scholarly journals Maternal RNA-directed DNA methylation is required for seed development in Brassica rapa

2017 ◽  
Author(s):  
Jeffrey W. Grover ◽  
Timmy Kendall ◽  
Abdul Baten ◽  
Graham J. King ◽  
Rebecca A. Mosher
Keyword(s):  
Dna Methylation ◽  
Brassica Rapa ◽  
Small Rna ◽  
Small Rnas ◽  
Parental Influence ◽  
Genome Integrity ◽  
Accessory Cells ◽  
Somatic Tissues ◽  
Common Strategy

AbstractSome organisms deploy small RNAs from accessory cells to maintain genome integrity in the zygote, a mechanism that has been proposed but not demonstrated in plants. Here we show that maternal mutations in the Pol IV-dependent small RNA pathway cause abortion of developing seeds in Brassica rapa. Surprisingly, small RNA production is required in maternal somatic tissues, but not in maternal gametes or the developing zygote. We propose that parental influence over zygotic genomes is a common strategy in eukaryotes and that outbreeding species such as B. rapa are key to understanding the role of small RNAs during reproduction.

scholarly journals Protease-mediated processing of Argonaute proteins controls small RNA association

2020 ◽  
Author(s):  
Rajani Kanth Gudipati ◽  
Kathrin Braun ◽  
Foivos Gypas ◽  
Daniel Hess ◽  
Jan Schreier ◽  
...  
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Proteolytic Processing ◽  
Genome Integrity ◽  
Wild Type ◽  
Selfish Genetic Elements ◽  
Argonaute Proteins ◽  
Processing Activity ◽  
Rna Pathways

SummarySmall RNA pathways defend the germlines of animals against selfish genetic elements and help to maintain genomic integrity. At the same time, their activity needs to be well-controlled to prevent silencing of ‘self’ genes. Here, we reveal a proteolytic mechanism that controls endogenous small interfering (22G) RNA activity in the Caenorhabditis elegans germline to protect genome integrity and maintain fertility. We find that WAGO-1 and WAGO-3 Argonaute (Ago) proteins are matured through proteolytic processing of their unusually proline-rich N-termini. In the absence of DPF-3, a P-granule-localized N-terminal dipeptidase orthologous to mammalian DPP8/9, processing fails, causing a change of identity of 22G RNAs bound to these WAGO proteins. Desilencing of repeat- and transposon-derived transcripts, DNA damage and acute sterility ensue. These phenotypes are recapitulated when WAGO-1 and WAGO-3 are rendered resistant to DFP-3-mediated processing, identifying them as critical substrates of DPF-3. We conclude that N-terminal processing of Ago proteins regulates their activity and promotes discrimination of self from non-self by ensuring association with the proper complement of small RNAs.Graphical Abstract: The role of DPF-3 in the fertility of the animalsIn wild type animals, the WAGO-1 and WAGO-3 Argonaute proteins are produced as immature pro-proteins with N-termini (N) that are unusually rich in prolines (P). N-terminal processing by DPF-3 is required for loading of the proper small RNA cargo and stabilization of WAGO-3. Accordingly, loss of this processing activity causes desilencing of transposable elements (TE), cell death and sterility.

scholarly journals Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis

2021 ◽  
Author(s):  
Jincheng Long ◽  
James Walker ◽  
Wenjing She ◽  
Billy Aldridge ◽  
Hongbo Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Small Rnas ◽  
Nurse Cell ◽  
De Novo ◽  
Epigenetic Inheritance ◽  
Genome Integrity ◽  
Nurse Cells ◽  
Male Germline ◽  
Methylation Patterns

AbstractThe plant male germline undergoes DNA methylation reprogramming, which methylates genes de novo and thereby alters gene expression and facilitates meiosis. Why reprogramming is limited to the germline and how specific genes are chosen is unknown. Here, we demonstrate that genic methylation in the male germline, from meiocytes to sperm, is established by germline-specific siRNAs transcribed from transposons with imperfect sequence homology. These siRNAs are synthesized by meiocyte nurse cells (tapetum) via activity of the tapetum-specific chromatin remodeler CLASSY3. Remarkably, tapetal siRNAs govern germline methylation throughout the genome, including the inherited methylation patterns in sperm. Finally, we demonstrate that these nurse cell-derived siRNAs (niRNAs) silence germline transposons, thereby safeguarding genome integrity. Our results reveal that tapetal niRNAs are sufficient to reconstitute germline methylation patterns and drive extensive, functional methylation reprogramming analogous to piRNA-mediated reprogramming in animal germlines.

scholarly journals Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.

