Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing
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ABSTRACT:
ORGANISM(S): Medicago truncatula
PROVIDER: GSE29154 | GEO | 2012/05/09
SECONDARY ACCESSION(S): PRJNA140007
REPOSITORIES: GEO
Similar Datasets
Project description:Two hundreds eighty three and 293 known miRNAs were identified from the control and drought stress libraries, respectively. In addition, 253 potential candidate miRNAs were identified, and among them 48 novel miRNAs/ novel members of known miRNA families whose complementary miRNAs were also detected. Both high-throughput sequencing and RT-qPCR confirmed that 22 members of 4 miRNA families were up-regulated and 10 members of 6 miRNA families were down-regulated in response to drought stress. Among the 48 novel miRNAs, 24 miRNAs were responsive to drought stress with 21 and 3 miRNAs being up- and down-regulated, respectively. The known and predicted targets of these miRNAs in response to drought stress are involved in diverse cellular processes in plants, such as development, transcription, protein degradation, detoxification, nutrient status and cross adaptation. To identify miRNAs in response to drought stress in M. truncatula, control and drought stress shoots were used to construct small RNA libraries, respectively. The date from Solexa sequencer (Illumina) was compared to identify miRNAs in response to drought stress.
2012-05-08 | E-GEOD-29154 | biostudies-arrayexpress
Project description:Drought stress response is a complex trait regulated at multiple levels. In the past few years, molecular and genomic studies have shown that several drought responsive genes (DRGs) with various functions are induced by drought stresses, and that various transcription factors (TFs) are involved in the regulation of stress-inducible genes. In addition to those DRGs mentioned above, microRNAs (miRNAs) are important regulators of gene expression at the posttranscriptional level by repressing mRNA expression. There is a complex interplay between transcriptional and post-transcriptional regulation of drought response that has not been extensively characterized in tobacco. In order to fully understand DRGs (including TFs) and different roles of miRNAs involved in the stress response, we sequenced and analysed three Digital Gene Expression (DGE) libraries in roots from drought treated tobacco plants, and four small RNA populations in roots, stems and leaves from control or drought treated tobacco plants. We identified 276 candidate DRGs in tobacco with sequence similarities to 64 known DRGs from model plants and crops and about 40% were TFs including WRKY, NAC, ERF and bZIP families. Furthermore, Out of these tobacco DRGs, 54differentially expressed DRGs included 21 TFs, which belonged to 24 TFs families such as NAC (6), MYB (4), ERF (10) and bZIP (1). Additionally, we confirmed expression of 39 known miRNA families (122 members) and five conserved miRNA families, which showed differential regulation under drought stress. Targets of miRNAs were further surveyed based on a recently published study, in which ten targets were DRGs. Finally, an integrated gene regulatory network has been proposed for the molecular mechanisms of the response of tobacco roots to drought stress using differentially expressed DRGs, the changed expression profiles of miRNAs and their target transcripts as a basis base on previous studies. In general, our data provide valuable information for future studies of the molecular mechanisms underlying tobacco roots in response to drought resistance in tobacco and other plants. Three tobacco (Nicotiana tabacum L.) roots tag-based DGE libraries treated at three time points (0, 6 and 48 h) with 20% PEG6000 were generated using Illumina 1G technology. The samples for four small RNA libraries was used based on the result of physiological index measurement as follows: equal quantities (10 ug) of total RNA isolated from tobacco roots treated with two time points (6 and 48 h) were mixed together to construct the drought -treated small RNA library (Root-treat), and total RNA prepared from the control roots sample was used to construct the control small RNA library (Root-ck). In addition, we also constructed another two libraries (stem and leaf) from leaves and stems of control plants, respectively. These libraries were constructed using the Small RNA Sample Prep Kit (Illumina, San Diego, CA) and then sent for Solexa sequencing.
2013-12-20 | E-GEOD-43058 | biostudies-arrayexpress
Project description:Drought stress response is a complex trait regulated at multiple levels. In the past few years, molecular and genomic studies have shown that several drought responsive genes (DRGs) with various functions are induced by drought stresses, and that various transcription factors (TFs) are involved in the regulation of stress-inducible genes. In addition to those DRGs mentioned above, microRNAs (miRNAs) are important regulators of gene expression at the posttranscriptional level by repressing mRNA expression. There is a complex interplay between transcriptional and post-transcriptional regulation of drought response that has not been extensively characterized in tobacco. In order to fully understand DRGs (including TFs) and different roles of miRNAs involved in the stress response, we sequenced and analysed three Digital Gene Expression (DGE) libraries in roots from drought treated tobacco plants, and four small RNA populations in roots, stems and leaves from control or drought treated tobacco plants. We identified 276 candidate DRGs in tobacco with sequence similarities to 64 known DRGs from model plants and crops and about 40% were TFs including WRKY, NAC, ERF and bZIP families. Furthermore, Out of these tobacco DRGs, 54differentially expressed DRGs included 21 TFs, which belonged to 24 TFs families such as NAC (6), MYB (4), ERF (10) and bZIP (1). Additionally, we confirmed expression of 39 known miRNA families (122 members) and five conserved miRNA families, which showed differential regulation under drought stress. Targets of miRNAs were further surveyed based on a recently published study, in which ten targets were DRGs. Finally, an integrated gene regulatory network has been proposed for the molecular mechanisms of the response of tobacco roots to drought stress using differentially expressed DRGs, the changed expression profiles of miRNAs and their target transcripts as a basis base on previous studies. In general, our data provide valuable information for future studies of the molecular mechanisms underlying tobacco roots in response to drought resistance in tobacco and other plants.
