1
|
Simko I. Differentially methylated genomic regions of lettuce seeds relate to divergence across morphologically distinct horticultural types. AOB PLANTS 2023; 15:plad060. [PMID: 37680204 PMCID: PMC10482144 DOI: 10.1093/aobpla/plad060] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 08/22/2023] [Indexed: 09/09/2023]
Abstract
Heritable cytosine methylation plays a role in shaping plant phenotypes; however, no information is available about DNA methylation in cultivated lettuce (Lactuca sativa), one of the most important leafy vegetables. Whole-genome bisulfite sequencing (WGBS) performed on seeds of 95 accessions from eight morphologically distinct horticultural types (Batavia, butterhead, iceberg, Latin, leaf, oilseed, romaine and stem) revealed a high level of methylation in lettuce genome with an average methylation of 90.6 % in the CG context, 72.9 % in the CHG context and 7.5 % in the CHH context. Although WGBS did not show substantial differences in overall methylation levels across eight horticultural types, 350 differentially methylated regions (DMR) were identified. Majority of the 41 pivotal DMR overlapped with genomic features predicted or confirmed to be involved in plant growth and development. These results provide the first insight into lettuce DNA methylation and indicate a potential role for heritable variation in cytosine methylation in lettuce morphology. The results reveal that differences in methylation profiles of morphologically distinct horticultural types are already detectable in seeds. Identified DMR can be a focus of the future functional studies.
Collapse
Affiliation(s)
- Ivan Simko
- Crop Improvement and Protection Research Unit, US Department of Agriculture, Agricultural Research Service, Salinas, CA 93905, USA
| |
Collapse
|
2
|
Pei LL, Zhang LL, Liu X, Jiang J. Role of microRNA miR171 in plant development. PeerJ 2023; 11:e15632. [PMID: 37456878 PMCID: PMC10340099 DOI: 10.7717/peerj.15632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/02/2023] [Indexed: 07/18/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenous non-coding small RNA with 19-24 nucleotides (nts) in length, which play an essential role in regulating gene expression at the post-transcriptional level. As one of the first miRNAs found in plants, miR171 is a typical class of conserved miRNAs. The miR171 sequences among different species are highly similar, and the vast majority of them have both "GAGCCG" and "CAAUAU" fragments. In addition to being involved in plant growth and development, hormone signaling and stress response, miR171 also plays multiple and important roles in plants through interactions with microbe and other small-RNAs. The miRNA functions by regulating the expression of target genes. Most of miR171's target genes are in the GRAS gene family, but also include some NSP, miRNAs, lncRNAs, and other genes. This review is intended to summarize recent updates on miR171 regarding its function in plant life and hopefully provide new ideas for understanding miR171 function and regulatory mechanisms.
Collapse
Affiliation(s)
- Ling Ling Pei
- College of Horticulture, Shenyang Agricultural University, Shenyang, Shenhe District, China
| | - Ling Ling Zhang
- College of Horticulture, Shenyang Agriculture University, Shenyang, Shenhe District, China
| | - Xin Liu
- Horticulture Department, Shenyang Agricultural University, Shenyang, Shenhe District, China
| | - Jing Jiang
- Horticulture Department, Shenyang Agricultural University, Shenyang, Shenhe District, China
| |
Collapse
|
3
|
Wan J, Zhou Y, Beardall J, Raven JA, Lin J, Huang J, Lu Y, Liang S, Ye M, Xiao M, Zhao JY, Dai X, Xia J, Jin P. DNA methylation and gene transcription act cooperatively in driving the adaptation of a marine diatom to global change. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad150. [PMID: 37100754 DOI: 10.1093/jxb/erad150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Indexed: 06/19/2023]
Abstract
Genetic changes together with epigenetic modifications such as DNA methylation have been demonstrated to regulate many biological processes and thereby govern the response of organisms to environmental changes. However, how DNA methylation might act cooperatively with gene transcription and thereby mediate the long-term adaptive responses of marine microalgae to global change is virtually unknown. Here we performed a transcriptomic analysis, and a whole-genome bisulfite sequencing, along with phenotypic analysis of a model marine diatom Phaeodactylum tricornutum adapted for two years to high CO2 and/or warming conditions. Our results show that the methylated islands (peaks of methylation) mCHH were positively correlated with expression of genes in the sub-region of the gene body when the populations were grown under high CO2 or its combination with warming for ~2 years. We further identified the differentially expressed genes (DEGs) and hence the metabolic pathways in which they function, at the transcriptomics level in differentially methylated regions (DMRs). Although DEGs in DMRs contributed only 18-24% of the total DEGs, we found that those DEGs acted cooperatively with DNA methylation and then regulated key processes such as central carbon metabolism, amino acid metabolism, ribosome biogenesis, terpenoid backbone biosynthesis, and degradation of misfolded proteins. Taken together, by integrating transcriptomic, epigenetic and phenotypic analysis, our study provides evidence for DNA methylation acting cooperatively with gene transcription to contribute to the adaptation of microalgae to global changes.