DNA Research ◽  
2018 ◽  
Vol 25 (5) ◽  
pp. 511-520 ◽  
Author(s):  
Satoshi Takahashi ◽  
Kenji Osabe ◽  
Naoki Fukushima ◽  
Shohei Takuno ◽  
Naomi Miyaji ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Brassica Rapa ◽  
Small Rna ◽  
Histone H3 ◽  
Rna Expression ◽  
Genome Wide

scholarly journals Different classes of small RNAs are essential for head regeneration in the planarian Dugesia japonica

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhonghong Cao ◽  
David Rosenkranz ◽  
Suge Wu ◽  
Hongjin Liu ◽  
Qiuxiang Pang ◽  
...  
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Evolutionary Conservation ◽  
Body Parts ◽  
Promising Candidate ◽  
Dugesia Japonica ◽  
Head Regeneration

Abstract Background Planarians reliably regenerate all body parts after injury, including a fully functional head and central nervous system. But until now, the expression dynamics and functional role of miRNAs and other small RNAs during the process of head regeneration are not well understood. Furthermore, little is known about the evolutionary conservation of the relevant small RNAs pathways, rendering it difficult to assess whether insights from planarians will apply to other taxa. Results In this study, we applied high throughput sequencing to identify miRNAs, tRNA fragments and piRNAs that are dynamically expressed during head regeneration in Dugesia japonica. We further show that knockdown of selected small RNAs, including three novel Dugesia-specific miRNAs, during head regeneration induces severe defects including abnormally small-sized eyes, cyclopia and complete absence of eyes. Conclusions Our findings suggest that a complex pool of small RNAs takes part in the process of head regeneration in Dugesia japonica and provide novel insights into global small RNA expression profiles and expression changes in response to head amputation. Our study reveals the evolutionary conserved role of miR-124 and brings further promising candidate small RNAs into play that might unveil new avenues for inducing restorative programs in non-regenerative organisms via small RNA mimics based therapies.

scholarly journals A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6080
Author(s):  
Clicia Grativol ◽  
Flavia Thiebaut ◽  
Sara Sangi ◽  
Patricia Montessoro ◽  
Walaci da Silva Santos ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Small Rna ◽  
Genome Assembly ◽  
Inverted Repeat ◽  
Small Rnas ◽  
Distribution Patterns ◽  
Plant Genomes ◽  
Sugarcane Genome

Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter pipeline. These sequences were found to be upstream, downstream or inserted into 67 genic regions in the genome. The position of the most abundant MITE (Stowaway-like) in genic regions, which we call AddIn-MITE, was confirmed in a WD40 gene. The analysis of four monocot species showed conservation of the AddIn-MITE sequence, with a large number of copies in their genomes. We also investigated the conservation of the AddIn-MITE’ position in the WD40 genes from sorghum, maize and, in sugarcane cultivars and wild Saccharum species. In all analyzed plants, AddIn-MITE has located in WD40 intronic region. Furthermore, the role of AddIn-MITE-related sRNA in WD40 genic region was investigated. We found sRNAs preferentially mapped to the AddIn-MITE than to other regions in the WD40 gene in sugarcane. In addition, the analysis of the small RNA distribution patterns in the WD40 gene and the structure of AddIn-MITE, suggests that the MITE region is a proto-miRNA locus in sugarcane. Together, these data provide insights into the AddIn-MITE role in Andropogoneae grasses.

scholarly journals Genomic asymmetry of the Brassica napus seed: Epigenetic contributions of DNA methylation and small RNAs to subgenome bias

2020 ◽  
Author(s):  
Dylan J. Ziegler ◽  
Deirdre Khan ◽  
Nadège Pulgar-Vidal ◽  
Isobel A.P. Parkin ◽  
Stephen J. Robinson ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Brassica Napus ◽  
Seed Development ◽  
Epigenetic Regulation ◽  
Small Rnas ◽  
Flowering Plants ◽  
Genetic History ◽  
History Of ◽  
Syntenic Regions

