scholarly journals Conserved units of co-expression in bacterial genomes: an evolutionary insight into gene regulation

2014 ◽  
Author(s):  
Ivan Junier ◽  
Olivier Rivoire
Keyword(s):  
Gene Regulation ◽  
Strongly Correlated ◽  
Rna Seq ◽  
Regulatory Factor ◽  
Bacterial Genomes ◽  
Promoter Regions ◽  
Dna And Rna ◽  
Genome Wide ◽  
Associated Proteins ◽  
Underlying Mechanisms

Genome-wide measurements of transcriptional activity in bacteria indicate that the transcription of successive genes is strongly correlated beyond the scale of operons. However, the underlying mechanisms are poorly characterized and a systematic method for identifying local groups of co-transcribed genes is lacking. Here, we identify supra-operonic segments of consecutive genes by comparing gene proximity in thousands of bacterial genomes. Structurally, the segments are contained within micro-domains delineated by known nucleoid-associated proteins, and they contain operons with specific relative orientations. Functionally, the operons within a same segment are highly co-transcribed, even in the absence of regulatory factors at their promoter regions. Hence, operons with no common regulatory factor can be co-regulated if they share a regulatory factor at the level of segments. To rationalize these findings, we put forward the hypothesis supported by RNA-seq data that facilitated co-transcription, the feedback of transcription into itself involving only DNA and RNA-polymerases, may represent both an evolutionary primitive and a functionally primary mode of gene regulation.

scholarly journals Cytokinin-Regulated Expression of Arabidopsis thaliana PAP Genes and Its Implication for the Expression of Chloroplast-Encoded Genes

Biomolecules ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1658
Author(s):  
Aleksandra A. Andreeva ◽  
Radomira Vankova ◽  
Ivan A. Bychkov ◽  
Natalia V. Kudryakova ◽  
Maria N. Danilova ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Nuclear Genes ◽  
Promoter Regions ◽  
Knock Out ◽  
Regulatory Circuit ◽  
Associated Proteins ◽  
Gene Transcripts ◽  
Plastid Rna Polymerase ◽  
Underlying Mechanisms

Cytokinins (CKs) are known to regulate the biogenesis of chloroplasts under changing environmental conditions and at different stages of plant ontogenesis. However, the underlying mechanisms are still poorly understood. Apparently, the mechanisms can be duplicated in several ways, including the influence of nuclear genes that determine the expression of plastome through the two-component CK regulatory circuit. In this study, we evaluated the role of cytokinins and CK signaling pathway on the expression of nuclear genes for plastid RNA polymerase-associated proteins (PAPs). Cytokinin induced the expression of all twelve Arabidopsis thalianaPAP genes irrespective of their functions via canonical CK signaling pathway but this regulation might be indirect taking into consideration their different functions and versatile structure of promoter regions. The disruption of PAP genes contributed to the abolishment of positive CK effect on the accumulation of the chloroplast gene transcripts and transcripts of the nuclear genes for plastid transcription machinery as can be judged from the analysis of pap1 and pap6 mutants. However, the CK regulatory circuit in the mutants remained practically unperturbed. Knock-out of PAP genes resulted in cytokinin overproduction as a consequence of the strong up-regulation of the genes for CK synthesis.

scholarly journals Genome-wide Identification and Expression Analysis of the Eyloglucan Endotransglucosylase/hydrolase Gene Family in Poplar

2021 ◽  
Author(s):  
Zihan Cheng ◽  
Xuemei Zhang ◽  
Wenjing Yao ◽  
Yuan Gao ◽  
Kai Zhao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Plant Cell Wall ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Rna Seq ◽  
Promoter Regions ◽  
Salt Stress Response ◽  
Populus Simonii ◽  
Cis Acting ◽  
Genome Wide

Abstract Background: Xyloglucan endotransglucosylase/hydrolase (XTH) plays an important role in the process of plant cell wall reconstruction, and also involved in plants stress resistance. However, its characteristics of XTH family genes have not been reported in poplar. Results: In this study, we found 43 PtrXTH genes from Populus simonii × Populus nigra, and most of them contain two conserved structures (Glyco_hydro_16 and XET_C domain). The promoter regions of the PtrXTH genes contain many cis-acting elements related to growth and development and adverse stresses responses. Collinearity analysis revealed that the XTH family from poplarhave an evolutionary relationship with other five species, including Eucalyptus robusta, Solanum lycopersicum, Glycine max, Arabidopsis, Zea mays and Oryza sativa. Through RNA-Seq analysis, we found that the PtrXTH genes have different expression patterns in the roots, stems and leaves, and many of them are highly expressed in the roots. In addition, we found 11 differentially expressed PtrXTH genes in the roots, 9 in the stems, and 7 in the leaves under salt stress, and verified the accuracy of RNA-Seq analysis by RT-qPCR.Conclusion: All the results indicated that XTH family genes may play an important role in tissue specificity and salt stress response. This study laid a theoretical foundation for further study on the functions of XTH genes in poplar.