Collapse
Affiliation(s)
- Jiaofeng Wan
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Yunyue Zhou
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - John Beardall
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - John A Raven
- Division of Plant Science, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- School of Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- Climate Change Cluster, University of Technology, Sydney, Ultimo, NSW 2007, Australia
| | - Jiamin Lin
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jiali Huang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Yucong Lu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Shiman Liang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Mengcheng Ye
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Mengting Xiao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jing Yuan Zhao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Xiaoying Dai
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jianrong Xia
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Peng Jin
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| |
Collapse
|
4
|
Long Non-Coding RNAs of Plants in Response to Abiotic Stresses and Their Regulating Roles in Promoting Environmental Adaption. Cells 2023; 12:cells12050729. [PMID: 36899864 PMCID: PMC10001313 DOI: 10.3390/cells12050729] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/10/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Abiotic stresses triggered by climate change and human activity cause substantial agricultural and environmental problems which hamper plant growth. Plants have evolved sophisticated mechanisms in response to abiotic stresses, such as stress perception, epigenetic modification, and regulation of transcription and translation. Over the past decade, a large body of literature has revealed the various regulatory roles of long non-coding RNAs (lncRNAs) in the plant response to abiotic stresses and their irreplaceable functions in environmental adaptation. LncRNAs are recognized as a class of ncRNAs that are longer than 200 nucleotides, influencing a variety of biological processes. In this review, we mainly focused on the recent progress of plant lncRNAs, outlining their features, evolution, and functions of plant lncRNAs in response to drought, low or high temperature, salt, and heavy metal stress. The approaches to characterize the function of lncRNAs and the mechanisms of how they regulate plant responses to abiotic stresses were further reviewed. Moreover, we discuss the accumulating discoveries regarding the biological functions of lncRNAs on plant stress memory as well. The present review provides updated information and directions for us to characterize the potential functions of lncRNAs in abiotic stresses in the future.
Collapse
|
5
|
Ding Y, Zou LH, Wu J, Ramakrishnan M, Gao Y, Zhao L, Zhou M. The pattern of DNA methylation alteration, and its association with the expression changes of non-coding RNAs and mRNAs in Moso bamboo under abiotic stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111451. [PMID: 36075278 DOI: 10.1016/j.plantsci.2022.111451] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/01/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Epigenetic changes play an important role in plant growth and development and in stress response. However, DNA methylation pattern and its relationship with the expression changes of non-coding RNAs and mRNAs of Moso bamboo in response to abiotic stress is still largely unknown. In this work, we used whole-genome bisulfite sequencing in combination with whole-transcriptome sequencing to analyze the DNA methylation and transcription patterns of mRNAs and non-coding RNAs in Moso bamboo under abiotic stresses such as cold, heat, ultraviolet (UV) and salinity. We found that CHH methylation in the promoter region was positively correlated with gene expression, while CHG and CHH methylations in the gene body regions were negatively associated with gene expression. Moreover, CG and CHG methylations in the promoter regions were negatively correlated with the transcript abundance of long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and circular RNAs (circRNAs). Similarly, the methylation levels of three contexts in the genic regions were negatively correlated with the transcript abundance of lncRNAs and miRNAs but positively correlated with that of circRNAs. In addition, we suggested that the reduction of 21-nt and 24-nt small interfering RNA (siRNA) expression tended to increase methylation levels in the genic regions. We found that stress-responsive genes such as CRPK1, HSFB2A and CIPK were differentially methylated and expressed. Our results also proposed that DNA methylation may regulate the expression of the transcription factors (TFs) and plant hormone signalling genes such as IAA9, MYC2 and ERF110 in response to abiotic stress. This study firstly reports the abiotic stress-responsive DNA methylation pattern and its involvement of expression of coding RNAs and non-coding RNAs in Moso bamboo. The results expand the knowledge of epigenetic mechanisms in Moso bamboo under abiotic stress and support in-depth deciphering of the function of specific non-coding RNAs in future studies.