2013-12-20 | GSE43058 | GEO
Project description:MicroRNAs (miRNAs) are part of gene regulatory networks that direct all most all biological processes in plants including their growth and development, as well as adaptation to biotic and abiotic stresses. Sorghum is largely grown for its grain production, but recently it also emerged a major feedstock for biofuel production. Interestingly, Sorghum is relatively drought tolerant crop and largely grown in semi-arid tropical and sub-tropical regions where the drought or high temperature or their combination co-occur in the field. Although miRNA profiles have been reported in Sorghum leaves exposed to drought, but thus far miRNAs in heat- or drought and heat-exposed conditions have not been reported. In this study, we report miRNA profiles in Sorghum leaves exposed to drought or heat or their combination. The bioinformatic analysis of small RNA libraries revealed the expression of approximately 30 conserved miRNA families represented by 81 individual miRNAs as well as 11 novel miRNA families in Sorghum leaves. Of these, 26 miRNAs were found to be differentially regulated in response to one or more of the stress treatments. Overall, the number of miRNAs regulated by heat was more than the drought. Furthermore, miRNA profiles revealed more similarities between heat and the combination of drought and heat stresses. We also have analyzed degradome profiles in control and drought-exposed plants to identify potential targets for the miRNAs. This study provides a frame work for better understanding of miRNA-guided gene regulations that vary between individual drought or heat or combination of drought and heat treatments.
2021-12-31 | GSE157523 | GEO
Project description:MicroRNAs (miRNAs) are part of gene regulatory networks that direct all most all biological processes in plants including their growth and development, as well as adaptation to biotic and abiotic stresses. Sorghum is largely grown for its grain production, but recently it also emerged a major feedstock for biofuel production. Interestingly, Sorghum is relatively drought tolerant crop and largely grown in semi-arid tropical and sub-tropical regions where the drought or high temperature or their combination co-occur in the field. Although miRNA profiles have been reported in Sorghum leaves exposed to drought, but thus far miRNAs in heat- or drought and heat-exposed conditions have not been reported. In this study, we report miRNA profiles in Sorghum leaves exposed to drought or heat or their combination. The bioinformatic analysis of small RNA libraries revealed the expression of approximately 30 conserved miRNA families represented by 81 individual miRNAs as well as 11 novel miRNA families in Sorghum leaves. Of these, 26 miRNAs were found to be differentially regulated in response to one or more of the stress treatments. Overall, the number of miRNAs regulated by heat was more than the drought. Furthermore, miRNA profiles revealed more similarities between heat and the combination of drought and heat stresses. We also have analyzed degradome profiles in control and drought-exposed plants to identify potential targets for the miRNAs. This study provides a frame work for better understanding of miRNA-guided gene regulations that vary between individual drought or heat or combination of drought and heat treatments.
2021-12-31 | GSE157521 | GEO
Project description:MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition in plants and animals. At present there is relatively little information regarding the role of miRNAs in the response to drought stress in maize. In this study, two small RNA libraries were sequenced, and a total of 11,973,711 and 14,326,010 raw sequences were generated from growing leaves of drought-tolerant and drought-sensitive maize seedlings, respectively. Further analysis identified 192 mature miRNAs, which include 124 known maize (zma) miRNAs and 68 potential novel miRNA candidates. Additionally, 167 target genes (259 transcripts) of known and novel miRNAs were predicted to be differentially expressed between two maize inbred lines. Of these, three novel miRNAs were up-regulated and two were down-regulated under drought stress. The expression of these five miRNAs and nine target genes was confirmed using quantitative reverse transcription PCR. The expression of three of the miRNAs and their putative target genes exhibited an inverse correlation, and expression analysis suggested that all five may play important roles in maize leaves. Finally, GO annotations of the target genes indicated a potential role in photosynthesis, may therefore contribute to the drought stress response. This study describes the identification and characterization of novel miRNAs that are the differentially expressed in drought-tolerant and drought-sensitive inbred maize lines. This provides the foundation for further investigation into the mechanism of miRNA function in response to drought stress in maize.