Genome-wide expression analysis in a dwarf soybean mutant

2014 ◽  
Vol 12 (S1) ◽  
pp. S70-S73 ◽  
Author(s):  
Feng Zhang ◽  
Yanting Shen ◽  
Shi Sun ◽  
Jianqiu Guo ◽  
Congcong Li ◽  
...  
Keyword(s):  
Plant Hormone ◽  
Dwarf Mutant ◽  
Biosynthetic Pathways ◽  
Rna Seq ◽  
Wild Type ◽  
Yield Improvement ◽  
Genome Wide ◽  
Γ Ray ◽  
Underlying Mechanisms ◽  
Genome Wide Expression

Plant height is important for crop yield improvement. In this study, a dwarf mutant, Gmdwarf1, was screened from a γ-ray-treated soybean population. Compared with the wild type, the mutant exhibited later germination, smaller and darker green leaves, and less-elongated shoots. Genome-wide transcriptome detection through RNA-seq analysis revealed that not only gibberellin-related genes but many other genes involved in hormone biosynthetic pathways were also significantly influenced in the mutant. We presumed that Gmdwarf1 might play essential roles in the plant hormone pathways. Future functional analysis of this dwarf mutant would help us to understand the underlying mechanisms and be beneficial for improving soybean yield.

scholarly journals Exploration of the cyanidioschyzon merolae intron landscape

2021 ◽  
Author(s):  
◽  
Viktor Slat
Keyword(s):  
Genome Engineering ◽  
Cyanidioschyzon Merolae ◽  
Rna Seq ◽  
Protein Coding ◽  
Genome Wide ◽  
Accurate Picture ◽  
Small Nuclear Rnas ◽  
Associated Proteins ◽  
Splice Site Usage

The eukaryotic process of pre-mRNA splicing involves the removal of noncoding intron sequences and the fusion of the remaining protein-coding exon sequences. The splicing reaction is catalyzed by the spliceosome, a dynamic multi-megadalton ribonucleoprotein complex that, in humans, is composed of 5 small nuclear RNAs (snRNAs) and over 200 associated proteins acting on more that 200,000 introns present within 25,000 genes. The unicellular red alga Cyanidioschyzon merolae possesses a more tractable splicing environment, with only 4 snRNAs and 75 associated proteins interacting with 27 annotated introns found in 26 our of 5,331 genes. Intron-rich genomes can confer benefits to their host species such as improved gene expression, incredible proteomic diversity, and increased genetic stability. This raises the question of why intron-poor C. merolae has retained such a small number of introns and a dramatically reduced spliceosome. A comprehensive investigation into the precise role that introns play in C. merolae would require the systematic removal of introns and an analysis of the effects thereof. The ability to elucidate the role of splicing in C. merolae via genome-wide intron deletion, however, hinges on the feasibility of establishing the efficiently scalable CRISPR genome engineering tool in C. merolae. It also follows that such an endeavour would require an accurate picture of the intron landscape of C. merolae, and since the number of annotated introns in C. merolae is relatively small, it is especially vital to determine whether any introns are missing from the C. merolae annotation. To that end, a stable and inducible Cas9-expressing strain of C. merolae was successfully developed. Transcriptome analysis using RNA-seq data revealed the discovery of 11 novel introns and 1 misannotated intron, as well as the presence of alternative splicing in the form of alternative splice site usage.

scholarly journals Genome-Wide Identification of Tomato Golden 2-Like Transcription Factors and Abiotic Stress Related Members Screening

2021 ◽  
Author(s):  
Ziyu Wang ◽  
Junfang Liu ◽  
Haiyan Zhao ◽  
Xuying Sun ◽  
Tairu Wu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stresses ◽  
Regulatory Elements ◽  
Biosynthesis Pathway ◽  
Rna Seq ◽  
Promoter Regions ◽  
Multiple Functions ◽  
Genome Wide ◽  
Comprehensive Information ◽  
Motif Composition