Collapse
Affiliation(s)
- Yiqian Ding
- The State Key Laboratory of Subtropical Silviculture; Institute of Bamboo, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Long-Hai Zou
- The State Key Laboratory of Subtropical Silviculture; Institute of Bamboo, Zhejiang A&F University, Lin'an, Hangzhou 311300, China.
| | - Jiajun Wu
- The State Key Laboratory of Subtropical Silviculture; Institute of Bamboo, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Muthusamy Ramakrishnan
- The State Key Laboratory of Subtropical Silviculture; Institute of Bamboo, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Yubang Gao
- The State Key Laboratory of Subtropical Silviculture; Institute of Bamboo, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Liangzhen Zhao
- The State Key Laboratory of Subtropical Silviculture; Institute of Bamboo, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mingbing Zhou
- The State Key Laboratory of Subtropical Silviculture; Institute of Bamboo, Zhejiang A&F University, Lin'an, Hangzhou 311300, China.
| |
Collapse
|
6
|
Genome-wide chromatin accessibility analysis unveils open chromatin convergent evolution during polyploidization in cotton. Proc Natl Acad Sci U S A 2022; 119:e2209743119. [PMID: 36279429 PMCID: PMC9636936 DOI: 10.1073/pnas.2209743119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Allopolyploidization, resulting in divergent genomes in the same cell, is believed to trigger a “genome shock”, leading to broad genetic and epigenetic changes. However, little is understood about chromatin and gene-expression dynamics as underlying driving forces during allopolyploidization. Here, we examined the genome-wide DNase I-hypersensitive site (DHS) and its variations in domesticated allotetraploid cotton (
Gossypium hirsutum
and
Gossypium barbadense
, AADD) and its extant AA (
Gossypium arboreum
) and DD (
Gossypium raimondii
) progenitors. We observed distinct DHS distributions between
G. arboreum
and
G. raimondii
. In contrast, the DHSs of the two subgenomes of
G. hirsutum
and
G. barbadense
showed a convergent distribution. This convergent distribution of DHS was also present in the wild allotetraploids
Gossypium darwinii
and
G. hirsutum
var.
yucatanense
, but absent from a resynthesized hybrid of
G. arboreum
and
G. raimondii
, suggesting that it may be a common feature in polyploids, and not a consequence of domestication after polyploidization. We revealed that putative
cis
-regulatory elements (CREs) derived from polyploidization-related DHSs were dominated by several families, including Dof, ERF48, and BPC1. Strikingly, 56.6% of polyploidization-related DHSs were derived from transposable elements (TEs). Moreover, we observed positive correlations between DHS accessibility and the histone marks H3K4me3, H3K27me3, H3K36me3, H3K27ac, and H3K9ac, indicating that coordinated interplay among histone modifications, TEs, and CREs drives the DHS landscape dynamics under polyploidization. Collectively, these findings advance our understanding of the regulatory architecture in plants and underscore the complexity of regulome evolution during polyploidization.
Collapse
|
7
|
Yang Z, Yan H, Wang J, Nie G, Feng G, Xu X, Li D, Huang L, Zhang X. DNA hypermethylation promotes the flowering of orchardgrass during vernalization. PLANT PHYSIOLOGY 2022; 190:1490-1505. [PMID: 35861426 PMCID: PMC9516772 DOI: 10.1093/plphys/kiac335] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Vernalization, influenced by environmental factors, is an essential process associated with the productivity of temperate crops, during which epigenetic regulation of gene expression plays an important role. Although DNA methylation is one of the major epigenetic mechanisms associated with the control of gene expression, global changes in DNA methylation in the regulation of gene expression during vernalization-induced flowering of temperate plants remain largely undetermined. To characterize vernalization-associated DNA methylation dynamics, we performed whole-genome bisulfite-treated sequencing and transcriptome sequencing in orchardgrass (Dactylis glomerata) during vernalization. The results revealed that increased levels of genome DNA methylation during the early vernalization of orchardgrass were associated with transcriptional changes in DNA methyltransferase and demethylase genes. Upregulated expression of vernalization-related genes during early vernalization was attributable to an increase in mCHH in the promoter regions of these genes. Application of an exogenous DNA methylation accelerator or overexpression of orchardgrass NUCLEAR POLY(A) POLYMERASE (DgPAPS4) promoted earlier flowering, indicating that DNA hypermethylation plays an important role in vernalization-induced flowering. Collectively, our findings revealed that vernalization-induced hypermethylation is responsible for floral primordium initiation and development. These observations provide a theoretical foundation for further studies on the molecular mechanisms underlying the control of vernalization in temperate grasses.