AbstractPolyploidy has predominated the genetic history of the angiosperms, and allopolyploidy is known to have contributed to the vast speciation of flowering plants. Brassica napus, one of the world’s most important oilseeds, is one such polyploid species originating from the interspecific hybridization of Brassica rapa (An) and Brassica oleracea (Cn). Nascent amphidiploids must balance progenitor genomes during reproduction, though the role of epigenetic regulation in subgenome maintenance is unknown. The seed is the pivotal developmental transition into the new sporophytic generation and as such undergoes substantial epigenetic modifications. We investigated subgenome bias between the An and Cn subgenomes as well as across syntenic regions by profiling DNA methylation and siRNAs characteristic of B. napus seed development. DNA methylation and siRNA accumulation were prevalent in the Cn subgenome and most pronounced early during seed morphogenesis. Hypermethylation during seed maturation was most pronounced on non-coding elements, including promoters, repetitive elements, and siRNAs. Methylation on siRNA clusters was more prevalent in syntenic regions of the Cn subgenome and implies selective silencing of genomic loci of the seed. Together, we find compelling evidence for the asymmetrical epigenetic regulation of the An and Cn subgenomes of Brassica napus across seed development.

Osteoblastic Cell-Derived Extracellular Vesicles Transfer Small RNAs That Alter the Physiology of Hematopoietic Cells In Vivo

Blood ◽  
2017 ◽  
Vol 130 (Suppl_1) ◽  
pp. 93-93
Author(s):  
Youmna Kfoury ◽  
Anthony Anselmo ◽  
Jefferson Seidl ◽  
Ani Papazian ◽  
Francois Mercier ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
Flow Cytometry ◽  
Small Rna ◽  
Small Rnas ◽  
Mesenchymal Cell ◽  
Target Cells ◽  
Hematopoietic System

Abstract Background The bone marrow microenvironment (BMEV) regulates the highly regenerative hematopoietic system. However, there are a limited number of BMEV-derived molecules with a definitive role in maintaining hematopoietic stem and progenitor cells (HSPCs). Extracellular vesicles (EVs) encapsulate bioactive molecules, and may modify the physiology of their target cells. In hematopoiesis, EVs derived from culture-expanded mesenchymal cells can rescue irradiation damage, expand human umbilical cord blood cells and support HSPCs in vitro . However, in vivo evidence of EV function is lacking. We therefore sought to investigate the role of EVs in the interaction between the BMEV and the hematopoietic system and took advantage of existing mice bearing genetic reporters of key mesenchymal cell types. Results While analyzing the bone marrow (BM) of different mesenchymal cell-GFP reporter mice, we unexpectedly found CD45+ GFP+ cells. These were confirmed as single cells with intracellular GFP as demonstrated by imaging flow cytometry and confocal microscopy (Fig. 1A). Moreover, their hematopoietic identity was confirmed by their ability to form myeloid colonies in methylcellulose. Transplanted CD45.1 BM into Osteocalcin-Topaz (Ocn-Topaz) and Collagen1-GFP (Col1-GFP) mice that label osteoblasts, as well as Nestin-GFP (Nes-GFP) that labels mesenchymal stem cells demonstrated that donor cells are comparably labeled with GFP in Ocn-Topaz and Col1-GFP (2.2%) but at a much lower frequency (0.05%) in Nes-GFP. We therefore decided to proceed with the Ocn-Topaz model to investigate the role of osteoblast derived EVs in hematopoietic communication. Within the lineage negative compartment, the frequency of GFP+ cells increased with maturation. The highest frequency found in GMPs (0.06% of live cells were GFP+), followed by CMPs (0.01%), MEPs (0.002%) and LKS (0.004%) (Fig. 1B). Of particular interest, Lin- GFP+ cells formed ~5 fold more colonies as compared to their GFP- counterparts. However, transplantation assays demonstrated that the GFP+ cells possessed a decreased ability for long term reconstitution. Given the molecular weight of GFP, we hypothesized that EVs were the basis for transfer. Transmission electron microscopy coupled with immunogold staining revealed microvesicular structures of ~100 nm in size that contained GFP and that were labeled with the exosome marker TSG101 (Fig. 1C). Western blotting and flow cytometry detected labeling with exosome markers CD81 and CD9. Heparin sulfate proteoglycans (HSPGs) have been implicated in the biogenesis and uptake of EVs. Osteoblast-specific disruption of HSPGs by the knock out of the glycosyl transferase EXT1 resulted in a (40%) drop in the frequency of GFP+ cells in the GMP compartment. These findings demonstrate the EV-dependent transfer of GFP from osteoblasts to BM hematopoietic cells, and confirm GFP as a marker for the isolation and characterization of EV target cells. Exosomes from the BM of Ocn-Topaz mice in addition to GFP+ and GFP- GMPs were isolated for small RNA sequencing. In parallel, GMP populations were collected for mRNA sequencing. Global analysis of small RNA libraries from EVs and GMPs demonstrated that piRNAs was the most abundant species in both EVs (30%) and GMPs (18%). Surprisingly, EVs had low miRNA content (1.4%) compared to GMPs (9.2%) (Fig. 1D). When comparing GFP+ GMPs to GFP- ones, 6 miRNAs (mir-143, mir-122, mir-423-5p, mir-451, mir-206, mir-146b*) showed at least 100% increase in the GFP+GMPs. Predicted targets of mir-143, mir-206, mir-146 emerged as enriched sets when comparing gene expression of GFP+ and GFP- GMPs. In contrast, tRNAs was the most enriched species in EVs (10.5%) when compared to GMPs (2.5%) (Fig. 1D) and interestingly, GFP+ GMPs had higher content of tRNA when compared to GFP- (3.3% vs 1.7%) respectively. Given the role of tRNAs in translation and the emerging role of tRNA fragments (tRFs) in translation regulation and stress signaling, it was of interest to see translation and ribosome genesis among the top enriched gene sets when comparing GFP+ and GFP- GMPs. In conclusion, we present evidence for the in vivo transfer of bioactive EVs from osteoblasts to BM progenitor populations, and that this transfer alters hematopoietic cell function and gene expression. Moreover, we identify piRNAs and tRNAs as the most enriched species of small RNAs within BM derived EVs. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

