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  • 1
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    Online Resource
    Absence of CG methylation alters the long noncoding transcriptome landscape in multiple species
    Wiley ; 2021
    In:  FEBS Letters Vol. 595, No. 12 ( 2021-06), p. 1734-1747
    Details
    In: FEBS Letters, Wiley, Vol. 595, No. 12 ( 2021-06), p. 1734-1747
    Abstract: The noncoding regions throughout the genome are in large part comprised of transposable elements (TEs), some of which are functionalized with long intergenic noncoding RNAs (lincRNAs). DNA methylation is predominantly associated with TEs, but little is known about its contribution to the transcription of lincRNAs. Here, we examine the lincRNA profiles of DNA methylation‐related mutants of five species, Arabidopsis , rice, tomato, maize, and mouse, to elucidate patterns in lincRNA regulation under altered DNA methylation status. Significant activation of lincRNAs was observed in the absence of CG DNA methylation rather than non‐CG. Our study establishes a working model of the contribution of DNA methylation to regulation of the dynamic activity of lincRNA transcription.
    Type of Medium: Online Resource
    ISSN: 0014-5793 , 1873-3468
    URL: Issue
    URL: Article
    DOI: 10.1002/feb2.v595.12
    DOI: 10.1002/1873-3468.14100
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 1460391-3
    SSG: 12
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  • 2
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    Efficient chromatin profiling of H3K4me3 modification in cotton using CUT&Tag
    Springer Science and Business Media LLC ; 2020
    In:  Plant Methods Vol. 16, No. 1 ( 2020-12)
    Details
    In: Plant Methods, Springer Science and Business Media LLC, Vol. 16, No. 1 ( 2020-12)
    Abstract: In 2019, Kaya-Okur et al. reported on the cleavage under targets and tagmentation (CUT & Tag) technology for efficient profiling of epigenetically modified DNA fragments. It was used mainly for cultured cell lines and was especially effective for small samples and single cells. This strategy generated high-resolution and low-background-noise chromatin profiling data for epigenomic analysis. CUT & Tag is well suited to be used in plant cells, especially in tissues from which small samples are taken, such as ovules, anthers, and fibers. Results Here, we present a CUT & Tag protocol step by step using plant nuclei. In this protocol, we quantified the nuclei that can be used in each CUT & Tag reaction, and compared the efficiency of CUT & Tag with chromatin immunoprecipitation with sequencing (ChIP-seq) in the leaves of cotton. A general workflow for the bioinformatic analysis of CUT & Tag is also provided. Results indicated that, compared with ChIP-seq, the CUT & Tag procedure was faster and showed a higher-resolution, lower-background signal than did ChIP. Conclusion A CUT & Tag protocol has been refined for plant cells using intact nuclei that have been isolated.
    Type of Medium: Online Resource
    ISSN: 1746-4811
    URL: Article
    DOI: 10.1186/s13007-020-00664-8
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2203723-8
    SSG: 12
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  • 3
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    Profiling of H3K4me3 Modification in Plants using Cleavage under Targets and Tagmentation
    MyJove Corporation ; 2022
    In:  Journal of Visualized Experiments , No. 182 ( 2022-04-22)
    Details
    In: Journal of Visualized Experiments, MyJove Corporation, , No. 182 ( 2022-04-22)
    Type of Medium: Online Resource
    ISSN: 1940-087X
    URL: Article
    DOI: 10.3791/62534
    Language: English
    Publisher: MyJove Corporation
    Publication Date: 2022
    detail.hit.zdb_id: 2259946-0
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  • 4
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    Role of phasiRNAs from two distinct phasing frames of GhMYB2 loci in cis- gene regulation in the cotton genome
    Springer Science and Business Media LLC ; 2020
    In:  BMC Plant Biology Vol. 20, No. 1 ( 2020-12)
    Details
    In: BMC Plant Biology, Springer Science and Business Media LLC, Vol. 20, No. 1 ( 2020-12)
    Abstract: Phased small interfering RNA (phasiRNA) is primarily derived from the 22-nt miRNA targeting loci. GhMYB2 , a gene with potential roles in cotton fiber cell fate determination, is a target gene of miR828 and miR858 in the generation of phasiRNAs. Results In the presented work, through the evaluation of phasing scores and phasiRNA distribution pattern, we found that phasiRNAs from GhMYB2 were derived from the 3′ cleavage fragments of 22-nt miR828 and 21-nt miR858 respectively. These two miRNA targeting sites initiated two phasing frames on transcripts of one locus. By means of RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE), we further demonstrated that phasiRNAs derived from the two phasing frames played a role in cis -regulation of GhMYB2 . The phasiRNAs derived from GhMYB2 were expressed in the somatic tissues, especially in anther and hypocotyl. We further employed our previous small RNA sequencing data as well as the degradome data of cotton fiber bearing ovules, anthers, hypocotyls and embryogenic calli tissues published in public databases, to validate the expression, phasing pattern and functions of phasiRNAs. Conclusions The presenting research provide insights of the molecular mechanism of phasiRNAs in regulation of GhMYB2 loci.