Collapse
Affiliation(s)
| | | | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, Florida 32611, USA
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Dandan Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | | | | |
Collapse
|
8
|
A Method to Produce vsiRNAs in Plants with Cross-Kingdom Gene Silencing Capacity. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12115329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Plants have evolved defense mechanisms to suppress viral transcription and replication by transcriptional and post-transcriptional gene silencing mediated by virus-derived small interfering RNAs (vsiRNAs). Based on this response, virus-induced gene silencing (VIGS)-based technology has been developed to silence target genes on either host plants or insect pests. This mechanism could also be used for the silencing of genes of interest in the medical field. We used the VIGS vector pEuMV-YP:Krt18, which was obtained by inserting the Mus musculus (M. musculus) Krt18 sequence into pEuMV-YP:ΔAV1. The objective was to evaluate the capacity of pEuMV-YP:Krt18 to induce Nicotiana benthamiana (N. benthamiana) production of vsiRNAs of a specific sequence that belongs to neither the plant genome nor the wild virus genome, which were used to induce cross-kingdom gene silencing between plants and mammals. The percentage of vsiRNA for each viral gene was calculated from an sRNA library of N. benthamiana plants infected by pEuMV-YP: Krt18. When the vsiRNAs were characterized, it was found that they corresponded to all the genes of the pEuMV-YP:Krt18 vector. These vsiRNAs induced the silencing of the Krt18 gene in M. musculus macrophages, supporting the ability to use VIGS vectors in plants as biofactories for the production of sRNAs that induce gene silencing in mammals.
Collapse
|
9
|
Xiao L, Lu L, Zeng W, Shang X, Cao S, Yan H. DNA Methylome and LncRNAome Analysis Provide Insights Into Mechanisms of Genome-Dosage Effects in Autotetraploid Cassava. FRONTIERS IN PLANT SCIENCE 2022; 13:915056. [PMID: 35860527 PMCID: PMC9289687 DOI: 10.3389/fpls.2022.915056] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/02/2022] [Indexed: 05/16/2023]
Abstract
Whole genome duplication (WGD) increases the dosage of all coding and non-coding genes, yet the molecular implications of genome-dosage effects remain elusive. In this study, we generated integrated maps of the methylomes and lncRNAomes for diploid and artificially generated autotetraploid cassava (Manihot esculenta Crantz). We found that transposable elements (TEs) suppressed adjacent protein coding gene (PCG)-expression levels, while TEs activated the expression of nearby long non-coding RNAs (lncRNAs) in the cassava genome. The hypermethylation of DNA transposons in mCG and mCHH sites may be an effective way to suppress the expression of nearby PCGs in autotetraploid cassava, resulting in similar expression levels for most of PCGs between autotetraploid and diploid cassava. In the autotetraploid, decreased methylation levels of retrotransposons at mCHG and mCHH sites contributed to reduced methylation of Gypsy-neighboring long intergenic non-coding RNAs, potentially preserving diploid-like expression patterns in the major of lncRNAs. Collectively, our study highlighted that WGD-induced DNA methylation variation in DNA transposons and retrotransposons may be as direct adaptive responses to dosage of all coding-genes and lncRNAs, respectively.
Collapse
Affiliation(s)
- Liang Xiao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Liuying Lu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Wendan Zeng
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiaohong Shang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Sheng Cao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Huabing Yan
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- *Correspondence: Huabing Yan,
| |
Collapse
|
10
|
Tong W, Li R, Huang J, Zhao H, Ge R, Wu Q, Mallano AI, Wang Y, Li F, Deng W, Li Y, Xia E. Divergent DNA methylation contributes to duplicated gene evolution and chilling response in tea plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1312-1327. [PMID: 33730390 DOI: 10.1111/tpj.15237] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/05/2021] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
The tea plant (Camellia sinensis) is a thermophilic cash crop and contains a highly duplicated and repeat-rich genome. It is still unclear how DNA methylation regulates the evolution of duplicated genes and chilling stress in tea plants. We therefore generated a single-base-resolution DNA methylation map of tea plants under chilling stress. We found that, compared with other plants, the tea plant genome is highly methylated in all three sequence contexts, including CG, CHG and CHH (where H = A, T, or C), which is further proven to be correlated with its repeat content and genome size. We show that DNA methylation in the gene body negatively regulates the gene expression of tea plants, whereas non-CG methylation in the flanking region enables a positive regulation of gene expression. We demonstrate that transposable element-mediated methylation dynamics significantly drives the expression divergence of duplicated genes in tea plants. The DNA methylation and expression divergence of duplicated genes in the tea plant increases with evolutionary age and selective pressure. Moreover, we detect thousands of differentially methylated genes, some of which are functionally associated with chilling stress. We also experimentally reveal that DNA methyltransferase genes of tea plants are significantly downregulated, whereas demethylase genes are upregulated at the initial stage of chilling stress, which is in line with the significant loss of DNA methylation of three well-known cold-responsive genes at their promoter and gene body regions. Overall, our findings underscore the importance of DNA methylation regulation and offer new insights into duplicated gene evolution and chilling tolerance in tea plants.
