Structural and Functional Annotation of Transposable Elements Revealed a Potential Regulation of Genes Involved in Rubber Biosynthesis by TE-Derived siRNA Interference in Hevea brasiliensis

The natural rubber biosynthetic pathway is well described in Hevea, although the final stages of rubber elongation are still poorly understood. Small Rubber Particle Proteins and Rubber Elongation Factors (SRPPs and REFs) are proteins with major function in rubber particle formation and stabilization. Their corresponding genes are clustered on a scaffold1222 of the reference genomic sequence of the Hevea brasiliensis genome. Apart from gene expression by transcriptomic analyses, to date, no deep analyses have been carried out for the genomic environment of SRPPs and REFs loci. By integrative analyses on transposable element annotation, small RNAs production and gene expression, we analysed their role in the control of the transcription of rubber biosynthetic genes. The first in-depth annotation of TEs (Transposable Elements) and their capacity to produce TE-derived siRNAs (small interfering RNAs) is presented, only possible in the Hevea brasiliensis clone PB 260 for which all data are available. We observed that 11% of genes are located near TEs and their presence may interfere in their transcription at both genetic and epigenetic level. We hypothesized that the genomic environment of rubber biosynthesis genes has been shaped by TE and TE-derived siRNAs with possible transcriptional interference on their gene expression. We discussed possible functionalization of TEs as enhancers and as donors of alternative transcription start sites in promoter sequences, possibly through the modelling of genetic and epigenetic landscapes.

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Endogenous siRNAs: regulators of internal affairs

Biochemical Society Transactions ◽

10.1042/bst20140068 ◽

2014 ◽

Vol 42 (4) ◽

pp. 1174-1179 ◽

Cited By ~ 37

Author(s):

Monica J. Piatek ◽

Andreas Werner

Keyword(s):

Gene Expression ◽

Gene Regulation ◽

Drosophila Melanogaster ◽

Transposable Elements ◽

Essential Role ◽

Viral Infections ◽

Biological Functions ◽

Small Interfering Rnas ◽

Argonaute Proteins ◽

Genome Protection

Endo-siRNAs (endogenous small-interfering RNAs) have recently emerged as versatile regulators of gene expression. They derive from double-stranded intrinsic transcripts and are processed by Dicer and associate with Argonaute proteins. In Caenorhabditis elegans, endo-siRNAs are known as 22G and 26G RNAs and are involved in genome protection and gene regulation. Drosophila melanogaster endo-siRNAs are produced with the help of specific Dicer and Argonaute isoforms and play an essential role in transposon control and the protection from viral infections. Biological functions of endo-siRNAs in vertebrates include repression of transposable elements and chromatin organization, as well as gene regulation at the transcriptional and post-transcriptional levels.

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Vacuolar-type inorganic pyrophosphatase located on the rubber particle in the latex is an essential enzyme in regulation of the rubber biosynthesis in Hevea brasiliensis

Plant Science ◽

10.1016/j.plantsci.2009.01.009 ◽

2009 ◽

Vol 176 (5) ◽

pp. 602-607 ◽

Cited By ~ 20

Author(s):

Zeng Rizhong ◽

Duan Cuifang ◽

Li Xiaoyuan ◽

Tian Weimin ◽

Nie Zhiyi

Keyword(s):

Hevea Brasiliensis ◽

Rubber Particle ◽

Inorganic Pyrophosphatase ◽

Rubber Biosynthesis ◽

Essential Enzyme

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Tobacco rattle virus -induced gene silencing in Hevea brasiliensis

10.21203/rs.3.rs-32707/v1 ◽

2020 ◽

Author(s):

Hui-Liang Li ◽

Dong Guo ◽

Ying Wang ◽

Jia-Hong Zhu ◽

Long Qu ◽

...

