scholarly journals Identifying stress responsive genes using overlapping communities in co-expression networks

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Camila Riccio-Rengifo ◽  
Jorge Finke ◽  
Camilo Rocha
Keyword(s):  
Salt Stress ◽  
Target Genes ◽  
Specific Treatment ◽  
Search Space ◽  
Shoot Biomass ◽  
Lasso Regression ◽  
Overlapping Communities ◽  
Regulatory Domains ◽  
Treatment Conditions ◽  
Highly Sensitive

Abstract Background This paper proposes a workflow to identify genes that respond to specific treatments in plants. The workflow takes as input the RNA sequencing read counts and phenotypical data of different genotypes, measured under control and treatment conditions. It outputs a reduced group of genes marked as relevant for treatment response. Technically, the proposed approach is both a generalization and an extension of WGCNA. It aims to identify specific modules of overlapping communities underlying the co-expression network of genes. Module detection is achieved by using Hierarchical Link Clustering. The overlapping nature of the systems’ regulatory domains that generate co-expression can be identified by such modules. LASSO regression is employed to analyze phenotypic responses of modules to treatment. Results The workflow is applied to rice (Oryza sativa), a major food source known to be highly sensitive to salt stress. The workflow identifies 19 rice genes that seem relevant in the response to salt stress. They are distributed across 6 modules: 3 modules, each grouping together 3 genes, are associated to shoot K content; 2 modules of 3 genes are associated to shoot biomass; and 1 module of 4 genes is associated to root biomass. These genes represent target genes for the improvement of salinity tolerance in rice. Conclusions A more effective framework to reduce the search-space for target genes that respond to a specific treatment is introduced. It facilitates experimental validation by restraining efforts to a smaller subset of genes of high potential relevance.

scholarly journals MES7 Modulates Seed Germination via Regulating Salicylic Acid Content in Arabidopsis

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 903
Author(s):  
Wenrui Gao ◽  
Yan Liu ◽  
Juan Huang ◽  
Yaqiu Chen ◽  
Chen Chen ◽  
...  
Keyword(s):  
Salicylic Acid ◽  
Salt Stress ◽  
Abiotic Stress ◽  
Seed Germination ◽  
Environmental Conditions ◽  
Acid Content ◽  
Hydrolytic Enzyme ◽  
Stress Conditions ◽  
Transitional Period ◽  
Highly Sensitive

Seed germination is an important phase transitional period of angiosperm plants during which seeds are highly sensitive to different environmental conditions. Although seed germination is under the regulation of salicylic acid (SA) and other hormones, the molecular mechanism underlying these regulations remains mysterious. In this study, we determined the expression of SA methyl esterase (MES) family genes during seed germination. We found that MES7 expression decreases significantly in imbibed seeds, and the dysfunction of MES7 decreases SA content. Furthermore, MES7 reduces and promotes seed germination under normal and salt stress conditions, respectively. The application of SA restores the seed germination deficiencies of mes7 mutants under different conditions. Taking together, our observations uncover a MeSA hydrolytic enzyme, MES7, regulates seed germination via altering SA titer under normal and abiotic stress conditions.

scholarly journals Post-ejaculation thermal stress causes changes to the RNA profile of sperm in an external fertilizer

2020 ◽  
Vol 287 (1938) ◽  
pp. 20202147
Author(s):  
Rowan A. Lymbery ◽  
Jonathan P. Evans ◽  
W. Jason Kennington
Keyword(s):  
Stress Responses ◽  
Messenger Rna ◽  
Mytilus Galloprovincialis ◽  
Target Genes ◽  
Sperm Function ◽  
Mrna Levels ◽  
Embryo Viability ◽  
Paired Samples ◽  
Degradation Rates ◽  
Highly Sensitive