Collapse
Affiliation(s)
- Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ruopei Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jin Huang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Huijuan Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ruoheng Ge
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ali I Mallano
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yanli Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Weiwei Deng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yeyun Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| |
Collapse
|
11
|
Li J, Li N, Zhu L, Zhang Z, Li X, Wang J, Xun H, Zhao J, Wang X, Wang T, Wang H, Liu B, Li Y, Gong L. Mutation of a major CG methylase alters genome-wide lncRNA expression in rice. G3-GENES GENOMES GENETICS 2021; 11:6146525. [PMID: 33617633 PMCID: PMC8049413 DOI: 10.1093/g3journal/jkab049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/08/2021] [Indexed: 11/14/2022]
Abstract
Plant long non-coding RNAs (lncRNAs) function in diverse biological processes, and lncRNA expression is under epigenetic regulation, including by cytosine DNA methylation. However, it remains unclear whether 5-methylcytosine (5mC) plays a similar role in different sequence contexts (CG, CHG, and CHH). In this study, we characterized and compared the profiles of genome-wide lncRNA profiles (including long intergenic non-coding RNAs [lincRNAs] and long noncoding natural antisense transcripts [lncNATs]) of a null mutant of the rice DNA methyltransferase 1, OsMET1-2 (designated OsMET1-2-/-) and its isogenic wild type (OsMET1-2+/+). The En/Spm transposable element (TE) family, which was heavily methylated in OsMET1-2+/+, was transcriptionally de-repressed in OsMET1-2-/- due to genome-wide erasure of CG methylation, and this led to abundant production of specific lncRNAs. In addition, RdDM-mediated CHH hypermethylation was increased in the 5'-upstream genomic regions of lncRNAs in OsMET1-2-/-. The positive correlation between the expression of lincRNAs and that of their proximal protein-coding genes was also analyzed. Our study shows that CG methylation negatively regulates the TE-related expression of lncRNA and demonstrates that CHH methylation is also involved in the regulation of lncRNA expression.
Collapse
Affiliation(s)
- Juzuo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ling Zhu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Xiaochong Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Jinbin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Hongwei Xun
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Jing Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Xiaofei Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Hongyan Wang
- Laboratory of Plant Epigenetics and Evolution, School of Life Science, Liaoning University, Shenyang 110036, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yu Li
- Engineering Research Center of the Ministry of Education (MOE) for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin 130118, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| |
Collapse
|
12
|
Wu B, Sun M, Zhang H, Yang D, Lin C, Khan I, Wang X, Zhang X, Nie G, Feng G, Yan Y, Li Z, Peng Y, Huang L. Transcriptome analysis revealed the regulation of gibberellin and the establishment of photosynthetic system promote rapid seed germination and early growth of seedling in pearl millet. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:94. [PMID: 33840392 PMCID: PMC8040237 DOI: 10.1186/s13068-021-01946-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/01/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Seed germination is the most important stage for the formation of a new plant. This process starts when the dry seed begins to absorb water and ends when the radicle protrudes. The germination rate of seed from different species varies. The rapid germination of seed from species that grow on marginal land allows seedlings to compete with surrounding species, which is also the guarantee of normal plant development and high yield. Pearl millet is an important cereal crop that is used worldwide, and it can also be used to extract bioethanol. Previous germination experiments have shown that pearl millet has a fast seed germination rate, but the molecular mechanisms behind pearl millet are unclear. Therefore, this study explored the expression patterns of genes involved in pearl millet growth from the germination of dry seed to the early growth stages. RESULTS Through the germination test and the measurement of the seedling radicle length, we found that pearl millet seed germinated after 24 h of swelling of the dry seed. Using transcriptome sequencing, we characterized the gene expression patterns of dry seed, water imbibed seed, germ and radicle, and found more differentially expressed genes (DEGs) in radicle than germ. Further analysis showed that different genome clusters function specifically at different tissues and time periods. Weighted gene co-expression network analysis (WGCNA) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that many genes that positively regulate plant growth and development are highly enriched and expressed, especially the gibberellin signaling pathway, which can promote seed germination. We speculated that the activation of these key genes promotes the germination of pearl millet seed and the growth of seedlings. To verify this, we measured the content of gibberellin and found that the gibberellin content after seed imbibition rose sharply and remained at a high level. CONCLUSIONS In this study, we identified the key genes that participated in the regulation of seed germination and seedling growth. The activation of key genes in these pathways may contribute to the rapid germination and growth of seed and seedlings in pearl millet. These results provided new insight into accelerating the germination rate and seedling growth of species with slow germination.
