scholarly journals Reprogramming of 24nt siRNAs in rice gametes

2019 ◽  
Author(s):  
Chenxin Li ◽  
Hengping Xu ◽  
Fang-Fang Fu ◽  
Scott D. Russell ◽  
Venkatesan Sundaresan ◽  
...  
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Large Scale ◽  
Dna Methyltransferases ◽  
Critical Stage ◽  
Vegetative Tissues ◽  
Plant Life ◽  
Genome Wide ◽  
Strong Indicator ◽  
Plant Life Cycle

ABSTRACTGametes constitute a critical stage of the plant life cycle, during which the genome undergoes reprogramming in preparation for embryogenesis. Here we characterized the small RNA transcriptomes of egg cells and sperm cells from rice to elucidate genome-wide distributions of 24nt siRNAs, which are a hallmark of RNA-directed DNA methylation (RdDM) in plants and are typically concentrated at boundaries of heterochromatin. We found that 24nt siRNAs were depleted from heterochromatin boundaries in both gametes, reminiscent of siRNA patterns in DDM1-type nucleosome remodeler mutants. In sperm, 24nt siRNAs were spread across broad heterochromatic regions, while in eggs, 24nt siRNAs were concentrated at a smaller number of heterochromatic loci throughout the genome, which were shared with vegetative tissues and sperm. In both gametes, patterns of CHH methylation, typically a strong indicator of RdDM, were similar to vegetative tissues, although lower in magnitude. These findings indicate that the small RNA transcriptome undergoes large-scale re-programming in both male and female gametes, which is not correlated with recruitment of DNA methyltransferases in gametes and suggestive of unexplored regulatory activities of gamete small RNAs in seeds after fertilization.

scholarly journals Genome-wide identification and analysis of class III peroxidases in Betula pendula

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Kewei Cai ◽  
Huixin Liu ◽  
Song Chen ◽  
Yi Liu ◽  
Xiyang Zhao ◽  
...  
Keyword(s):  
Stress Responses ◽  
Betula Pendula ◽  
Expression Patterns ◽  
Class Iii ◽  
Physiological Processes ◽  
Plant Life ◽  
Genome Wide ◽  
Plant Life Cycle ◽  
Class Iii Peroxidases ◽  
And Function

Abstract Background Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. At present, POD genes have been studied in Arabidopsis, rice, poplar, maize and Chinese pear, but there are no reports on the identification and function of POD gene family in Betula pendula. Results We identified 90 nonredundant POD genes in Betula pendula. (designated BpPODs). According to phylogenetic relationships, these POD genes were classified into 12 groups. The BpPODs are distributed in different numbers on the 14 chromosomes, and some BpPODs were located sequentially in tandem on chromosomes. In addition, we analyzed the conserved domains of BpPOD proteins and found that they contain highly conserved motifs. We also investigated their expression patterns in different tissues, the results showed that some BpPODs might play an important role in xylem, leaf, root and flower. Furthermore, under low temperature conditions, some BpPODs showed different expression patterns at different times. Conclusions The research on the structure and function of the POD genes in Betula pendula plays a very important role in understanding the growth and development process and the molecular mechanism of stress resistance. These results lay the theoretical foundation for the genetic improvement of Betula pendula.

scholarly journals Transcriptional and Small RNA Responses of the White Mold Fungus Sclerotinia sclerotiorum to Infection by a Virulence-Attenuating Hypovirus

Viruses ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 713 ◽  
Author(s):  
Shin-Yi Lee Marzano ◽  
Achal Neupane ◽  
Leslie Domier
Keyword(s):  
Sclerotinia Sclerotiorum ◽  
Small Rna ◽  
Small Rnas ◽  
Large Scale ◽  
White Mold ◽  
Enhanced Production ◽  
Mold Fungus ◽  
Depth Analysis ◽  
Sclerotial Formation ◽  
In Trans

Mycoviruses belonging to the family Hypoviridae cause persistent infection of many different host fungi. We previously determined that the white mold fungus, Sclerotinia sclerotiorum, infected with Sclerotinia sclerotiorum hypovirus 2-L (SsHV2-L) exhibits reduced virulence, delayed/reduced sclerotial formation, and enhanced production of aerial mycelia. To gain better insight into the cellular basis for these changes, we characterized changes in mRNA and small RNA (sRNA) accumulation in S. sclerotiorum to infection by SsHV2-L. A total of 958 mRNAs and 835 sRNA-producing loci were altered after infection by SsHV2-L, among which >100 mRNAs were predicted to encode proteins involved in the metabolism and trafficking of carbohydrates and lipids. Both S. sclerotiorum endogenous and virus-derived sRNAs were predominantly 22 nt in length suggesting one dicer-like enzyme cleaves both. Novel classes of endogenous small RNAs were predicted, including phasiRNAs and tRNA-derived small RNAs. Moreover, S. sclerotiorum phasiRNAs, which were derived from noncoding RNAs and have the potential to regulate mRNA abundance in trans, showed differential accumulation due to virus infection. tRNA fragments did not accumulate differentially after hypovirus infection. Hence, in-depth analysis showed that infection of S. sclerotiorum by a hypovirulence-inducing hypovirus produced selective, large-scale reprogramming of mRNA and sRNA production.

