scholarly journals Temporal Small RNA Expression Profiling Under Drought Reveals a Potential Regulatory Role of snoRNAs in Drought Responses of Maize

2018 ◽  
Author(s):  
Jun Zheng ◽  
Erliang Zeng ◽  
Yicong Du ◽  
Cheng He ◽  
Ying Hu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Sequence Data ◽  
Expression Profiles ◽  
Regulatory Role ◽  
Chromatin Modifications ◽  
Small Nuclear Rnas ◽  
Genome Copy Number ◽  
Rna Expression Profiling ◽  
Genomic Regions

AbstractSmall RNAs (sRNAs) are short noncoding RNAs that play roles in many biological processes, including drought responses in plants. However, how the expression of sRNAs dynamically changes with the gradual imposition of drought stress in plants is largely unknown. We generated time-series sRNA sequence data from maize seedlings under drought stress and under well-watered conditions at the same time points. Analyses of length, functional annotation, and abundance of 736,372 non-redundant sRNAs from both drought and well-watered data, as well as genome copy number and chromatin modifications at the corresponding genomic regions, revealed distinct patterns of abundance, genome organization, and chromatin modifications for different sRNA classes of sRNAs. The analysis identified 6,646 sRNAs whose regulation was altered in response to drought stress. Among drought-responsive sRNAs, 1,325 showed transient down-regulation by the seventh day, coinciding with visible symptoms of drought stress. The profiles revealed drought-responsive microRNAs, as well as other sRNAs that originated from ribosomal RNAs (rRNAs), splicing small nuclear RNAs, and small nucleolar RNAs (snoRNA). Expression profiles of their sRNA derivers indicated that snoRNAs might play a regulatory role through regulating stability of rRNAs and splicing small nuclear RNAs under drought condition.

scholarly journals Divergence of chemosensing during the early stages of speciation

2020 ◽  
Vol 117 (28) ◽  
pp. 16438-16447 ◽  
Author(s):  
Bas van Schooten ◽  
Jesyka Meléndez-Rosa ◽  
Steven M. Van Belleghem ◽  
Chris D. Jiggins ◽  
John D. Tan ◽  
...  
Keyword(s):  
Host Plant ◽  
Expression Profiles ◽  
Life Stage ◽  
Gene Expression Profiles ◽  
Color Pattern ◽  
Mate Finding ◽  
Strong Candidate ◽  
Genomic Regions ◽  
Heliconius Cydno

Chemosensory communication is essential to insect biology, playing indispensable roles during mate-finding, foraging, and oviposition behaviors. These traits are particularly important during speciation, where chemical perception may serve to establish species barriers. However, identifying genes associated with such complex behavioral traits remains a significant challenge. Through a combination of transcriptomic and genomic approaches, we characterize the genetic architecture of chemoperception and the role of chemosensing during speciation for a young species pair ofHeliconiusbutterflies,Heliconius melpomeneandHeliconius cydno. We provide a detailed description of chemosensory gene-expression profiles as they relate to sensory tissue (antennae, legs, and mouthparts), sex (male and female), and life stage (unmated and mated female butterflies). Our results untangle the potential role of chemical communication in establishing barriers during speciation and identify strong candidate genes for mate and host plant choice behaviors. Of the 252 chemosensory genes,HmOBP20(involved in volatile detection) andHmGr56(a putative synephrine-related receptor) emerge as strong candidates for divergence in pheromone detection and host plant discrimination, respectively. These two genes are not physically linked to wing-color pattern loci or other genomic regions associated with visual mate preference. Altogether, our results provide evidence for chemosensory divergence betweenH. melpomeneandH. cydno, two rarely hybridizing butterflies with distinct mate and host plant preferences, a finding that supports a polygenic architecture of species boundaries.

Gene expression profiles predict the possible regulatory role of OPN-mediated signaling pathways in rat liver regeneration

Gene ◽  
2016 ◽  
Vol 576 (2) ◽  
pp. 782-790 ◽  
Author(s):  
Gaiping Wang ◽  
Shasha Chen ◽  
Congcong Zhao ◽  
Xiaofang Li ◽  
Ling Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Liver Regeneration ◽  
Signaling Pathways ◽  
Rat Liver ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Regulatory Role ◽  
Rat Liver Regeneration

scholarly journals Histone modifications during the life cycle of the brown alga Ectocarpus

2020 ◽  
Author(s):  
Simon Bourdareau ◽  
Leila Tirichine ◽  
Bérangère Lombard ◽  
Damarys Loew ◽  
Delphine Scornet ◽  
...  
Keyword(s):  
Life Cycle ◽  
Brown Algae ◽  
Land Plant ◽  
Chromatin Modifications ◽  
Post Translational Modifications ◽  
Transcription Start Sites ◽  
Histone Ptms ◽  
Genomic Regions ◽  
Active Genes