Collapse
Affiliation(s)
- Bingchao Wu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 6111130, China
| | - Min Sun
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 6111130, China
| | - Huan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 6111130, China
| | - Dan Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 6111130, China
| | - Chuang Lin
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 6111130, China
| | - Imran Khan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 6111130, China
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 6111130, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 6111130, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 6111130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 6111130, China
| | - Yanhong Yan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 6111130, China
| | - Zhou Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 6111130, China
| | - Yan Peng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 6111130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 6111130, China.
| |
Collapse
|
13
|
Genome-wide analysis of long noncoding RNAs, 24-nt siRNAs, DNA methylation and H3K27me3 marks in Brassica rapa. PLoS One 2021; 16:e0242530. [PMID: 33788851 PMCID: PMC8011741 DOI: 10.1371/journal.pone.0242530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/18/2021] [Indexed: 11/30/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are RNA fragments that generally do not code for a protein but are involved in epigenetic gene regulation. In this study, lncRNAs of Brassica rapa were classified into long intergenic noncoding RNAs, natural antisense RNAs, and intronic noncoding RNAs and their expression analyzed in relation to genome-wide 24-nt small interfering RNAs (siRNAs), DNA methylation, and histone H3 lysine 27 trimethylation marks (H3K27me3). More than 65% of the lncRNAs analyzed consisted of one exon, and more than 55% overlapped with inverted repeat regions (IRRs). Overlap of lncRNAs with IRRs or genomic regions encoding for 24-nt siRNAs resulted in increased DNA methylation levels when both were present. LncRNA did not overlap greatly with H3K27me3 marks, but the expression level of intronic noncoding RNAs that did coincide with H3K27me3 marks was higher than without H3K27me3 marks. The Brassica genus comprises important vegetables and oil seed crops grown across the world. B. rapa is a diploid (AA genome) thought to be one of the ancestral species of both B. juncea (AABB genome) and B. napus (AACC) through genome merging (allotetrapolyploidization). Complex genome restructuring and epigenetic alterations are thought to be involved in these allotetrapolyploidization events. Comparison of lncRNAs between B. rapa and B. nigra, B. oleracea, B. juncea, and B. napus showed the highest conservation with B. oleracea. This study presents a comprehensive analysis of the epigenome structure of B. rapa at multi-epigenetic levels (siRNAs, DNA methylation, H3K27me3, and lncRNAs) and identified a suite of candidate lncRNAs that may be epigenetically regulated in the Brassica genus.
Collapse
|
14
|
Urquiaga MCDO, Thiebaut F, Hemerly AS, Ferreira PCG. From Trash to Luxury: The Potential Role of Plant LncRNA in DNA Methylation During Abiotic Stress. FRONTIERS IN PLANT SCIENCE 2021; 11:603246. [PMID: 33488652 PMCID: PMC7815527 DOI: 10.3389/fpls.2020.603246] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/07/2020] [Indexed: 05/27/2023]
Abstract
Remarkable progress has been made in elucidating important roles of plant non-coding RNAs. Among these RNAs, long noncoding RNAs (lncRNAs) have gained widespread attention, especially their role in plant environmental stress responses. LncRNAs act at different levels of gene expression regulation, and one of these mechanisms is by recruitment of DNA methyltransferases or demethylases to regulate the target gene transcription. In this mini-review, we highlight the function of lncRNAs, including their potential role in RNA-directed DNA Methylation (RdDM) silencing pathway and their potential function under abiotic stresses conditions. Moreover, we also present and discuss studies of lncRNAs in crops. Finally, we propose a path outlook for future research that may be important for plant breeding.