scholarly journals Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Martina Legris ◽  
Yetkin Çaka Ince ◽  
Christian Fankhauser
Keyword(s):  
Conformational Changes ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Plant Life ◽  
Signaling Mechanisms ◽  
Open Questions ◽  
Whole Plant ◽  
Promoter Usage ◽  
Plant Life Cycle ◽  
Compare And Contrast

AbstractPhytochromes are bilin-binding photosensory receptors which control development over a broad range of environmental conditions and throughout the whole plant life cycle. Light-induced conformational changes enable phytochromes to interact with signaling partners, in particular transcription factors or proteins that regulate them, resulting in large-scale transcriptional reprograming. Phytochromes also regulate promoter usage, mRNA splicing and translation through less defined routes. In this review we summarize our current understanding of plant phytochrome signaling, emphasizing recent work performed in Arabidopsis. We compare and contrast phytochrome responses and signaling mechanisms among land plants and highlight open questions in phytochrome research.

scholarly journals Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host

2015 ◽  
Vol 43 (13) ◽  
pp. 6191-6206 ◽  
Author(s):  
Eric Roberto Guimarães Rocha Aguiar ◽  
Roenick Proveti Olmo ◽  
Simona Paro ◽  
Flavia Viana Ferreira ◽  
Isaque João da Silva de Faria ◽  
...  
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Large Scale ◽  
Virus Detection ◽  
Virus Surveillance ◽  
Size Profile ◽  
Reference Databases ◽  
Similarity Searches ◽  
Viral Sequences

Abstract Virus surveillance in vector insects is potentially of great benefit to public health. Large-scale sequencing of small and long RNAs has previously been used to detect viruses, but without any formal comparison of different strategies. Furthermore, the identification of viral sequences largely depends on similarity searches against reference databases. Here, we developed a sequence-independent strategy based on virus-derived small RNAs produced by the host response, such as the RNA interference pathway. In insects, we compared sequences of small and long RNAs, demonstrating that viral sequences are enriched in the small RNA fraction. We also noted that the small RNA size profile is a unique signature for each virus and can be used to identify novel viral sequences without known relatives in reference databases. Using this strategy, we characterized six novel viruses in the viromes of laboratory fruit flies and wild populations of two insect vectors: mosquitoes and sandflies. We also show that the small RNA profile could be used to infer viral tropism for ovaries among other aspects of virus biology. Additionally, our results suggest that virus detection utilizing small RNAs can also be applied to vertebrates, although not as efficiently as to plants and insects.

scholarly journals Genome-wide analyses across Viridiplantae reveal the origin and diversification of small RNA pathway-related genes

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Sibo Wang ◽  
Hongping Liang ◽  
Yan Xu ◽  
Linzhou Li ◽  
Hongli Wang ◽  
...  
Keyword(s):  
Small Rna ◽  
Stress Responses ◽  
Small Rnas ◽  
Common Ancestor ◽  
Regulation Of Gene Expression ◽  
Mirna Biogenesis ◽  
Last Common Ancestor ◽  
Evolutionary Transitions ◽  
Genome Wide ◽  
Post Transcriptional Regulation

AbstractSmall RNAs play a major role in the post-transcriptional regulation of gene expression in eukaryotes. Despite the evolutionary importance of streptophyte algae, knowledge on small RNAs in this group of green algae is almost non-existent. We used genome and transcriptome data of 34 algal and plant species, and performed genome-wide analyses of small RNA (miRNA & siRNA) biosynthetic and degradation pathways. The results suggest that Viridiplantae started to evolve plant-like miRNA biogenesis and degradation after the divergence of the Mesostigmatophyceae in the streptophyte algae. We identified two major evolutionary transitions in small RNA metabolism in streptophyte algae; during the first transition, the origin of DCL-New, DCL1, AGO1/5/10 and AGO4/6/9 in the last common ancestor of Klebsormidiophyceae and all other streptophytes could be linked to abiotic stress responses and evolution of multicellularity in streptophytes. During the second transition, the evolution of DCL 2,3,4, and AGO 2,3,7 as well as DRB1 in the last common ancestor of Zygnematophyceae and embryophytes, suggests their possible contribution to pathogen defense and antibacterial immunity. Overall, the origin and diversification of DICER and AGO along with several other small RNA pathway-related genes among streptophyte algae suggested progressive adaptations of streptophyte algae during evolution to a subaerial environment.