Keyword(s):

Gene Silencing ◽

Hevea Brasiliensis ◽

Rubber Tree ◽

Tobacco Rattle Virus ◽

Functional Gene ◽

Small Interfering Rnas ◽

Virus Induced Gene Silencing ◽

Rubber Biosynthesis ◽

Natural Rubber Biosynthesis ◽

First Time

Abstract BackgroundSince it is very difficult to obtain gene knockouts in rubber tree (Hevea Brasiliensis) due to low genetic transformation efficiency. Virus-induced gene silencing (VIGS) is a powerful gene silencing tool that has been intensively applied in plant. Up to now, the application of VIGS in rubber tree has not yet been reported.ResultsHevea brasiliensis phytoene desaturase (HbPDS) was identified in H. brasiliensis genome. The prediction of small interfering RNAs (siRNAs) from HbPDS and the silencing gene fragment (SGF) were predicted and a length of 409 bp SGF was chosen to be tested. We show that the tobacco rattle virus (TRV) -VIGS is able to induce effective HbPDS silencing in rubber tree. The TRV-VIGS system has the potential for functional gene studies in rubber tree.ConclusionsThis is the first time to report VIGS in rubber tree. The present TRV-VIGS method could be further applied to produce gene silenced rubber tree plants, to advance functional gene of rubber tree. The applied TRV-VIGS method will achieve deeper underground into the natural rubber biosynthesis and regulation in this important rubber-producing plant.

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Faculty Opinions recommendation of Inhibiting gene expression at transcription start sites in chromosomal DNA with antigene RNAs.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1030294.342278 ◽

2005 ◽

Author(s):

Marjori Matzke

Keyword(s):

Gene Expression ◽

Chromosomal Dna ◽

Transcription Start ◽

Transcription Start Sites

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Faculty Opinions recommendation of Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1162434.626838 ◽

2009 ◽

Author(s):

Magnus Nordborg

Keyword(s):

Gene Expression ◽

Transposable Elements ◽

Epigenetic Silencing ◽

Neighboring Gene ◽

Trade Off

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Latex-specific transcriptome analysis reveals mechanisms for latex metabolism and natural rubber biosynthesis in laticifers of Hevea brasiliensis

Industrial Crops and Products ◽

10.1016/j.indcrop.2021.113835 ◽

2021 ◽

Vol 171 ◽

pp. 113835

Author(s):

Xiangyu Long ◽

Yongjun Fang ◽

Yunxia Qin ◽

Jianghua Yang ◽

Xiaohu Xiao

Keyword(s):

Natural Rubber ◽

Transcriptome Analysis ◽

Hevea Brasiliensis ◽

Rubber Biosynthesis ◽

Natural Rubber Biosynthesis

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Association between the nucleosome footprint of plasma DNA and neoadjuvant chemotherapy response for breast cancer

npj Breast Cancer ◽

10.1038/s41523-021-00237-5 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Xu Yang ◽

Geng-Xi Cai ◽

Bo-Wei Han ◽

Zhi-Wei Guo ◽

Ying-Song Wu ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Neoadjuvant Chemotherapy ◽

Cancer Patients ◽

Cell Receptor ◽

Chemotherapy Response ◽

Breast Cancer Patients ◽

Plasma Dna ◽

Transcription Start Sites ◽

Response To Chemotherapy

AbstractGene expression signatures have been used to predict the outcome of chemotherapy for breast cancer. The nucleosome footprint of cell-free DNA (cfDNA) carries gene expression information of the original tissues and thus may be used to predict the response to chemotherapy. Here we carried out the nucleosome positioning on cfDNA from 85 breast cancer patients and 85 healthy individuals and two cancer cell lines T-47D and MDA-MB-231 using low-coverage whole-genome sequencing (LCWGS) method. The patients showed distinct nucleosome footprints at Transcription Start Sites (TSSs) compared with normal donors. In order to identify the footprints of cfDNA corresponding with the responses to neoadjuvant chemotherapy in patients, we mapped on nucleosome positions on cfDNA of patients with different responses: responders (pretreatment, n = 28; post-1 cycle, post-3/4 cycles, and post-8 cycles of treatment, n = 12) and nonresponders (pretreatment, n = 10; post-1 cycle, post-3/4 cycles, and post-8 cycles of treatment, n = 10). The coverage depth near TSSs in plasma cfDNA differed significantly between responders and nonresponders at pretreatment, and also after neoadjuvant chemotherapy treatment cycles. We identified 232 TSSs with differential footprints at pretreatment and 321 after treatment and found enrichment in Gene Ontology terms such as cell growth inhibition, tumor suppressor, necrotic cell death, acute inflammatory response, T cell receptor signaling pathway, and positive regulation of vascular endothelial growth factor production. These results suggest that cfDNA nucleosome footprints may be used to predict the efficacy of neoadjuvant chemotherapy for breast cancer patients and thus may provide help in decision making for individual patients.

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