    Type of Medium: Online Resource
    ISSN: 1471-2229
    URL: Article
    DOI: 10.1186/s12870-020-02430-3
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2059868-3
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  • 5
    Online Resource
    Online Resource
    Profiling of H3K4me3 Modification in Plants using Cleavage under Targets and Tagmentation
    MyJove Corporation ; 2022
    In:  Journal of Visualized Experiments , No. 182 ( 2022-04-22)
    Details
    In: Journal of Visualized Experiments, MyJove Corporation, , No. 182 ( 2022-04-22)
    Type of Medium: Online Resource
    ISSN: 1940-087X
    URL: Article
    DOI: 10.3791/62534-v
    Language: English
    Publisher: MyJove Corporation
    Publication Date: 2022
    detail.hit.zdb_id: 2259946-0
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  • 6
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    Functional analysis of the cotton CLE polypeptide signaling gene family in plant growth and development
    Springer Science and Business Media LLC ; 2021
    In:  Scientific Reports Vol. 11, No. 1 ( 2021-03-03)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2021-03-03)
    Abstract: The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (ESR)–RELATED ( CLE ) gene family encodes a large number of polypeptide signaling molecules involved in the regulation of shoot apical meristem division and root and vascular bundle development in a variety of plants. CLE family genes encode important short peptide hormones; however, the functions of these signaling polypeptides in cotton remain largely unknown. In the current work, we studied the effects of the CLE family genes on growth and development in cotton. Based on the presence of a conserved CLE motif of 13 amino acids, 93 genes were characterized as GhCLE gene family members, and these were subcategorized into 7 groups. A preliminary analysis of the cotton CLE gene family indicated that the activity of its members tends to be conserved in terms of both the 13-residue conserved domain at the C-terminus and their subcellular localization pattern. Among the 14 tested genes, the ectopic overexpression of GhCLE5::GFP partially mimicked the phenotype of the clv3 mutant in Arabidopsis . GhCLE5 could affect the endogenous CLV3 in binding to the receptor complex, comprised of CLV1, CLV2, and CRN, in the yeast two-hybrid assay and split-luciferase assay. Silencing GhCLE5 in cotton caused a short seedling phenotype. Therefore, we concluded that the cotton GhCLE gene family is functionally conserved in apical shoot development regulation. These results indicate that CLE also plays roles in cotton development as a short peptide hormone.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-021-84312-8
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2615211-3
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  • 7
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    Neofunctionalization of a polyploidization-activated cotton long intergenic non-coding RNA DAN1 during drought stress regulation
    Oxford University Press (OUP) ; 2021
    In:  Plant Physiology Vol. 186, No. 4 ( 2021-08-03), p. 2152-2168
    Details
    In: Plant Physiology, Oxford University Press (OUP), Vol. 186, No. 4 ( 2021-08-03), p. 2152-2168
    Abstract: The genomic shock of whole-genome duplication (WGD) and hybridization introduces great variation into transcriptomes, for both coding and noncoding genes. An altered transcriptome provides a molecular basis for improving adaptation during the evolution of new species. The allotetraploid cotton, together with the putative diploid ancestor species compose a fine model for study the rapid gene neofunctionalization over the genome shock. Here we report on Drought-Associated Non-coding gene 1 (DAN1), a long intergenic noncoding RNA (lincRNA) that arose from the cotton progenitor A-diploid genome after hybridization and WGD events during cotton evolution. DAN1 in allotetraploid upland cotton (Gossypium hirsutum) is a drought-responsive lincRNA predominantly expressed in the nucleoplasm. Chromatin isolation by RNA purification profiling and electrophoretic mobility shift assay analysis demonstrated that GhDAN1 RNA can bind with DNA fragments containing AAAG motifs, similar to DNA binding with one zinc finger transcription factor binding sequences. The suppression of GhDAN1 mainly regulates genes with AAAG motifs in auxin-response pathways, which are associated with drought stress regulation. As a result, GhDAN1-silenced plants exhibit improved tolerance to drought stress. This phenotype resembles the drought-tolerant phenotype of the A-diploid cotton ancestor species, which has an undetectable expression of DAN1. The role of DAN1 in cotton evolution and drought tolerance regulation suggests that the genomic shock of interspecific hybridization and WGD stimulated neofunctionalization of non-coding genes during the natural evolutionary process.