Sperm cells experience considerable post-ejaculation environmental variation. However, little is known about whether this affects their molecular composition, probably owing to the assumption that sperm are transcriptionally quiescent. Nevertheless, recent evidence shows sperm have distinct RNA profiles that affect fertilization and embryo viability. Moreover, RNAs are expected to be highly sensitive to extracellular changes. One such group of RNAs are heat shock protein (hsp) transcripts, which function in stress responses and are enriched in sperm. Here, we exploit the experimental tractability of the mussel Mytilus galloprovincialis by exposing paired samples of ejaculated sperm to ambient (19°C) and increased (25°C) temperatures, then measure (i) sperm motility phenotypes, and (ii) messenger RNA (mRNA) levels of two target genes ( hsp70 and hsp90 ) and several putative reference genes. We find no phenotypic changes in motility, but reduced mRNA levels for hsp90 and the putative reference gene gapdh at 25°C. This could reflect either decay of specific RNAs, or changes in translation and degradation rates of transcripts to maintain sperm function under stress. These findings represent, to our knowledge, the first evidence for changes in sperm RNA profiles owing to post-ejaculation environments, and suggest that sperm may be more vulnerable to stress from rising temperatures than currently thought.

scholarly journals Notch family members follow stringent requirements for intracellular domain dimerization at sequence-paired sites

2020 ◽  
Author(s):  
Jacob J. Crow ◽  
Allan R. Albig
Keyword(s):  
Transcriptional Activation ◽  
Target Genes ◽  
Regulatory Mechanism ◽  
Family Members ◽  
Regulatory Function ◽  
Specific Nature ◽  
Intracellular Domain ◽  
Notch Intracellular Domain ◽  
Highly Sensitive ◽  
Cellular Identity

ABSTRACTNotch signaling is essential for multicellular life, regulating core functions such as cellular identity, differentiation, and fate. These processes require highly sensitive systems to avoid going awry, and one such regulatory mechanism is through Notch intracellular domain dimerization. Select Notch target genes contain sequence-paired sites (SPS); motifs in which two Notch transcriptional activation complexes can bind and interact through Notch’s ankyrin domain, resulting in enhanced transcriptional activation. This mechanism has been mostly studied through Notch1, and to date, the abilities of the other Notch family members have been left unexplored. Through the utilization of minimalized, SPS-driven luciferase assays, we were able to test the functional capacity of Notch dimers. Here we show that each family member is capable of dimerization-induced signaling, following the same stringent requirements as seen with Notch1. Interestingly, we identified a mechanical difference between canonical and cryptic SPSs, leading to differences in their dimerization-induced regulation. Finally, we profiled the Notch family members’ SPS gap distance preferences and found that they all prefer a 16-nucleotide gap, with little room for variation. In summary, this work highlights the potent and highly specific nature of Notch dimerization and refines the scope of this regulatory function.

scholarly journals P476SREBF1, SREBF2 and their target genes expression is different in wistar and SHR rats under high cholesterol treatment conditions

2014 ◽  
Vol 103 (suppl 1) ◽  
pp. S87.1-S87
Author(s):  
HV Portnichenko ◽  
SV Goncharov ◽  
LV Tumanovska ◽  
DO Stroy ◽  
OS Moibenko ◽  
...  
Keyword(s):  
Target Genes ◽  
Shr Rats ◽  
High Cholesterol ◽  
Treatment Conditions ◽  
Cholesterol Treatment ◽  
Genes Expression

scholarly journals Multiple Regulatory Domains of IRF-5 Control Activation, Cellular Localization, and Induction of Chemokines That Mediate Recruitment of T Lymphocytes

2002 ◽  
Vol 22 (16) ◽  
pp. 5721-5740 ◽  
Author(s):  
Betsy J. Barnes ◽  
Merrill J. Kellum ◽  
Ann E. Field ◽  
Paula M. Pitha
Keyword(s):  
Cellular Localization ◽  
Target Genes ◽  
Nuclear Translocation ◽  
Transient Transfection Assay ◽  
Nuclear Localization Signals ◽  
Regulatory Domains ◽  
Inflammatory Protein ◽  
Infected Cells ◽  
Simplex Virus ◽  
And Function

