sRNAs. At present, there is no information on the presence of small non-coding RNAs and their genes in the Agrobacterium tumefaciens genome. To identify potential sRNAs in this important bacterium, deep sequencing of the short RNA populations isolated from Agrobacterium tumefaciens C58 was carried out. From a data set of more than 10,000 short sequences, 16 candidate sRNAs have been tentatively identified based on computational analysis. All of these candidates can form stem-loop structures by RNA folding predictions and the majority of the secondary structures are rich in GC base-pairs：：Some are followed by a short stretch of U residues, indicative of a rho-independent transcription terminator, whereas some of the short RNAs are found in the stem region of the hairpin, indicative of eukaryotic-like sRNAs. Experimental strategies will need to be used to verify these candidates. The study of an expanded list of candidate sRNAs in Agrobacterium will allow a more complete understanding of the range of roles played by regulatory RNAs in prokaryotes.

基于转录组测序分析猪子宫内膜妊娠中的关键非编码RNA及其调控通路

【目的】探究调控具有不同产仔数的川乡黑猪和藏猪的猪子宫内膜妊娠过程的相关miRNA、lncRNA及靶基因,进一步揭示影响不同品种猪子宫内膜妊娠相关非编码RNA富集的信号通路。【方法】对平均产仔数为11.35和6.70的川乡黑猪和藏猪第2、5胎次的子宫内膜进行分离,提取RNA,质检合格后进行转录组测序,测序数据经过拼接、比对到miRNA和lncRNA并预测其靶基因,进行GO和KEGG富集分析筛选到调控川乡黑猪和藏猪不同产仔数的候选基因以及信号富集通路。【结果】不同胎次的川乡黑猪和藏猪之间存在多个miRNA、lncRNA及靶基因的差异表达,其中第2胎次具有1571个miRNA和2042个lncRNA差异表达,第5胎次具有1042个miRNA和2096个lncRNA差异表达。进一步根据靶基因的GO和KEGG富集分析发现川乡黑猪在促性腺激素释放激素(GnRH)分泌、ECM受体互作以及Wnt信号通路等的富集程度高于藏猪。同时发现川乡黑猪相比藏猪有醛固酮调节钠重吸收、谷胱甘肽代谢、果糖和甘露糖代谢等过程的富集。此外,已鉴定的关键候选调控基因包括FSHR(Follicle stimulating hormone receptor)、DBX1(Developing brain homeobox 1)、ARID2(AT-rich interaction domain 2)、TNC(Tenascin C)、NT5C2(Neuropilin 2)、LAMC3(Laminin subunit gamma 3)、MADD(MAP kinase activating death domain)等。【结论】高产仔数的川乡黑猪相比低产仔数的藏猪在子宫内膜妊娠过程中有更高的促性腺激素释放激素(GnRH)分泌、ECM受体互作以及Wnt信号通路富集(GO分析结果),同时也有代谢途径的参与(KEGG分析结果)。涉及到的关键调控基因主要有FSHR、DBX1等。本研究为探究非编码RNA在猪子宫内膜妊娠过程中的功能及其分子调控机制提供了新的思路。

基于单细胞RNA测序数据的基因调控网络推断算法综述

通过基因表达的变化可以推断基因调控网络.单细胞RNA测序(scRNA-seq)为推断细胞周期或分化等时间依赖性生物过程的基因调控网络提供了新的可能性,基于scRNA-seq数据的基因调控网络推断算法成为一个相对活跃的研究方向.本文首先对26种基因调控网络推断算法进行介绍,包括3种针对批量RNA测序数据的推断算法和23种针对scRNA-seq数据的推断算法(基于布尔网络的算法2种、基于微分方程的算法3种、基于伪时序基因相关性集成策略的算法5种、基于共表达基因的算法4种、基于细胞特异性的算法3种、基于深度学习的算法6种),详细描述了每类算法的方法原理和算法优缺点,对算法进行综合比较;然后分析了推断算法比较研究的相关成果,并使用scRNA-seq数据简单评估了26种算法的性能;最后探讨当前基因调控网络推断算法面临的机遇与挑战.