scholarly journals The role of small RNAs in wide hybridisation and allopolyploidisation between Brassica rapa and Brassica nigra

2014 ◽  
Vol 14 (1) ◽  
Author(s):  
Muhammad Awais Ghani ◽  
Junxing Li ◽  
Linli Rao ◽  
Muhammad Ammar Raza ◽  
Liwen Cao ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Small Rnas ◽  
Brassica Nigra ◽  
Wide Hybridisation

scholarly journals Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting

2021 ◽  
Vol 118 (29) ◽  
pp. e2104445118
Author(s):  
Jessica A. Rodrigues ◽  
Ping-Hung Hsieh ◽  
Deling Ruan ◽  
Toshiro Nishimura ◽  
Manoj K. Sharma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Genomic Imprinting ◽  
Small Rnas ◽  
Imprinted Genes ◽  
Dna Hypomethylation ◽  
Transcription Start ◽  
Specific Expression ◽  
Parent Of Origin

Parent-of-origin–dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin–specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions—the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution.

scholarly journals Abolished miR158 activity leads to 21-nucleotide tertiary phasiRNA biogenesis that targets NHX2 in Arabidopsis thaliana

2021 ◽  
Author(s):  
Abhinandan Mani Tripathi ◽  
Rajneesh Singh ◽  
Akanksha Singh ◽  
Ashwani Kumar Verma ◽  
Parneeta Mishra ◽  
...  
Keyword(s):  
Gene Expression ◽  
Small Rna ◽  
Small Rnas ◽  
Small Interfering Rnas ◽  
Primary Transcript ◽  
Over Expression ◽  
Additional Layer ◽  
Natural Variants ◽  
Non Coding Rnas

ABSTRACTSmall RNAs including microRNAs (miRNAs) are short 20-24-nucleotide non-coding RNAs. They are key regulators of gene expression in plants and other organisms. Some small RNAs, mostly 22-nucleotide long trigger biogenesis of secondary small interfering RNAs (siRNAs). Those siRNAs having distinctive phased configuration are known as phased siRNAs (phasiRNAs) and act either in cis or trans enhancing silencing cascade. Here, we report natural variants of MIR158 having deletions or insertions led to negligible or reduced expression of miR158. The deletion/insertion events affected processing of primary transcript of miR158 to precursor and to mature miR158. We show that miR158 targets a pseudo-pentatricopeptide gene and its abolished activity led to 21-nucleotide tertiary phasiRNA generation from its target. The biogenesis of these phasiRNAS is triggered by TAS2 derived two siRNAs. Accordingly, small RNA analyses of these natural variants, mutants and over-expression lines of MIR158 or its target exhibited enhanced or reduced phasiRNA biogenesis. Finally, we functionally validated the highest expressed tertiary phasiRNA that targets NHX2 thereby regulating transpiration and stomatal conductance. Overall, we deciphered a new module of small RNA network, miRNA-TAS-siRNA-pseudogene-tertiary phasiRNA-NHX2, suggesting an additional layer of gene regulation and larger role of pseudogene in plants.

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