scholarly journals High resolution RNA‐seq profiling of genes encoding ribosomal proteins across different organs and developmental stages in Arabidopsis thaliana

Plant Direct ◽  
2021 ◽  
Vol 5 (5) ◽  
Author(s):  
Wei Xiong ◽  
Jiancong Zhang ◽  
Ting Lan ◽  
Wenwen Kong ◽  
Xiaoyan Wang ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
High Resolution ◽  
Ribosomal Proteins ◽  
Developmental Stages ◽  
Rna Seq ◽  
Genes Encoding

scholarly journals Plant Histone HTB (H2B) Variants in Regulating Chromatin Structure and Function

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1435
Author(s):  
Janardan Khadka ◽  
Anat Pesok ◽  
Gideon Grafi
Keyword(s):  
Arabidopsis Thaliana ◽  
Chromatin Structure ◽  
Developmental Stages ◽  
Histone Variants ◽  
Structure And Function ◽  
Core Histone ◽  
Histone H2b ◽  
Histone Proteins ◽  
Genes Encoding ◽  
And Function

Besides chemical modification of histone proteins, chromatin dynamics can be modulated by histone variants. Most organisms possess multiple genes encoding for core histone proteins, which are highly similar in amino acid sequence. The Arabidopsis thaliana genome contains 11 genes encoding for histone H2B (HTBs), 13 for H2A (HTAs), 15 for H3 (HTRs), and 8 genes encoding for histone H4 (HFOs). The finding that histone variants may be expressed in specific tissues and/or during specific developmental stages, often displaying specific nuclear localization and involvement in specific nuclear processes suggests that histone variants have evolved to carry out specific functions in regulating chromatin structure and function and might be important for better understanding of growth and development and particularly the response to stress. In this review, we will elaborate on a group of core histone proteins in Arabidopsis, namely histone H2B, summarize existing data, and illuminate the potential function of H2B variants in regulating chromatin structure and function in Arabidopsis thaliana.

scholarly journals Unique Shine–Dalgarno Sequences in Cyanobacteria and Chloroplasts Reveal Evolutionary Differences in Their Translation Initiation

2019 ◽  
Vol 11 (11) ◽  
pp. 3194-3206 ◽  
Author(s):  
Yulong Wei ◽  
Xuhua Xia
Keyword(s):  
Arabidopsis Thaliana ◽  
Nicotiana Tabacum ◽  
Translation Initiation ◽  
Ribosomal Proteins ◽  
Selection Pressure ◽  
Rna Seq ◽  
Prominent Feature ◽  
Transcriptomic Data ◽  
Reduced Genome ◽  
Cyanobacterial Genes

Abstract Microorganisms require efficient translation to grow and replicate rapidly, and translation is often rate-limited by initiation. A prominent feature that facilitates translation initiation in bacteria is the Shine–Dalgarno (SD) sequence. However, there is much debate over its conservation in Cyanobacteria and in chloroplasts which presumably originated from endosymbiosis of ancient Cyanobacteria. Elucidating the utilization of SD sequences in Cyanobacteria and in chloroplasts is therefore important to understand whether 1) SD role in Cyanobacterial translation has been reduced prior to chloroplast endosymbiosis or 2) translation in Cyanobacteria and in plastid has been subjected to different evolutionary pressures. To test these alternatives, we employed genomic, proteomic, and transcriptomic data to trace differences in SD usage among Synechocystis species, Microcystis aeruginosa, cyanophages, Nicotiana tabacum chloroplast, and Arabidopsis thaliana chloroplast. We corrected their mis-annotated 16S rRNA 3′ terminus using an RNA-Seq-based approach to determine their SD/anti-SD locational constraints using an improved measurement DtoStart. We found that cyanophages well-mimic Cyanobacteria in SD usage because both have been under the same selection pressure for SD-mediated initiation. Whereas chloroplasts lost this similarity because the need for SD-facilitated initiation has been reduced in plastids having much reduced genome size and different ribosomal proteins as a result of host-symbiont coevolution. Consequently, SD sequence significantly increases protein expression in Cyanobacteria but not in chloroplasts, and only Cyanobacterial genes compensate for a lack of SD sequence by having weaker secondary structures at the 5′ UTR. Our results suggest different evolutionary pressures operate on translation initiation in Cyanobacteria and in chloroplast.