ABSTRACT Transcription factors of the interferon regulatory factor (IRF) family have been identified as critical mediators of early inflammatory gene transcription in infected cells. We recently determined that, besides IRF-3 and IRF-7, IRF-5 serves as a direct transducer of virus-mediated signaling. In contrast to that mediated by the other two IRFs, IRF-5-mediated activation is virus specific. We show that, in addition to Newcastle disease virus (NDV) infection, vesicular stomatitis virus (VSV) and herpes simplex virus type 1 (HSV-1) infection activates IRF-5, leading to the induction of IFNA gene subtypes that are distinct from subtypes induced by NDV. The IRF-5-mediated stimulation of inflammatory genes is not limited to IFNA since in BJAB/IRF-5-expressing cells IRF-5 stimulates transcription of RANTES, macrophage inflammatory protein 1β, monocyte chemotactic protein 1, interleukin-8, and I-309 genes in a virus-specific manner. By transient- transfection assay, we identified constitutive-activation (amino acids [aa] 410 to 489) and autoinhibitory (aa 490 to 539) domains in the IRF-5 polypeptide. We identified functional nuclear localization signals (NLS) in the amino and carboxyl termini of IRF-5 and showed that both of these NLS are sufficient for nuclear translocation and retention in infected cells. Furthermore, we demonstrated that serine residues 477 and 480 play critical roles in the response to NDV infection. Mutation of these residues from serine to alanine dramatically decreased phosphorylation and resulted in a substantial loss of IRF-5 transactivation in infected cells. Thus, this study defines the regulatory phosphorylation sites that control the activity of IRF-5 in NDV-infected cells and provides further insight into the structure and function of IRF-5. It also shows that the range of IRF-5 immunoregulatory target genes includes members of the cytokine and chemokine superfamilies.

scholarly journals Towards a Sustainable Agriculture: Strategies Involving Phytoprotectants against Salt Stress

Agronomy ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 194 ◽  
Author(s):  
José Ramón Acosta-Motos ◽  
Consuelo Penella ◽  
José A. Hernández ◽  
Pedro Díaz-Vivancos ◽  
María Jesús Sánchez-Blanco ◽  
...  
Keyword(s):  
Salt Stress ◽  
Mycorrhizal Fungi ◽  
Arbuscular Mycorrhizal ◽  
Plant Growth Promoting Rhizobacteria ◽  
Antioxidant Metabolism ◽  
Water Demands ◽  
Industrial Sectors ◽  
Treatment Conditions ◽  
Plant Growth Promoting ◽  
Related Compounds

Salinity is one of the main constraints for agriculture productivity worldwide. This important abiotic stress has worsened in the last 20 years due to the increase in water demands in arid and semi-arid areas. In this context, increasing tolerance of crop plants to salt stress is needed to guarantee future food supply to a growing population. This review compiles knowledge on the use of phytoprotectants of microbial origin (arbuscular mycorrhizal fungi and plant growth-promoting rhizobacteria), osmoprotectants, melatonin, phytohormones and antioxidant metabolism-related compounds as alleviators of salt stress in numerous plant species. Phytoprotectants are discussed in detail, including their nature, applicability, and role in the plant in terms of physiological and phenotype effects. As a result, increased crop yield and crop quality can be achieved, which in turn positively impact food security. Herein, efforts from academic and industrial sectors should focus on defining the treatment conditions and plant-phytoprotectant associations providing higher benefits.

scholarly journals Overexpression of GSK3-like Kinase 5 (OsGSK5) in rice (Oryza sativa) enhances salinity tolerance in part via preferential carbon allocation to root starch

2017 ◽  
Vol 44 (7) ◽  
pp. 705 ◽  
Author(s):  
Maysaya Thitisaksakul ◽  
Maria C. Arias ◽  
Shaoyun Dong ◽  
Diane M. Beckles
Keyword(s):  
Oryza Sativa ◽  
Salt Stress ◽  
Salinity Tolerance ◽  
Carbon Allocation ◽  
Oryza Sativa L ◽  
Rice Seedling ◽  
Shoot Biomass ◽  
Salt Shock ◽  
Seedling Roots ◽  
Root Starch