侧流与主流磷回收工艺对比及调控因子分析

从污水中回收磷是缓解磷资源危机的有效途径,目前,污水处理厂常用的磷回收工艺主要为从剩余污泥中回收磷的侧流工艺,存在工艺复杂、回收效率低等问题.以生物膜为主体的主流磷回收工艺可实现磷的同步去除与富集,工艺简单且高效,因此更具发展前景.两种工艺在运行原理及模式上存在显著差异,因此对两者的调控措施不尽相同.本文分别以A^(2)O工艺和生物膜序批式反应器工艺为代表,对比了侧流和主流磷回收工艺在运行原理及模式上的异同,并以聚磷菌的代谢机理为基础,总结了温度、pH值、水力停留时间、溶解氧、碳源和蓄磷量等调控因子对两种工艺产生的影响,并阐述了其差异化机制,以期为生物膜磷回收工艺的进一步发展提供参考.

Transcriptomic and bioinformatics analysis of the mechanism by which erythropoietin promotes recovery from traumatic brain injury in mice

Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate traumatic brain injury in mice by intrape ritoneal injection of erythro poietin for 3 consecutive days.RNA sequencing detected a total of 4065 differentially expressed RNAs,including 1059 mRNAs,92 microRNAs,799 long non-coding RNAs,and 2115circular RNAs.Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses revealed that the coding and non-coding RNAs that were differentially expressed after traumatic brain injury and treatment with erythropoietin play roles in the axon guidance pathway,Wnt pathway,and MAPK pathway.Constructing competing endogenous RNA networks showed that regulatory relationship between the differentially expressed non-coding RNAs and mRNAs.Because the axon guidance pathway was repeatedly enriched,the expression of Wnt5a and Ephb6,key factors in the axonal guidance pathway,was assessed.Ephb6 expression decreased and Wnt5a expression increased after traumatic brain injury,and these effects were reversed by treatment with erythro poietin.These findings suggest that erythro poietin can promote recove ry of nerve function after traumatic brain injury through the axon guidance pathway.

New challenges in hepatocellular carcinoma:A role for PIWIinteracting RNAs?

Hepatocellular carcinoma(HCC)is the most common and deadliest subtype of liver cancer worldwide and,therefore,poses an enormous threat to global health.Understanding the molecular mechanisms underlying the development and progression of HCC is central to improving our clinical approaches.PIWIinteracting RNAs(piRNAs)are a class of small non-coding RNAs that bind to PIWI family proteins to regulate gene expression at transcriptional and posttranscriptional levels.A growing body of work shows that the dysregulation of piRNAs plays a crucial role in the progression of various human cancers.In this editorial,we report on the current knowledge of HCC-associated piRNAs and their potential clinical utility.Based on the editorial by Papadopoulos and Trifylli,on the role and clinical evaluation of exosomal circular RNAs in HCC,we highlight this other emerging class of non-coding RNAs.

