scholarly journals Genome-Wide Identification, Expression and Functional Analysis Reveal the Involvement of FCS-Like Zinc Finger Gene Family in Submergence Response in Rice

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Yamei Ma ◽  
Junliang Zhao ◽  
Hua Fu ◽  
Tifeng Yang ◽  
Jingfang Dong ◽  
...  
Keyword(s):  
Zinc Finger ◽  
Transcriptional Activation ◽  
Genome Wide ◽  
Comprehensive Information ◽  
Submergence Stress ◽  
A Genome ◽  
Poor Seed ◽  
Early Seedling ◽  
Cultivation Practice

Abstract Background Direct seeding is an efficient rice cultivation practice. However, its application is often limited due to O2 deficiency following submergence, leading to poor seed germination, seedling establishment, and consequently yield loss. Identification of genes associated with tolerance to submergence and understanding their regulatory mechanisms is the fundamental way to address this problem. Unfortunately, the molecular mechanism of rice response to submergence stress is still not well understood. Results Here, we have performed a genome-wide identification of FCS-like zinc finger (FLZ) proteins and assessed their involvement in submergence response in rice. We identified 29 FLZ genes in rice, and the expression analysis revealed that several genes actively responded to submergence stress. Eight OsFLZ proteins interact with SnRK1A. As a case study, we demonstrated that OsFLZ18 interacted with SnRK1A and inhibited the transcriptional activation activity of SnRK1A in modulating the expression of its target gene αAmy3, a positive regulator in rice flooding tolerance. In line with this, OsFLZ18-overexpression lines displayed retarded early seedling growth and shorter coleoptile following submergence. Conclusions These data provide the most comprehensive information of OsFLZ genes in rice, and highlight their roles in rice submergence response.

scholarly journals Low temperature triggers genome-wide hypermethylation of transposable elements and centromeres in maize

2019 ◽  
Author(s):  
Zeineb Achour ◽  
Johann Joets ◽  
Martine Leguilloux ◽  
Hélène Sellier ◽  
Jean-Philippe Pichon ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transposable Elements ◽  
Transcriptional Activation ◽  
Gene Expression Regulation ◽  
Environmental Cues ◽  
Specific Response ◽  
Genome Wide ◽  
A Genome ◽  
Response To Stress ◽  
Context Specific

ABSTRACTCharacterizing the molecular processes developed by plants to respond to environmental cues is a major task to better understand local adaptation. DNA methylation is a chromatin mark involved in the transcriptional silencing of transposable elements (TEs) and gene expression regulation. While the molecular bases of DNA methylation regulation are now well described, involvement of DNA methylation in plant response to environmental cues remains poorly characterized. Here, using the TE-rich maize genome and analyzing methylome response to prolonged cold at the chromosome and feature scales, we investigate how genomic architecture affects methylome response to stress in a cold-sensitive genotype. Interestingly, we show that cold stress induces a genome-wide methylation increase through the hypermethylation of TE sequences and centromeres. Our work highlights a cytosine context-specific response of TE methylation that depends on TE types, chromosomal location and proximity to genes. The patterns observed can be explained by the parallel transcriptional activation of multiple DNA methylation pathways that methylate TEs in the various chromatin locations where they reside. Our results open new insights into the possible role of genome-wide DNA methylation in phenotypic response to stress.

scholarly journals Plant genome response to incoming coding sequences: stochastic transcriptional activation independent of chromatin configuration

2020 ◽  
Author(s):  
Soichirou Satoh ◽  
Takayuki Hata ◽  
Naoto Takada ◽  
Makoto Tachikawa ◽  
Mitsuhiro Matsuo ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Cultured Cells ◽  
Plant Genome ◽  
Chromosomal Locus ◽  
Coding Sequences ◽  
Conventional View ◽  
Genome Wide ◽  
A Genome ◽  
Integration Sites ◽  
Chromatin Configuration

ABSTRACTHorizontal gene transfer can occur between phylogenetically distant organisms, such as prokaryotes and eukaryotes. In these cases, how do the translocated genes acquire transcriptional competency in the alien genome environment? According to the conventional view, specific loci of the eukaryotic genome are thought to provide transcriptional competency to the incoming coding sequences. To examine this possibility, we randomly introduced the promoterless luciferase (LUC)-coding sequences into the genome of Arabidopsis thaliana cultured cells and performed a genome-wide “transgene location vs. expression” scan. We found that one-third of the 4,504 mapped LUC genes were transcribed. However, only 10% of them were explained by conventional transcriptional fusions with the annotated genes, and the remainder of the genes exhibited novel transcription that occurred independently of the chromatin configuration or transcriptional activity inherent to the given chromosomal locus; rather, their transcriptional activation occurred stochastically at about 30% of each insertion event, but independent of the integration sites. We termed this activation phenomenon as an integration-dependent stochastic transcriptional activation, a new type of response of the plant genome to incoming coding sequences. We discuss the possible roles of this phenomenon in the evolution of eukaryotic genomes.