Collapse
Affiliation(s)
| | - Flávia Thiebaut
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | |
Collapse
|
15
|
Sarpan N, Taranenko E, Ooi SE, Low ETL, Espinoza A, Tatarinova TV, Ong-Abdullah M. DNA methylation changes in clonally propagated oil palm. PLANT CELL REPORTS 2020; 39:1219-1233. [PMID: 32591850 DOI: 10.1007/s00299-020-02561-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
Several hypomethylated sites within the Karma region of EgDEF1 and hotspot regions in chromosomes 1, 2, 3, and 5 may be associated with mantling. One of the main challenges faced by the oil palm industry is fruit abnormalities, such as the "mantled" phenotype that can lead to reduced yields. This clonal abnormality is an epigenetic phenomenon and has been linked to the hypomethylation of a transposable element within the EgDEF1 gene. To understand the epigenome changes in clones, methylomes of clonal oil palms were compared to methylomes of seedling-derived oil palms. Whole-genome bisulfite sequencing data from seedlings, normal, and mantled clones were analyzed to determine and compare the context-specific DNA methylomes. In seedlings, coding and regulatory regions are generally hypomethylated while introns and repeats are extensively methylated. Genes with a low number of guanines and cytosines in the third position of codons (GC3-poor genes) were increasingly methylated towards their 3' region, while GC3-rich genes remain demethylated, similar to patterns in other eukaryotic species. Predicted promoter regions were generally hypomethylated in seedlings. In clones, CG, CHG, and CHH methylation levels generally decreased in functionally important regions, such as promoters, 5' UTRs, and coding regions. Although random regions were found to be hypomethylated in clonal genomes, hypomethylation of certain hotspot regions may be associated with the clonal mantling phenotype. Our findings, therefore, suggest other hypomethylated CHG sites within the Karma of EgDEF1 and hypomethylated hotspot regions in chromosomes 1, 2, 3 and 5, are associated with mantling.
Collapse
Affiliation(s)
- Norashikin Sarpan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Elizaveta Taranenko
- Department of Biology, University of La Verne, La Verne, CA, USA
- Department of Fundamental Biology and Biotechnology, Siberian Federal University, 660074, Krasnoyarsk, Russia
| | - Siew-Eng Ooi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | | | - Tatiana V Tatarinova
- Department of Biology, University of La Verne, La Verne, CA, USA.
- Department of Fundamental Biology and Biotechnology, Siberian Federal University, 660074, Krasnoyarsk, Russia.
- Vavilov Institute for General Genetics, Moscow, Russia.
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
| |
Collapse
|
16
|
Zeng B, Zhang Y, Zhang A, Qiao D, Ren J, Li M, Cai K, Zhang J, Huang L. Transcriptome profiling of two Dactylis glomerata L. cultivars with different tolerance in response to submergence stress. PHYTOCHEMISTRY 2020; 175:112378. [PMID: 32315838 DOI: 10.1016/j.phytochem.2020.112378] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 06/11/2023]
Abstract
Submergence is one of the environmental stresses that limit plant growth and development. Dactylis glomerata L. is an important cool-season forage grass globally. To investigate the genes related to submergence response and the molecular mechanism associated with submergence tolerance, the transcriptome of D. glomerata in response to waterlogging treatment was analyzed. RNA-sequencing was performed in two D. glomerata cultivars, submergence tolerant 'Dianbei' and submergence sensitive 'Anba'. A total of 50,045 unique genes matched the known proteins in the NCBI nr database by BLAST searches and 60.8% (30,418) of these genes were annotated with GO terms. Among these, 1395 genes only differentially expressed in 'Dianbei' and 18 genes shown different expression all the time were detected between the submergence tolerant 'Dianbei' and sensitive 'Anba'. Gene ontology (GO) and KEGG pathway enrichment analyses demonstrated that the DEGs were mainly implicated in oxidation-reduction system, nucleic acid binding transcription factor activity, and glycerol kinase activity. The D. glomerata assembled transcriptome provided substantial molecular resource for further genomic analysis of forage grasses in response to submergence stress. The significant difference in expression of specific unigenes may account for waterlogging tolerance or acclimation in the two different D. glomerata cultivars. This study provided new insights into the molecular basis of submergence tolerance in D. glomerata.
Collapse
Affiliation(s)
- Bing Zeng
- College of Animal Science, Rongchang Campus, Southwest University, Chongqing, 402460, China
| | - Yajie Zhang
- College of Animal Science, Rongchang Campus, Southwest University, Chongqing, 402460, China
| | - Ailing Zhang
- Department of Grassland Science, Faculty of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dandan Qiao
- College of Animal Science, Rongchang Campus, Southwest University, Chongqing, 402460, China
| | - Juncai Ren
- College of Animal Science, Rongchang Campus, Southwest University, Chongqing, 402460, China
| | - Mingyang Li
- College of Animal Science, Rongchang Campus, Southwest University, Chongqing, 402460, China
| | - Kai Cai
- College of Animal Science, Rongchang Campus, Southwest University, Chongqing, 402460, China
| | - Jinhua Zhang
- Guizhou animal Husbandry and Veterinary Institute, Guiyang, 550005, China.