干扰素调节因子3促结直肠癌细胞增殖与侵袭相关探索

目的·分析结直肠癌中干扰素调节因子3(interferon regulatory factor 3,IRF3)表达水平与临床病理特征及患者预后的关系,观察IRF3过表达对结直肠癌细胞增殖与侵袭能力的影响及其相关蛋白通路。方法·下载癌症基因组图谱(The Cancer Genome Atlas,TCGA)数据,分析IRF3表达水平与恶性肿瘤患者(肾癌、结直肠癌、肝癌、前列腺癌)预后的关系。采用免疫组织化学法检测10例结直肠癌或肾癌患者的癌组织与癌旁正常组织切片中IRF3表达水平的差异。针对IRF3蛋白的C端残基位点进行改造,构建拟磷酸化IRF3-5D(396/398/402/404/405-D)高表达的HEK-293T细胞。分别在细胞培养12、24 h时,采用TANK结合激酶1(TANK-binding kinase 1,TBK1)抑制剂进行处理,并采用蛋白质印迹法检测细胞IRF3、p-IRF3(Ser386)蛋白表达水平。采用RNA测序技术探索IRF3-5D高表达与肿瘤相关蛋白表达水平的相关性。构建野生型IRF3(IRF3-WT)和IRF3-5D过表达的结直肠癌细胞CT26、COLON26,采用细胞计数法、细胞划痕试验和克隆形成试验检测细胞增殖及迁移能力。结果·TCGA数据分析提示癌组织中IRF3蛋白表达水平与患者的不良预后呈正相关。癌症患者病理组织免疫组织化学法显示,结直肠癌、肾癌组织中IRF3的表达水平显著上调,且蛋白表达集中于细胞核内。TBK1抑制剂分别在细胞培养12、24 h时间点作用后,HEK-293T细胞p-IRF3(Ser386)蛋白表达减弱。RNA测序和蛋白质印迹法结果显示,多个与癌症预后不良相关的蛋白[IRF9、细胞程序性死亡-配体1(programmed cell death 1-ligand 1,PD-L1)等]表达水平在IRF3-5D高表达的条件下显著上调。结直肠癌细胞中过表达IRF3-5D,可导致癌细胞的增殖、迁移能力显著上调。结论·结直肠癌中IRF3表达水平与患者不良预后呈正相关。IRF3-5D蛋白在结直肠癌细胞内高表达后,促进癌细胞恶性生物学行为。此外,IRF3-5D依赖于TBK1介导的IRF3活化激活通路,并上调多个肿瘤相关蛋白的表达水平。

瓜实蝇雄性决定因子基因MoY功能及其上游调控序列活性分析

【目的】本研究旨在鉴定瓜实蝇Zeugodacus cucurbitae雄性决定因子基因MoY上游调控序列,并探索该序列在胚胎早期驱动MoY表达对瓜实蝇性别决定的影响,为后续的瓜实蝇转基因品系的构建提供参考依据以及可用元件。【方法】使用基因组步移法扩增瓜实蝇Y染色体连锁的MoY上游序列并测序,将获得的上游序列连接MoY的CDS区构建其驱动MoY表达的质粒;将MoY表达质粒注射进瓜实蝇新鲜的胚胎中,待胚胎孵化后观察成虫的表型以及性比并提取基因组DNA,通过使用基因组DNA扩增MoY以判断获得的MoY上游调控序列是否具有驱动MoY表达的功能,同时分析MoY在胚胎中的表达对性别决定的影响。【结果】克隆并获得瓜实蝇MoY上游1660 bp序列,构建该序列驱动MoY表达的质粒p1660。由注射胚胎发育而来的瓜实蝇雄成虫18头和雌成虫13头及另外发现3头成虫的生殖器发育异常且MoY的扩增结果为阴性,确认为间性个体。【结论】本研究通过对MoY进行基因组步移扩增发现所获得的瓜实蝇MoY上游调控序列具有驱动MoY表达的活性,当MoY于瓜实蝇胚胎早期表达可使原本发育为雌性的个体出现性别逆转的现象。

非编码遗传资源在作物重要农艺性状调控中的研究进展

在传统作物遗传研究中,蛋白质编码基因一直是研究的焦点。然而,近年来的科学进展揭示了非编码遗传资源在调控作物产量、品质和抗性等重要农艺性状中的关键作用。这些非编码遗传资源包括调控性非编码RNA、组成性非编码RNA、基因非编码区序列、核酸适配体以及由非编码序列衍生的小肽,它们在基因表达调控、细胞代谢、基因组稳定性以及生物技术应用中发挥着至关重要的作用。高通量测序技术、生物信息学和功能基因组学的快速发展,为非编码遗传资源的系统发掘和功能研究提供了技术支撑。在作物育种领域,非编码遗传资源的精准调控特性为提升农艺性状提供了全新手段,突破了传统编码基因研究的局限性。相关研究不仅揭示了非编码序列在作物复杂性状调控中的多样化功能与精细调控机制,也展现出巨大的应用潜力。该文综合评述非编码遗传资源在作物农艺性状调控中的研究进展,系统梳理这些非编码元件的分类、起源与演化背景,详细讨论其在调控作物重要农艺性状中的作用机制和调控网络,最后探讨非编码遗传资源在作物育种中的应用潜力,并对其在未来遗传改良中的发展方向提出展望。通过系统地总结现有研究成果,可为未来研究提供坚实的理论基础,并促进非编码遗传资源在作物遗传改良中的创新应用。

CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network

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 ruminantspecific conserved non-coding elements(active-RSCNEs).To interpret the function of these activeRSCNEs,we defined toolkit transcription factors(TTFs)and modeled their regulation on rumenspecific 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.