Abstract Background: Golden 2-Like (G2-like) transcription factors play an important role in plant development. However, the roles of these G2-like regulatory genes in response to abiotic stresses in tomato are not well understood.Results: In this study, we identified 66 putative G2-like genes in tomato (Solanum lycopersicum) and classified them into 5 groups (I to V) according to gene structure, motif composition and phylogenetic analysis. The G2-like genes were unevenly distributed across all 12 chromosomes. There were nine pairs of duplicated gene segments and four tandem duplicated SlGlk genes. Analysis of the cis-regulatory elements (CREs) showed that the promoter regions of SlGlks contain many kinds of stress- and hormone-related CREs. Based on RNA-seq, SlGlks were expressed in response to three abiotic stresses. Thirty-six differentially expressed SlGlks were identified; these genes have multiple functions according to Gene Ontology (GO) analysis and are enriched mainly in the zeatin biosynthesis pathway. Further studies exhibited that silencing SlGlk16 in tomato would reduce drought stress tolerance by earlier wilted, lower superoxide dismutase (SOD), peroxidase (POD) activities, less Pro contents and more MDA contents. Conclusion: Overall, the results of this study provide comprehensive information on G2-like transcription factors and G2-like genes that may be expressed in response to abiotic stresses.

Liver and Statins: A Critical Appraisal of the Evidence

2019 ◽  
Vol 25 (42) ◽  
pp. 5835-5846 ◽  
Author(s):  
Anna Licata ◽  
Antonina Giammanco ◽  
Maria Giovanna Minissale ◽  
Salvatore Pagano ◽  
Salvatore Petta ◽  
...  
Keyword(s):  
Adverse Events ◽  
Association Studies ◽  
Organic Anion ◽  
Genome Wide Association Studies ◽  
Drug Induced ◽  
Drug Induced Liver Injury ◽  
Organic Anion Transporting Polypeptide ◽  
Treatment And Prevention ◽  
Genome Wide ◽  
Underlying Mechanisms

Adverse drug reactions (ADRs) represent an important cause of morbidity and mortality worldwide. Statins are a class of drugs whose main adverse effects are drug-induced liver injury (DILI) and myopathy. Some of these may be predictable, due to their pharmacokinetic and pharmacodynamic properties, while others, unfortunately, are idiosyncratic. Genetic factors may also influence patient susceptibility to DILI and myopathy in the case of statins. This review will first discuss the role of statins in cardiovascular disease treatment and prevention and the underlying mechanisms of action. Furthermore, to explore the susceptibility of statin-induced adverse events such as myopathy and hepatotoxicity, it will then focus on the recent Genome-Wide Association Studies (GWAS) concerning the transporter genes, Cytochrome P450 (CYP), organic anion-transporting polypeptide (OATP) and ABCB1 and ABCC1, which seem to play a role in the development of clinically relevant adverse events. Finally, we appraise the evidence for and against the use of statins in metabolic syndrome and in HCV-infected patients, in terms of their safety and efficacy in cardiovascular events.

scholarly journals X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters

Genetics ◽  
2021 ◽  
Author(s):  
Thomas D Brekke ◽  
Emily C Moore ◽  
Shane C Campbell-Staton ◽  
Colin M Callahan ◽  
Zachary A Cheviron ◽  
...  
Keyword(s):  
Gene Expression ◽  
X Chromosome ◽  
Regulatory Networks ◽  
Mammalian Species ◽  
Strongly Correlated ◽  
Placental Development ◽  
Substitution Lines ◽  
Genome Wide ◽  
Highly Sensitive ◽  
First And Second Generation

AbstractEmbryonic development in mammals is highly sensitive to changes in gene expression within the placenta. The placenta is also highly enriched for genes showing parent-of-origin or imprinted expression, which is predicted to evolve rapidly in response to parental conflict. However, little is known about the evolution of placental gene expression, or if divergence of placental gene expression plays an important role in mammalian speciation. We used crosses between two species of dwarf hamsters (Phodopus sungorus and Phodopus campbelli) to examine the genetic and regulatory underpinnings of severe placental overgrowth in their hybrids. Using quantitative genetic mapping and mitochondrial substitution lines, we show that overgrowth of hybrid placentas was primarily caused by genetic differences on the maternally inherited P. sungorus X chromosome. Mitochondrial interactions did not contribute to abnormal hybrid placental development, and there was only weak correspondence between placental disruption and embryonic growth. Genome-wide analyses of placental transcriptomes from the parental species and first- and second-generation hybrids revealed a central group of co-expressed X-linked and autosomal genes that were highly enriched for maternally biased expression. Expression of this gene network was strongly correlated with placental size and showed widespread misexpression dependent on epistatic interactions with X-linked hybrid incompatibilities. Collectively, our results indicate that the X chromosome is likely to play a prominent role in the evolution of placental gene expression and the accumulation of hybrid developmental barriers between mammalian species.