AbstractBackgroundBrown algae evolved complex multicellularity independently of the animal and land plant lineages and are the third most developmentally complex phylogenetic group on the planet. An understanding of developmental processes in this group is expected to provide important insights into the evolutionary events necessary for the emergence of complex multicellularity. Here we have focused on mechanisms of epigenetic regulation involving post-translational modifications (PTMs) of histone proteins.ResultsA total of 47 histone PTMs were identified, including a novel mark H2AZR38me1, but Ectocarpus lacks both H3K27me3 and the major polycomb complexes. ChIP-seq identified PTMs associated with transcription start sites (TSSs) and gene bodies of active genes, and with transposons. H3K79me2 exhibited an unusual pattern, often marking large genomic regions spanning several genes. TSSs of closely spaced divergently transcribed gene pairs shared a common nucleosome depleted region and exhibited shared histone PTM peaks. Overall, patterns of histone PTMs were stable through the life cycle. Analysis of histone PTMs at generation-biased genes identified a correlation between the presence of specific chromatin marks and the level of gene expression.ConclusionsThe overview of histone PTMs in the brown algae presented here will provide a foundation for future studies aimed at understanding the role of chromatin modifications in the regulation of brown algal genomes.

scholarly journals Drought-induced ABA, H2O2 and JA positively regulate CmCAD genes and lignin synthesis in melon stems

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Wei Liu ◽  
Yun Jiang ◽  
Yazhong Jin ◽  
Chenghui Wang ◽  
Juan Yang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Expression Profiles ◽  
Lignin Biosynthesis ◽  
Cinnamyl Alcohol Dehydrogenase ◽  
Signal Molecules ◽  
Lignin Synthesis ◽  
Enzyme Functions ◽  
Stress Promoter ◽  
Important Enzyme

Abstract Background Cinnamyl alcohol dehydrogenase (CAD) is an important enzyme functions at the last step in lignin monomer synthesis pathway. Our previous work found that drought induced the expressions of CmCAD genes and promoted lignin biosynthesis in melon stems. Results Here we studied the effects of abscisic acid (ABA), hydrogen peroxide (H2O2) and jasmonic acid (JA) to CmCADs under drought stress. Results discovered that drought-induced ABA, H2O2 and MeJA were prevented efficiently from increasing in melon stems pretreated with fluridone (Flu, ABA inhibitor), imidazole (Imi, H2O2 scavenger) and ibuprofen (Ibu, JA inhibitor). ABA and H2O2 are involved in the positive regulations to CmCAD1, 2, 3, and 5, and JA is involved in the positive regulations to CmCAD2, 3, and 5. According to the expression profiles of lignin biosynthesis genes, ABA, H2O2 and MeJA all showed positive regulations to CmPAL2-like, CmPOD1-like, CmPOD2-like and CmLAC4-like. In addition, positive regulations were also observed with ABA to CmPAL1-like, CmC4H and CmCOMT, with H2O2 to CmPAL1-like, CmC4H, CmCCR and CmLAC17-like, and with JA to CmCCR, CmCOMT, CmLAC11-like and CmLAC17-like. As expected, the signal molecules positively regulated CAD activity and lignin biosynthesis under drought stress. Promoter::GUS assays not only further confirmed the regulations of the signal molecules to CmCAD1~3, but also revealed the important role of CmCAD3 in lignin synthesis due to the strongest staining of CmCAD3 promoter::GUS. Conclusions CmCADs but CmCAD4 are positively regulated by ABA, H2O2 and JA under drought stress and participate in lignin synthesis.

Role of small nuclear RNAs in eukaryotic gene expression

2013 ◽  
Vol 54 ◽  
pp. 79-90 ◽  
Author(s):  
Saba Valadkhan ◽  
Lalith S. Gunawardane
Keyword(s):  
Gene Expression ◽  
Protein Interactions ◽  
Rna Stability ◽  
Splice Sites ◽  
Branch Site ◽  
Small Nuclear Rnas ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene ◽  
Rna Biogenesis

Eukaryotic cells contain small, highly abundant, nuclear-localized non-coding RNAs [snRNAs (small nuclear RNAs)] which play important roles in splicing of introns from primary genomic transcripts. Through a combination of RNA–RNA and RNA–protein interactions, two of the snRNPs, U1 and U2, recognize the splice sites and the branch site of introns. A complex remodelling of RNA–RNA and protein-based interactions follows, resulting in the assembly of catalytically competent spliceosomes, in which the snRNAs and their bound proteins play central roles. This process involves formation of extensive base-pairing interactions between U2 and U6, U6 and the 5′ splice site, and U5 and the exonic sequences immediately adjacent to the 5′ and 3′ splice sites. Thus RNA–RNA interactions involving U2, U5 and U6 help position the reacting groups of the first and second steps of splicing. In addition, U6 is also thought to participate in formation of the spliceosomal active site. Furthermore, emerging evidence suggests additional roles for snRNAs in regulation of various aspects of RNA biogenesis, from transcription to polyadenylation and RNA stability. These snRNP-mediated regulatory roles probably serve to ensure the co-ordination of the different processes involved in biogenesis of RNAs and point to the central importance of snRNAs in eukaryotic gene expression.

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