ADAR-mediated RNA editing in non-coding RNA sequences

Adenosine to inosine （A-to-I） RNA editing is the most abundant editing event in animals. It converts adenosine to inosine in double-stranded RNA regions through the action of the adenosine deaminase acting on RNA （ADAR） proteins. Editing of pre-mRNA coding regions can alter the protein codon and increase functional diversity. However, most of the A-to-I editing sites occur in the non-coding regions of pre-mRNA or mRNA and non-coding RNAs. Untranslated regions （UTRs） and introns are located in pre-rnRNA non-coding regions, thus A-to-I editing can influence gene expression by nuclear retention, degrada- tion, alternative splicing, and translation regulation. Non-coding RNAs such as microRNA （miRNA）, small interfering RNA （siRNA） and long non-coding RNA （lncRNA） are related to pre-mRNA splicing, translation, and gene regulation. A-to-I edit- ing could therefore affect the stability, biogenesis, and target recognition of non-coding RNAs. Finally, it may influence the function of non-coding RNAs, resulting in regulation of gene expression. This review focuses on the function of ADAR-mediated RNA editing on mRNA non-coding regions （UTRs and introns） and non-coding RNAs （miRNA, siRNA, and IncRNA）.

Hide and Seek: Protein-coding Sequences Inside ‘‘Non-coding” RNAs

Calcium homeostasis is crucial for muscle contractilityMuscle cells are critically dependent on calcium homeostasis. Without having the right amount of calcium ions just on the spot and coordinated in between muscle cells, no contraction can take place. Therefore, calcium homeostasis is one of the critical regulatory mechanisms in all muscle cells, including skeletal muscle and heart [1,2]. Ca2＋ adenosine triphosphatase the relaxation of muscle cells Sarco-endoplasmic reticulum （SERCA） is responsible for by pumping Ca2＋ into the sarcoplasmic reticulum （SR） .

Reconstructing gene regulatory networks in single-cell transcriptomic data analysis

Gene regulatory networks play pivotal roles in our understanding of biological processes/mechanisms at the molecular level.Many studies have developed sample-specific or cell-type-specific gene regulatory networks from single-cell transcriptomic data based on a large amount of cell samples.Here,we review the state-of-the-art computational algorithms and describe various applications of gene regulatory networks in biological studies.

Expression and regulatory network of long noncoding RNA in rats after spinal cord hemisection injury

Long noncoding RNAs(lncRNAs)participate in a variety of biological processes and diseases.However,the expression and function of lncRNAs after spinal cord injury has not been extensively analyzed.In this study of right side hemisection of the spinal cord at T10,we detected the expression of lncRNAs in the proximal tissue of T10 lamina at different time points and found 445 lncRNAs and 6522 mRNA were differentially expressed.We divided the differentially expressed lncRNAs into 26 expression trends and analyzed Profile 25 and Profile 2,the two expression trends with the most significant difference.Our results showed that the expression of 68 lncRNAs in Profile 25 rose first and remained high 3 days post-injury.There were 387 mRNAs co-expressed with the 68 lncRNAs in Profile 25.The co-expression network showed that the co-expressed genes were mainly enriched in cell division,inflammatory response,FcγR-mediated cell phagocytosis signaling pathway,cell cycle and apoptosis.The expression of 56 lncRNAs in Profile2 first declined and remained low after 3 days post-injury.There were 387 mRNAs co-expressed with the 56 lncRNAs in Profile 2.The co-expression network showed that the co-expressed genes were mainly enriched in the chemical synaptic transmission process and in the signaling pathway of neuroactive ligand-receptor interaction.The results provided the expression and regulatory network of the main lncRNAs after spinal cord injury and clarified their co-expressed gene enriched biological processes and signaling pathways.These findings provide a new direction for the clinical treatment of spinal cord injury.