scholarly journals Genome-Wide Analysis of the Catharanthus roseus RLK1-Like in Soybean and GmCrRLK1L20 Responds to Drought and Salt Stresses

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhi-Qi Wang ◽  
Tai-Fei Yu ◽  
Guo-Zhong Sun ◽  
Jia-Cheng Zheng ◽  
Jun Chen ◽  
...  
Keyword(s):  
Catharanthus Roseus ◽  
Vital Role ◽  
Soybean Genome ◽  
Chromosomal Mapping ◽  
Genome Wide Analysis ◽  
Plant Life ◽  
Genome Wide ◽  
Localization Analysis ◽  
Drought And Salt Stresses ◽  
Plant Life Cycle

Abiotic stresses, such as drought and salinity, severely affects the growth, development and productivity of the plants. The Catharanthus roseus RLK1-like (CrRLK1L) protein kinase family is involved in several processes in the plant life cycle. However, there have been few studies addressing the functions of CrRLK1L proteins in soybean. In this study, 38 CrRLK1L genes were identified in the soybean genome (Glycine max Wm82.a2.v1). Phylogenetic analysis demonstrated that soybean CrRLK1L genes were grouped into clusters, cluster I, II, III. The chromosomal mapping demonstrated that 38 CrRLK1L genes were located in 14 of 20 soybean chromosomes. None were discovered on chromosomes 1, 4, 6, 7, 11, and 14. Gene structure analysis indicated that 73.6% soybean CrRLK1L genes were characterized by a lack of introns.15.7% soybean CrRLK1L genes only had one intron and 10.5% soybean CrRLK1L genes had more than one intron. Five genes were obtained from soybean drought- and salt-induced transcriptome databases and were found to be highly up-regulated. GmCrRLK1L20 was notably up-regulated under drought and salinity stresses, and was therefore studied further. Subcellular localization analysis revealed that the GmCrRLK1L20 protein was located in the cell membrane. The overexpression of the GmCrRLK1L20 gene in soybean hairy roots improved both drought tolerance and salt stresses and enhanced the expression of the stress-responsive genes GmMYB84, GmWRKY40, GmDREB-like, GmGST15, GmNAC29, and GmbZIP78. These results indicated that GmCrRLK1L20 could play a vital role in defending against drought and salinity stresses in soybean.

scholarly journals Stress Resets Transgenerational Small RNA Inheritance

2019 ◽  
Author(s):  
Leah Houri-Ze’evi ◽  
Guy Teichman ◽  
Hila Gingold ◽  
Oded Rechavi
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Memory Trace ◽  
Mapk Pathway ◽  
Transgenerational Inheritance ◽  
Cultivation Conditions ◽  
C Elegans ◽  
Genome Wide ◽  
A Genome ◽  
Basic Concepts

AbstractTransgenerational inheritance of small RNAs is challenging basic concepts of heredity and achieving control over such responses is of great interest. InC. elegansnematodes, small RNAs are transmitted across generations to establish a transgenerational memory trace of ancestral environments and distinguish self from non-self genes. Inheritance of small RNAs is regulated by dedicated machinery and carryover of aberrant heritable small RNA responses was shown to be maladaptive and to induce sterility. Here we show that various types of stress (starvation, high temperatures, and high osmolarity) but not non-stressful changes in cultivation conditions, lead to resetting of small RNA inheritance. We found that stress leads to a genome-wide reduction in heritable small RNA levels and that mutants defective in different stress pathways exhibit irregular RNAi inheritance dynamics. Moreover, we discovered that resetting of heritable RNAi is orchestrated by MAPK pathway factors, the transcription factor SKN-1, and the MET-2 methyltransferase. Termination of small RNA inheritance, and the fact that this process depends on stress, could protect from run-on of environment-irrelevant heritable gene regulation.

scholarly journals A small RNA pathway mediates global allelic dosage in endosperm

2017 ◽  
Author(s):  
Robert M. Erdmann ◽  
P.R. V. Satyaki ◽  
Maja Klosinska ◽  
Mary Gehring
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Inverse Relationship ◽  
Paternal Genome ◽  
Pol Iv ◽  
Genome Wide ◽  
A Genome ◽  
Normal Seed ◽  
Wide Scale ◽  
Parent Of Origin