2015-06-01 | GSE61700 | GEO
Project description:MicroRNAs (miRNAs), a group of small non-coding RNAs, have recently become a subject of intense study. They are a class of post-transcriptional, negative regulators playing vital roles in plant development and growth. However, little is known about their regulatory roles in treeâs responses to the stressful environments incurred over its long-term growth. Here, we reported the cloning of small RNAs from abiotic stressed tissues of P. trichocarpa and the identification of 68 putative miRNA sequences that can be classified into 27 families based on sequence homology. Among them, 9 families are novel, raising the number of the known ptc-miRNA families from 33 to 42. Total 346 targets are predicted for the cloned ptc-miRNAs using penalty scores of â¤2.5 for mismatched patterns in the miRNA:mRNA duplexes as the criterion. Six selected targets are experimentally validated. The expression of a majority of the novel miRNAs is altered in response to cold, heat, salt, dehydration, and mechanical stresses. Microarray analysis of known ptc-miRNAs identified 19 additional cold stress responsive ptc-miRNAs that originate from 14 miRNA gene families. Interestingly, we found that miRNAs of the same family respond differentially to the same stress. This suggests that members of a miRNA family may have different functions. These results reveal possible roles for miRNAs in the regulatory networks associated with development and stress response and therefore critical to plant long-term growth; and provide useful information for developing trees with a greater level of stress-resistance. Keywords: microRNA, cold stress, time course MicroRNA abundance of 21 samples from 7 cold stress time point were analyzed, each cold stress time point contain three replicates. 0 hour cold stress treatment were used as control.
2010-05-26 | E-GEOD-10582 | biostudies-arrayexpress
Project description:We present an efficient method to genome-wide discover new and drought stress responsive miRNAs in P. euphratica. High throughput sequencing of P. euphratica leaves found 197 conserved miRNAs between P. euphratica and Populus trichocarpa. Meanwhile, 189 new miRNAs which belonged to 120 families were identified, a large increasing to the number of P. euphratica miRNAs. Target prediction and degradome sequencing verification of 22 new and 21 conserved miRNA targets showed these targets were involved in multiple biological processes, including transcription regulation and response to stimulus. Furthermore, comparison of high-throughput sequencing with miRNA microarray profiling data indicated that 104 miRNA sequences were up-regulated, while 27 were down-regulated under drought stress. This preliminary characterization based on our findings provided a framework for future analysis of miRNA genes and their roles in key traits of poplar as stress resistance plant breeding and environment protection usage. Examination of sRNA expression in 2 poplar leaf samples in drought and normal growth conditions.
2011-04-25 | E-GEOD-25747 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs), a group of small non-coding RNAs, have recently become a subject of intense study. They are a class of post-transcriptional, negative regulators playing vital roles in plant development and growth. However, little is known about their regulatory roles in tree’s responses to the stressful environments incurred over its long-term growth. Here, we reported the cloning of small RNAs from abiotic stressed tissues of P. trichocarpa and the identification of 68 putative miRNA sequences that can be classified into 27 families based on sequence homology. Among them, 9 families are novel, raising the number of the known ptc-miRNA families from 33 to 42. Total 346 targets are predicted for the cloned ptc-miRNAs using penalty scores of ≤2.5 for mismatched patterns in the miRNA:mRNA duplexes as the criterion. Six selected targets are experimentally validated. The expression of a majority of the novel miRNAs is altered in response to cold, heat, salt, dehydration, and mechanical stresses. Microarray analysis of known ptc-miRNAs identified 19 additional cold stress responsive ptc-miRNAs that originate from 14 miRNA gene families. Interestingly, we found that miRNAs of the same family respond differentially to the same stress. This suggests that members of a miRNA family may have different functions. These results reveal possible roles for miRNAs in the regulatory networks associated with development and stress response and therefore critical to plant long-term growth; and provide useful information for developing trees with a greater level of stress-resistance. Keywords: microRNA, cold stress, time course
2008-02-21 | GSE10582 | GEO
Project description:We present an efficient method to genome-wide discover new and drought stress responsive miRNAs in P. euphratica. High throughput sequencing of P. euphratica leaves found 197 conserved miRNAs between P. euphratica and Populus trichocarpa. Meanwhile, 189 new miRNAs which belonged to 120 families were identified, a large increasing to the number of P. euphratica miRNAs. Target prediction and degradome sequencing verification of 22 new and 21 conserved miRNA targets showed these targets were involved in multiple biological processes, including transcription regulation and response to stimulus. Furthermore, comparison of high-throughput sequencing with miRNA microarray profiling data indicated that 104 miRNA sequences were up-regulated, while 27 were down-regulated under drought stress. This preliminary characterization based on our findings provided a framework for future analysis of miRNA genes and their roles in key traits of poplar as stress resistance plant breeding and environment protection usage.
2011-04-25 | GSE25747 | GEO