Predictive role of noncoding RNAs in growth-development and stress mechanisms of Amaranthus hypochondriacus.

IF 2.9 4区生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

3 Biotech Pub Date : 2025-10-01 Epub Date: 2025-09-17 DOI:10.1007/s13205-025-04515-y

Sarika Sahu, Indra Singh, Priyanka Jain, Rekha Dixit, Jaya Pandey, Ratna Kumari, Ambika Gaikwad, Kishor Gaikwad, Atmakuri Ramakrishna Rao

{"title":"Predictive role of noncoding RNAs in growth-development and stress mechanisms of Amaranthus hypochondriacus.","authors":"Sarika Sahu, Indra Singh, Priyanka Jain, Rekha Dixit, Jaya Pandey, Ratna Kumari, Ambika Gaikwad, Kishor Gaikwad, Atmakuri Ramakrishna Rao","doi":"10.1007/s13205-025-04515-y","DOIUrl":null,"url":null,"abstract":"The characterization of gene regulatory networks by noncoding RNAs (ncRNAs) may help understand the growth development and stress tolerance mechanisms of Amaranthus. The study aimed to identify (i) ncRNAs: long noncoding RNAs (lncRNAs), micro RNAs (miRNAs) and circular RNAs (circRNAs) on Amaranthus genome, (ii) ncRNA regulated genes and their role in plant processes, (iii) noncoding RNA bearing Simple Sequence Repeat (SSR) markers, and (iv) miRNA-lncRNA-mRNA triplet interactions, and study their involvement in growth development and stress tolerance mechanisms. We identified computationally a total of 2690 lncRNAs, 836 miRNAs, 31 circular RNAs and 3506 SSRs on genome and found SSRs on pre-miRNAs and lncRNAs. Majority of predicted lncRNAs were found specific to Amaranthus. The targeted genes of the identified ncRNAs are observed to be involved in growth-development and stress mechanisms. The lncRNA \"Ahy_lnc_0021\" acted as endogenous target mimic (eTM) to inhibit miRNA \"ahy-mir8717\" that targets the gene SHM6, largely involved in folate metabolism as well as in the synthesis of amino acids, vitamin B5 and nucleic acids. The likely involvement of lncRNAs and their targeted genes in growth development, phytophenols synthesis and stress tolerance mechanisms were validated. The key roles of lncRNA-miRNA-mRNA associations were also validated and found that the lncRNA \"Ahy_lnc_2243\" enhanced the expression of BRD-proteins by acting as RNA decoy for miRNA \"ahy-mir5298\". A database on findings from the study was populated and made available at https://cirssrdb.rf.gd/ and http://backlin.cabgrid.res.in/Amaranthus_database/index.php.Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04515-y.","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"15 10","pages":"353"},"PeriodicalIF":2.9000,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12443664/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"3 Biotech","FirstCategoryId":"5","ListUrlMain":"https://doi.org/10.1007/s13205-025-04515-y","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/9/17 0:00:00","PubModel":"Epub","JCR":"Q3","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

The characterization of gene regulatory networks by noncoding RNAs (ncRNAs) may help understand the growth development and stress tolerance mechanisms of Amaranthus. The study aimed to identify (i) ncRNAs: long noncoding RNAs (lncRNAs), micro RNAs (miRNAs) and circular RNAs (circRNAs) on Amaranthus genome, (ii) ncRNA regulated genes and their role in plant processes, (iii) noncoding RNA bearing Simple Sequence Repeat (SSR) markers, and (iv) miRNA-lncRNA-mRNA triplet interactions, and study their involvement in growth development and stress tolerance mechanisms. We identified computationally a total of 2690 lncRNAs, 836 miRNAs, 31 circular RNAs and 3506 SSRs on genome and found SSRs on pre-miRNAs and lncRNAs. Majority of predicted lncRNAs were found specific to Amaranthus. The targeted genes of the identified ncRNAs are observed to be involved in growth-development and stress mechanisms. The lncRNA "Ahy_lnc_0021" acted as endogenous target mimic (eTM) to inhibit miRNA "ahy-mir8717" that targets the gene SHM6, largely involved in folate metabolism as well as in the synthesis of amino acids, vitamin B5 and nucleic acids. The likely involvement of lncRNAs and their targeted genes in growth development, phytophenols synthesis and stress tolerance mechanisms were validated. The key roles of lncRNA-miRNA-mRNA associations were also validated and found that the lncRNA "Ahy_lnc_2243" enhanced the expression of BRD-proteins by acting as RNA decoy for miRNA "ahy-mir5298". A database on findings from the study was populated and made available at https://cirssrdb.rf.gd/ and http://backlin.cabgrid.res.in/Amaranthus_database/index.php.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04515-y.

查看原文本刊更多论文

非编码rna在苋属植物生长发育和胁迫机制中的预测作用。

利用非编码rna （ncRNAs）表征苋属植物的基因调控网络，有助于了解苋属植物的生长发育和耐胁迫机制。本研究旨在鉴定苋菜基因组中的ncRNAs：长链非编码RNA （lncRNAs）、微RNA （miRNAs）和环状RNA (circRNAs)， ncRNA调控基因及其在植物过程中的作用，携带简单序列重复（SSR）标记的非编码RNA，以及miRNA-lncRNA-mRNA三联体相互作用，并研究其在生长发育和胁迫耐受机制中的作用。我们在基因组上共鉴定了2690个lncrna、836个mirna、31个环状rna和3506个SSRs，并在pre- mirna和lncrna上发现了SSRs。大多数预测的lncrna都是苋属植物特有的。所鉴定的ncrna的靶基因被观察到参与生长发育和应激机制。lncRNA“Ahy_lnc_0021”作为内源性靶模拟物（eTM）抑制靶向SHM6基因的miRNA“ahy_mir8717”，该基因主要参与叶酸代谢以及氨基酸、维生素B5和核酸的合成。验证了lncRNAs及其靶基因可能参与生长发育、植物酚合成和胁迫耐受机制。lncRNA-miRNA- mrna关联的关键作用也得到了验证，发现lncRNA“Ahy_lnc_2243”通过作为miRNA“ahy-mir5298”的RNA诱饵来增强brd蛋白的表达。研究结果的数据库已被填充，并可在https://cirssrdb.rf.gd/和http://backlin.cabgrid.res.in/Amaranthus_database/index.php.Supplementary信息上获得：在线版本包含补充材料，可在10.1007/s13205-025-04515-y上获得。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

3 Biotech Agricultural and Biological Sciences-Agricultural and Biological Sciences (miscellaneous)

CiteScore

6.00

自引率

0.00%

发文量

314

期刊介绍： 3 Biotech publishes the results of the latest research related to the study and application of biotechnology to: - Medicine and Biomedical Sciences - Agriculture - The Environment The focus on these three technology sectors recognizes that complete Biotechnology applications often require a combination of techniques. 3 Biotech not only presents the latest developments in biotechnology but also addresses the problems and benefits of integrating a variety of techniques for a particular application. 3 Biotech will appeal to scientists and engineers in both academia and industry focused on the safe and efficient application of Biotechnology to Medicine, Agriculture and the Environment.