scholarly journals Epigenomic Analysis of RAD51 ChIP-seq Data Reveals cis-regulatory Elements Associated with Autophagy in Cancer Cell Lines

Cancers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2547
Author(s):  
Keunsoo Kang ◽  
Yoonjung Choi ◽  
Hyeonjin Moon ◽  
Chaelin You ◽  
Minjin Seo ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Homologous Recombination ◽  
Cell Lines ◽  
Regulatory Elements ◽  
Binding Motif ◽  
Genome Wide ◽  
E Box ◽  
Autophagy Pathway ◽  
Mcf 7

RAD51 is a recombinase that plays a pivotal role in homologous recombination. Although the role of RAD51 in homologous recombination has been extensively studied, it is unclear whether RAD51 can be involved in gene regulation as a co-factor. In this study, we found evidence that RAD51 may contribute to the regulation of genes involved in the autophagy pathway with E-box proteins such as USF1, USF2, and/or MITF in GM12878, HepG2, K562, and MCF-7 cell lines. The canonical USF binding motif (CACGTG) was significantly identified at RAD51-bound cis-regulatory elements in all four cell lines. In addition, genome-wide USF1, USF2, and/or MITF-binding regions significantly coincided with the RAD51-associated cis-regulatory elements in the same cell line. Interestingly, the promoters of genes associated with the autophagy pathway, such as ATG3 and ATG5, were significantly occupied by RAD51 and regulated by RAD51 in HepG2 and MCF-7 cell lines. Taken together, these results unveiled a novel role of RAD51 and provided evidence that RAD51-associated cis-regulatory elements could possibly be involved in regulating autophagy-related genes with E-box binding proteins.

scholarly journals VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide

Cell Reports ◽  
2021 ◽  
Vol 34 (3) ◽  
pp. 108629
Author(s):  
Kathrin Leppek ◽  
Gun Woo Byeon ◽  
Kotaro Fujii ◽  
Maria Barna
Keyword(s):  
Rna Seq ◽  
Expansion Segment ◽  
Genome Wide

scholarly journals Distinct regulation of hippocampal neuroplasticity and ciliary genes by corticosteroid receptors

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Karen R. Mifsud ◽  
Clare L. M. Kennedy ◽  
Silvia Salatino ◽  
Eshita Sharma ◽  
Emily M. Price ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Glucocorticoid Receptors ◽  
Acute Stress ◽  
Circadian Variation ◽  
Rna Seq ◽  
Physiological Regulation ◽  
Behavioural Adaptation ◽  
Neuronal Progenitor ◽  
Genome Wide ◽  
Transcriptional Changes

AbstractGlucocorticoid hormones (GCs) — acting through hippocampal mineralocorticoid receptors (MRs) and glucocorticoid receptors (GRs) — are critical to physiological regulation and behavioural adaptation. We conducted genome-wide MR and GR ChIP-seq and Ribo-Zero RNA-seq studies on rat hippocampus to elucidate MR- and GR-regulated genes under circadian variation or acute stress. In a subset of genes, these physiological conditions resulted in enhanced MR and/or GR binding to DNA sequences and associated transcriptional changes. Binding of MR at a substantial number of sites however remained unchanged. MR and GR binding occur at overlapping as well as distinct loci. Moreover, although the GC response element (GRE) was the predominant motif, the transcription factor recognition site composition within MR and GR binding peaks show marked differences. Pathway analysis uncovered that MR and GR regulate a substantial number of genes involved in synaptic/neuro-plasticity, cell morphology and development, behavior, and neuropsychiatric disorders. We find that MR, not GR, is the predominant receptor binding to >50 ciliary genes; and that MR function is linked to neuronal differentiation and ciliogenesis in human fetal neuronal progenitor cells. These results show that hippocampal MRs and GRs constitutively and dynamically regulate genomic activities underpinning neuronal plasticity and behavioral adaptation to changing environments.

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