scholarly journals RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3631 ◽  
Author(s):  
Van L.T. Hoang ◽  
Lisa N. Tom ◽  
Xiu-Cheng Quek ◽  
Jean-Marie Tan ◽  
Elizabeth J. Payne ◽  
...  
Keyword(s):  
Skin Cancer ◽  
Reference Genes ◽  
Ribosomal Proteins ◽  
Data Interpretation ◽  
Rna Seq ◽  
Non Melanoma Skin Cancer ◽  
Skin Cancers ◽  
Genes Encoding ◽  
Gene Expression Studies ◽  
Melanoma Skin

Identification of appropriate reference genes (RGs) is critical to accurate data interpretation in quantitative real-time PCR (qPCR) experiments. In this study, we have utilised next generation RNA sequencing (RNA-seq) to analyse the transcriptome of a panel of non-melanoma skin cancer lesions, identifying genes that are consistently expressed across all samples. Genes encoding ribosomal proteins were amongst the most stable in this dataset. Validation of this RNA-seq data was examined using qPCR to confirm the suitability of a set of highly stable genes for use as qPCR RGs. These genes will provide a valuable resource for the normalisation of qPCR data for the analysis of non-melanoma skin cancer.

A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling

2016 ◽  
Vol 88 (6) ◽  
pp. 1058-1070 ◽  
Author(s):  
Anna V. Klepikova ◽  
Artem S. Kasianov ◽  
Evgeny S. Gerasimov ◽  
Maria D. Logacheva ◽  
Aleksey A. Penin
Keyword(s):  
Arabidopsis Thaliana ◽  
High Resolution ◽  
Rna Seq ◽  
High Resolution Map ◽  
Resolution Map

Transciptome Analysis Molecular Mechanism of Starch Synthesis During Tuber Development in Chinese Yam (Dioscorea opposita)

2021 ◽  
Vol 15 (5) ◽  
pp. 589-597
Author(s):  
Yanfang Zhang ◽  
Shuchun Guo ◽  
Ying Shao ◽  
Lingmin Zhao ◽  
Linan Xing ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Starch Synthesis ◽  
Transcriptome Profiling ◽  
Starch Accumulation ◽  
Rna Seq ◽  
Sequencing Data ◽  
Tuber Development ◽  
Synthesis Mechanism ◽  
Dioscorea Opposita ◽  
Genes Encoding

Yam (Dioscorea opposita) is a kind of vegetables with important nutritional, medicinal and economic value. To reveal the relationship between starch synthesis and gene expression in yam tubers at gene transcription level, transcriptome profiling was conducted by RNA-Seq in Bikeqi yam (Dioscorea opposita Thunb.) tubers at five key developmental stages (105, 120, 135, 150, and 165 days after sowing, DAS). Based on transcriptome sequencing data, a total of 45,867 unigenes were obtained. The results showed that 135 days after sowing are the key period of starch accumulation. During yam tuber development, 1,941 candidate differentially expressed genes (DEGs) were successfully classified into three GO categories, respectively, and there were 292, 267 and 478 unigenes in cellular component, molecular function and biological process. There were 767, 90 and 73 DEGs enriched in metabolic, plant hormone signal transduction and Plant-pathogen interaction pathway by Kyoto Encyclopedia of Genes and Genomes (KEGG), individually. Especially 72 DEGs were enriched in starch and sucrose metabolism pathway. In this pathway, the metabolic process was mainly positive regulated by genes encoding sucrose synthase, glucose-1-phosphate adenylyltransferase, alpha-trehalase, and so on. There was negative regulated by genes encoding beta-glucosidase. 10 DEGs involved in starch synthesis were selected to prove the accuracy of the RNA-Seq data by qPCR, 85% (34/40) of the results were consistent. The results lay a theoretical foundation be used for further understanding the starch synthesis mechanism of yam tubers development and accelerating breeding progress.

scholarly journals RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers

2016 ◽  
Author(s):  
Van LT Hoang ◽  
Lisa N Tom ◽  
Xiu-Cheng Quek ◽  
Jean-Marie Tan ◽  
Elizabeth J Payne ◽  
...  
Keyword(s):  
Skin Cancer ◽  
Reference Genes ◽  
Ribosomal Proteins ◽  
Data Interpretation ◽  
Rna Seq ◽  
Non Melanoma Skin Cancer ◽  
Skin Cancers ◽  
Genes Encoding ◽  
Gene Expression Studies ◽  
Melanoma Skin

Identification of appropriate reference genes (RGs) is critical to accurate data interpretation in quantitative real-time PCR (qPCR) experiments. In this study, we have utilised next generation RNA-sequencing (RNA-seq) to analyse the transcriptome of a panel of non-melanoma skin cancer lesions, identifying genes, which are consistently expressed across all samples. Genes encoding ribosomal proteins were amongst the most stable in this dataset. Validation of this RNA-seq data was examined using qPCR to confirm the suitability of a set of highly stable genes for use as RGs. These genes will provide a valuable resource for the normalisation of qPCR data for the analysis of non-melanoma skin cancer.