    Type of Medium: Online Resource
    ISSN: 0032-0889 , 1532-2548
    URL: Article
    DOI: 10.1093/plphys/kiab179
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2004346-6
    detail.hit.zdb_id: 208914-2
    SSG: 12
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  • 8
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    Functional examination of lncRNAs in allotetraploid Gossypium hirsutum
    Springer Science and Business Media LLC ; 2021
    In:  BMC Genomics Vol. 22, No. 1 ( 2021-12)
    Details
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 22, No. 1 ( 2021-12)
    Abstract: An evolutionary model using diploid and allotetraploid cotton species identified 80 % of non-coding transcripts in allotetraploid cotton as being uniquely activated in comparison with its diploid ancestors. The function of the lncRNAs activated in allotetraploid cotton remain largely unknown. Results We employed transcriptome analysis to examine the relationship between the lncRNAs and mRNAs of protein coding genes (PCGs) in cotton leaf tissue under abiotic stresses. LncRNA expression was preferentially associated with that of the flanking PCGs. Selected highly-expressed lncRNA candidates (n = 111) were subjected to a functional screening pilot test in which virus-induced gene silencing was integrated with abiotic stress treatment. From this low-throughput screen, we obtained candidate lncRNAs relating to plant height and tolerance to drought and other abiotic stresses. Conclusions Low-throughput screen is an effective method to find functional lncRNA for further study. LncRNAs were more active in abiotic stresses than PCG expression, especially temperature stress. LncRNA XLOC107738 may take a cis- regulatory role in response to environmental stimuli. The degree to which lncRNAs are constitutively expressed may impact expression patterns and functions on the individual gene level rather than in genome-wide aggregate.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    URL: Article
    DOI: 10.1186/s12864-021-07771-3
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2041499-7
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  • 9
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    LncRNAs in polyploid cotton interspecific hybrids are derived from transposon neofunctionalization
    Springer Science and Business Media LLC ; 2018
    In:  Genome Biology Vol. 19, No. 1 ( 2018-12)
    Details
    In: Genome Biology, Springer Science and Business Media LLC, Vol. 19, No. 1 ( 2018-12)
    Type of Medium: Online Resource
    ISSN: 1474-760X
    URL: Article
    DOI: 10.1186/s13059-018-1574-2
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2018
    detail.hit.zdb_id: 2040529-7
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  • 10
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    Pseudomonas species isolated via high-throughput screening significantly protect cotton plants against verticillium wilt
    Springer Science and Business Media LLC ; 2020
    In:  AMB Express Vol. 10, No. 1 ( 2020-12)
    Details
    In: AMB Express, Springer Science and Business Media LLC, Vol. 10, No. 1 ( 2020-12)
    Abstract: Verticillium wilt (VW) caused by Verticillium dahliae is a devastating soil-borne disease that causes severe yield losses in cotton and other major crops worldwide. Here we conducted a high-throughput screening of isolates recovered from 886 plant rhizosphere samples taken from the three main cotton-producing areas of China. Fifteen isolates distributed in different genera of bacteria that showed inhibitory activity against V. dahliae were screened out. Of these, two Pseudomonas strains, P. protegens XY2F4 and P. donghuensis 22G5, showed significant inhibitory action against V. dahliae . Additional comparative genomic analyses and phenotypical assays confirmed that P. protegens XY2F4 and P. donghuensis 22G5 were the strains most efficient at protecting cotton plants against VW due to specific biological control products they produced. Importantly, we identified a significant efficacy of the natural tropolone compound 7-hydroxytropolone (7-HT) against VW. By phenotypical assay using the wild-type 22G5 and its mutant strain in 7-HT production, we revealed that the 7-HT produced by P. donghuensis is the major substance protecting cotton against VW. This study reveals that Pseudomonas specifically has gene clusters that allow the production of effective antipathogenic metabolites that can now be used as new agents in the biocontrol of VW.
    Type of Medium: Online Resource
    ISSN: 2191-0855
    URL: Article
    DOI: 10.1186/s13568-020-01132-1
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2621432-5
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