Rice (Oryza sativa L.) is very sensitive to soil salinity. To identify endogenous mechanisms that may help rice to better survive salt stress, we studied a rice GSK3-like isoform (OsGSK5), an orthologue of a Medicago GSK3 previously shown to enhance salinity tolerance in Arabidopsis by altering carbohydrate metabolism. We wanted to determine whether OsGSK5 functions similarly in rice. OsGSK5 was cloned and sequence, expression, evolutionary and functional analyses were conducted. OsGSK5 was expressed highest in rice seedling roots and was both salt and sugar starvation inducible in this tissue. A short-term salt-shock (150 mM) activated OsGSK5, whereas moderate (50 mM) salinity over the same period repressed the transcript. OsGSK5 response to salinity was due to an ionic effect since it was unaffected by polyethylene glycol. We engineered a rice line with 3.5-fold higher OsGSK5 transcript, which better tolerated cultivation on saline soils (EC = 8 and 10 dS m–2). This line produced more panicles and leaves, and a higher shoot biomass under high salt stress than the control genotypes. Whole-plant 14C-tracing and correlative analysis of OsGSK5 transcript with eco-physiological assessments pointed to the accelerated allocation of carbon to the root and its deposition as starch, as part of the tolerance mechanism.

Identification of ERG Specific Target Genes by Genome-Wide Screening in T-Lymphoblastic Leukemia

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 3788-3788
Author(s):  
Liliana H Mochmann ◽  
Konrad Neumann ◽  
Juliane Bock ◽  
Jutta Ortiz Tanchez ◽  
Arend Bohne ◽  
...  
Keyword(s):  
Target Genes ◽  
Lymphoblastic Leukemia ◽  
Specific Treatment ◽  
P Value ◽  
Dna Templates ◽  
Genome Wide ◽  
A Genome ◽  
On Chip ◽  
T Cell Leukemogenesis ◽  
The Impact

Abstract The Ets related gene, ERG, encodes a transcription factor with a vital role in hematopoiesis. Recent findings have shown that ERG knockout mice require a minimum of one functional allele to ensure embryonic blood development and adult stem cell maintenance. Moreover, it was earlier reported that enforced expression of ERG induced oncogenic transformation in 3T3 cells. Overexpression of ERG, observed in a subset of acute T-lymphoblastic and acute myeloid leukemia patients, was associated with an inferior outcome. However, the impact of ERG contributing to this unfavourable phenotype has yet to be determined, as downstream targets of ERG in leukemia remain unknown. Herein, we conducted a genome-wide analysis of ERG target genes in T-lymphoblastic leukemia. Chromatin immunoprecipitation-on-chip array (ChIP-on-chip) analyses were performed using two ERG specific antibodies for the enrichment of ERG-bound DNA templates in T-lymphoblastic leukemia cells (Jurkat) with input DNA or IgG precipitated DNA as controls. Enriched DNA templates and control DNA were differentially labelled and co-hybridized to high resolution promoter chip arrays with 50–75mer probes (770,000) representing 29,000 annotated human transcripts (NimbleGen). Based on two independent ChIP-on-chip assays, bioinformatic analysis (ACME) yielded statistically significant enriched peaks (using a sliding window of 1000 bp, and a P-value < 0.0001) identifying promoter regions of 365 potential ERG target genes. From these genes, clustering by functional annotation was performed using the DAVID database and subsequently genes related to leukemia were further selected for quantitative PCR validation. The design of promoter primers included the highly conserved ETS GGAA DNA binding site. Genes with greater than two-fold enrichment (ERG ChIP versus control) included WNT2 (17-fold), OLIG2 (14-fold), WNT11 (7-fold), CCND1 (5-fold), WNT9A (4-fold), CD7 (3-fold), EPO (3-fold), ERBB4 (3-fold), RPBJL (3-fold), TRADD (3-fold), PIWIL1 (2-fold), TNFRSF25 (2-fold), TWIST1 (2-fold), and HDAC4 (2-fold). Interestingly, enriched target genes involved in developmental processes (WNT2, WNT9A, WNT11, TWIST1, PIWIL1, ERBB4, and OLIG2) have shown oncogenic potential when mutated or overexpressed. Thus, we hypothesize that overexpression of ERG may contribute to T-cell leukemogenesis by the deregulation of these oncogenic targets. Further disclosure of ERG directed downstream pathways may contribute to the design of specific treatment strategies (such as WNT inhibitors) with particular effectiveness in ERG deregulated leukemia.

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