| | - Linkai Huang
- Department of Grassland Science, Faculty of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
| |
Collapse
|
17
|
Yan H, Bombarely A, Xu B, Wu B, Frazier TP, Zhang X, Chen J, Chen P, Sun M, Feng G, Wang C, Cui C, Li Q, Zhao B, Huang L. Autopolyploidization in switchgrass alters phenotype and flowering time via epigenetic and transcription regulation. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5673-5686. [PMID: 31419288 DOI: 10.1093/jxb/erz325] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 07/18/2019] [Indexed: 05/16/2023]
Abstract
Polyploidization is a significant source of genomic and organism diversification during plant evolution, and leads to substantial alterations in plant phenotypes and natural fitness. To help understand the phenotypic and molecular impacts of autopolyploidization, we conducted epigenetic and full-transcriptomic analyses of a synthesized autopolyploid accession of switchgrass (Panicum virgatum) in order to interpret the molecular and phenotypic changes. We found that mCHH levels were decreased in both genic and transposable element (TE) regions, and that TE methylation near genes was decreased as well. Among 142 differentially expressed genes involved in cell division, cellulose biosynthesis, auxin response, growth, and reproduction processes, 75 of them were modified by 122 differentially methylated regions, 10 miRNAs, and 15 siRNAs. In addition, up-regulated PvTOE1 and suppressed PvFT probably contribute to later flowering time of the autopolyploid. The expression changes were probably associated with modification of nearby methylation sites and siRNAs. We also experimentally demonstrated that expression levels of PvFT and PvTOE1 were regulated by DNA methylation, supporting the link between alterations in methylation induced by polyploidization and the phenotypic changes that were observed. Collectively, our results show epigenetic modifications in synthetic autopolyploid switchgrass for the first time, and support the hypothesis that polyploidization-induced methylation is an important cause of phenotypic alterations and is potentially important for plant evolution and improved fitness.
Collapse
Affiliation(s)
- Haidong Yan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Aureliano Bombarely
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
- Department of Life Sciences, University of Milan, Milan, Italy
| | - Bin Xu
- College of Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Bingchao Wu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Taylor P Frazier
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Xinquan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Jing Chen
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Peilin Chen
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Min Sun
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Guangyan Feng
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Chengran Wang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Chenming Cui
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Qi Li
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Bingyu Zhao
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
18
|
Ayyappan V, Sripathi VR, Kalavacharla V(K, Saha MC, Thimmapuram J, Bhide KP, Fiedler E. Genome-wide identification of histone methylation (H3K9 me2) and acetylation (H4K12 ac) marks in two ecotypes of switchgrass (Panicum virgatum L.). BMC Genomics 2019; 20:667. [PMID: 31438854 PMCID: PMC6704705 DOI: 10.1186/s12864-019-6038-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/16/2019] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Histone modifications play a significant role in the regulation of transcription and various biological processes, such as development and regeneration. Though a few genomic (including DNA methylation patterns) and transcriptomic studies are currently available in switchgrass, the genome-wide distribution of histone modifications has not yet been studied to help elucidate gene regulation and its application to switchgrass improvement. RESULTS This study provides a comprehensive epigenomic analyses of two contrasting switchgrass ecotypes, lowland (AP13) and upland (VS16), by employing chromatin immunoprecipitation sequencing (ChIP-Seq) with two histone marks (suppressive- H3K9me2 and active- H4K12ac). In this study, most of the histone binding was in non-genic regions, and the highest enrichment was seen between 0 and 2 kb regions from the transcriptional start site (TSS). Considering the economic importance and potential of switchgrass as a bioenergy crop, we focused on genes, transcription factors (TFs), and pathways that were associated with C4-photosynthesis, biomass, biofuel production, biotic stresses, and abiotic stresses. Using quantitative real-time PCR (qPCR) the relative expression of five genes selected from the phenylpropanoid-monolignol pathway showed preferential binding of acetylation marks in AP13 rather than in VS16. CONCLUSIONS The genome-wide histone modifications reported here can be utilized in understanding the regulation of genes important in the phenylpropanoid-monolignol biosynthesis pathway, which in turn, may help understand the recalcitrance associated with conversion of biomass to biofuel, a major roadblock in utilizing lignocellulosic feedstocks.
Collapse
Affiliation(s)
- Vasudevan Ayyappan
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE USA
| | - Venkateswara R. Sripathi
- Molecular Biology and Bioinformatics Laboratory, College of Agricultural, Life and Natural Sciences, Alabama A&M University, Normal, AL USA
| | - Venu ( Kal) Kalavacharla
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE USA
- Center for Integrated Biological and Environmental Research, Delaware State University, Dover, DE USA
| | | | | | - Ketaki P. Bhide
- Bioinformatics Core, Purdue University, West Lafayette, IN USA
| | - Elizabeth Fiedler
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE USA
| |
Collapse
|