SummaryBalance between maternal and paternal genomes within the triploid endosperm is necessary for normal seed development. The majority of genes in Arabidopsis endosperm are expressed in a 2:1 maternal:paternal ratio, reflecting endosperm genomic DNA content. Here we find that the 2:1 transcriptional ratio is not, unexpectedly, a passive default but is actively regulated. We describe an inverse relationship between the parent-of-origin of small RNAs and mRNAs in endosperm on a genome-wide scale. Disruption of the Pol IV small RNA pathway causes the entire transcriptome to become more maternally biased. Furthermore, paternal inheritance of a RNA Pol IV mutation is sufficient to rescue seed abortion caused by excess paternal genome dosage. These results indicate that maintenance of the maternal:paternal transcriptome ratio in endosperm is an active process and reveal a function for RNA Pol IV in mediating the global transcriptional balance between maternally and paternally inherited genomes in endosperm.

scholarly journals Genome-Wide Analysis of Single Non-Templated Nucleotides in Plant Endogenous siRNAs and miRNAs

2016 ◽  
Author(s):  
Feng Wang ◽  
Nathan R. Johnson ◽  
Ceyda Coruh ◽  
Michael J. Axtell
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Small Rna Sequencing ◽  
Plant Mirnas ◽  
Wild Type ◽  
Type Specimens ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Heterochromatic Sirna ◽  
Very High

AbstractPlant small RNAs are subject to various modifications. Previous reports revealed widespread 3' modifications (truncations and non-templated tailing) of plant miRNAs when the 2'-C-methyltransferase HEN1 is absent. However, non-templated nucleotides in plant heterochromatic siRNAs have not been deeply studied, especially in wild-type plants. We systematically studied non-templated nucleotide patterns in plant small RNAs by analyzing small RNA sequencing libraries from Arabidopsis. tomato, Medicago, rice, maize, and Physcomitrella. Elevated rates of non-templated nucleotides were observed at the 3' ends of both miRNAs and endogenous siRNAs from wild-type specimens of all species. 'Off-sized' small RNAs, such as 25 and 23 nt siRNAs arising from loci dominated by 24 nt siRNAs, often had very high rates of 3'-non-templated nucleotides. The same pattern was observed in all species that we studied. Further analysis of 24 nt siRNA clusters in Arabidopsis revealed distinct patterns of 3'-non-templated nucleotides of 23 nt siRNAs arising from heterochromatic siRNA loci. This pattern of non-templated 3' nucleotides on 23 nt siRNAs is not affected by loss of known small RNA 3'-end modifying enzymes, and may result from modifications added to longer heterochromatic siRNA precursors.

scholarly journals Resetting of 24-nt siRNA landscape is initiated in the unicellular zygote in rice

2020 ◽  
Author(s):  
Chenxin Li ◽  
Jonathan I. Gent ◽  
Hengping Xu ◽  
Hong Fu ◽  
Scott D. Russell ◽  
...  
Keyword(s):  
Stem Cell ◽  
Life Cycle ◽  
Small Rna ◽  
De Novo ◽  
Large Fraction ◽  
Egg Cell ◽  
Critical Stage ◽  
Vegetative Tissues ◽  
Differentiated Cells ◽  
Carry Over

ABSTRACTThe zygote, a totipotent stem cell, constitutes a critical stage of the life cycle for all sexually reproducing organisms. It is produced by fusion of two differentiated cells, egg and sperm, that in plants have radically different siRNA transcriptomes from each other and from multicellular embryos. Here we examined the small RNA transcriptome of unicellular rice zygotes. We find that the overall 24-nt siRNA landscape in the zygote resembles that of the unfertilized egg cell, consistent with maternal carry-over. A large fraction (∼75%) of the siRNAs in the zygote arise from a small proportion (∼2%) of siRNA loci, which corresponded to similar loci in the egg cell and ovary. However, these highly expressing loci were distinct from endosperm siren loci that were detected in later stage endosperm. miRNA abundances changed rapidly after fertilization, resulting in a miRNA profile distinct from the egg cell. Notably, the de novo 24-nt siRNAs expressed by the zygote had characteristics of canonical siRNAs, such as proximity to genes and tendency to overlap TIR DNA transposable elements, and resembled seedling siRNA loci, indicating a return to the canonical siRNA profile typical of vegetative tissues. Taken together, our results suggest that resetting of the gametic epigenome towards the canonical vegetative profile is initiated before the first embryonic division.

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