Characterization of Arabidopsis thaliana lines with T-DNA insertions in the mitochondrial ribosomal protein genes Rps14 and Rps19

2019 ◽  
Vol 79 (02) ◽  
Author(s):  
Suman Lata ◽  
Anshul Watts ◽  
S. R. Bhat
Keyword(s):  
Arabidopsis Thaliana ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Ribosomal Protein Genes ◽  
Protein Coding ◽  
Mitochondrial Ribosomal Protein ◽  
Genes Encoding ◽  
Coordinated Expression ◽  
Dna Insertion ◽  
Mutant Lines

In Arabidopsis, most of the genes encoding mitochondrial ribosomal proteins are located in the nucleus and only seven are present in the mitochondrial genome. Assembly of a functional ribosome requires coordinated expression of ribosomal protein encoding genes located in both these organelles. Genes and promoters of nuclear encoded mitochondrial ribosomal protein coding genes of plants have not been well characterized so far. In the present study we have characterized Arabidopsis thaliana SALK mutant lines with T-DNA insertion in Rps14 or Rps19 gene. The location of T-DNA insertion in the mutant lines was confirmed and plants homozygous and hemizygous for TDNA insertion were identified for both Rps14 and Rps19 genes. In homozygous T-DNA mutant lines of both Rps14 and Rps19 genes, the expression was estimated using RTPCR. Rps14 and Rps19 transcripts similar to wild type were present in homozygous mutant plants of Rps14 and Rps19 which indicated that T-DNA insertion has not affected their expression.

scholarly journals Transcriptome Sequence Reveals Candidate Genes Involving in the Post-Harvest Hardening of Trifoliate Yam Dioscorea dumetorum

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 787
Author(s):  
Christian Siadjeu ◽  
Eike Mayland-Quellhorst ◽  
Shruti Pande ◽  
Sascha Laubinger ◽  
Dirk C. Albach
Keyword(s):  
Candidate Genes ◽  
Molecular Breeding ◽  
Developmental Stages ◽  
Myb Transcription Factor ◽  
Rna Seq ◽  
Post Harvest ◽  
Qrt Pcr ◽  
Genes Encoding ◽  
Hypothetical Mechanism ◽  
Trifoliate Yam

Storage ability of trifoliate yam (Dioscorea dumetorum) is restricted by a severe post-harvest hardening (PHH) phenomenon, which starts within the first 24 h after harvest and renders tubers inedible. Previous work has only focused on the biochemical changes affecting PHH in D. dumetorum. To the best of our knowledge, the candidate genes responsible for the hardening of D. dumetorum have not been identified. Here, transcriptome analyses of D. dumetorum tubers were performed in yam tubers of four developmental stages: 4 months after emergence (4MAE), immediately after harvest (AH), 3 days after harvest (3DAH) and 14 days after harvest (14DAH) of four accessions (Bangou 1, Bayangam 2, Fonkouankem 1, and Ibo sweet 3) using RNA-Seq. In total, between AH and 3DAH, 165, 199, 128 and 61 differentially expressed genes (DEGs) were detected in Bayangam 2, Fonkouankem 1, Bangou 1 and Ibo sweet 3, respectively. Functional analysis of DEGs revealed that genes encoding for CELLULOSE SYNTHASE A (CESA), XYLAN O-ACETYLTRANSFERASE (XOAT), CHLOROPHYLL A/B BINDING PROTEIN1, 2, 3, 4 (LHCB1, LHCB2, LHCB3, and LCH4) and an MYB transcription factor were predominantly and significantly up-regulated 3DAH, implying that these genes were potentially involved in the PHH as confirmed by qRT-PCR. A hypothetical mechanism of this phenomenon and its regulation has been proposed. These findings provide the first comprehensive insights into gene expression in yam tubers after harvest and valuable information for molecular breeding against the PHH.

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