scholarly journals Genome urbanization: Clusters of topologically co-regulated genes delineate functional compartments in the genome of S. cerevisiae

2016 ◽  
Author(s):  
Maria Tsochatzidou ◽  
Maria Malliarou ◽  
Nikolas Papanikolaou ◽  
Joaquim Roca ◽  
Christoforos Nikolaou
Keyword(s):  
Transcriptional Activation ◽  
Topoisomerase Ii ◽  
Thermal Inactivation ◽  
Nuclear Periphery ◽  
Gene Clusters ◽  
Dna Supercoiling ◽  
Regulatory Control ◽  
Genome Wide ◽  
A Genome ◽  
Consistent Response

AbstractThe eukaryotic genome evolves under the dual constraint of maintaining co-ordinated gene transcription and performing effective DNA replication and cell division, the coupling of which brings about inevitable DNA topological tension. DNA supercoiling is resolved and, in some cases, even harnessed by the genome through the function of DNA topoisomerases, as has been shown in the concurrent transcriptional activation and suppression of genes upon transient deactivation of topoisomerase II (topoII). By analyzing a genome wide run-on experiment upon thermal inactivation of topoII in S.cerevisiae. we were able to define 116 gene clusters of consistent response (either positive or negative) to topological stress. A comprehensive analysis of these topologically co-regulated gene clusters revealed pronounced preferences regarding their functional, regulatory and structural attributes. Genes that negatively respond to topological stress, are positioned in gene-dense pericentromeric regions, are more conserved and associated to essential functions, while up-regulated gene clusters are preferentially located in the gene-sparse nuclear periphery, associated with secondary functions and under complex regulatory control. We propose that evolves with a core of essential genes occupying a compact genomic “old town”, whereas more recently acquired, condition-specific genes tend to be located in a more spacious “suburban” genomic periphery.

scholarly journals ZINC-FINGER interactions mediate transcriptional regulation of hypocotyl growth in Arabidopsis

2018 ◽  
Vol 115 (19) ◽  
pp. E4503-E4511 ◽  
Author(s):  
Giorgio Perrella ◽  
Mhairi L. H. Davidson ◽  
Liz O’Donnell ◽  
Ana-Marie Nastase ◽  
Pawel Herzyk ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Zinc Finger ◽  
Transcriptional Regulators ◽  
Hypocotyl Elongation ◽  
Transcriptional Level ◽  
Hypocotyl Growth ◽  
Environmental Signals ◽  
Genome Wide ◽  
A Genome

Integration of environmental signals and interactions among photoreceptors and transcriptional regulators is key in shaping plant development. TANDEM ZINC-FINGER PLUS3 (TZP) is an integrator of light and photoperiodic signaling that promotes flowering in Arabidopsis thaliana. Here we elucidate the molecular role of TZP as a positive regulator of hypocotyl elongation. We identify an interacting partner for TZP, the transcription factor ZINC-FINGER HOMEODOMAIN 10 (ZFHD10), and characterize its function in coregulating the expression of blue-light–dependent transcriptional regulators and growth-promoting genes. By employing a genome-wide approach, we reveal that ZFHD10 and TZP coassociate with promoter targets enriched in light-regulated elements. Furthermore, using a targeted approach, we show that ZFHD10 recruits TZP to the promoters of key coregulated genes. Our findings not only unveil the mechanism of TZP action in promoting hypocotyl elongation at the transcriptional level but also assign a function to an uncharacterized member of the ZFHD transcription factor family in promoting plant growth.

scholarly journals Genome-wide (ChIP-seq) Identification of Target Genes Regulated by WRKY33 During Submergence Stress in Arabidopsis

2020 ◽  
Author(s):  
Zhang Junlin ◽  
Liu bao ◽  
Song Yan ◽  
Chen yang ◽  
Fu jiao ◽  
...  
Keyword(s):  
Stress Responses ◽  
Crop Production ◽  
Target Genes ◽  
Reduction Process ◽  
Binding Motif ◽  
Genome Wide ◽  
Submergence Stress ◽  
A Genome ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Transgenic Lines

Abstract Background: Hypoxia induced by flooding causes significant losses to crop production almost every year. However, the molecular network of hypoxia signaling pathway is still poorly understood. According to previous studies, transgenic plants overexpressing the WRKY33 gene showed enhanced resistance to submergence stress. Thus, the transcription factor WRKY33 may regulate a series of target genes in response to submergence. Here, to determine the putative downstream targets of WRKY33 at a genome-wide scale in Arabidopsis thaliana, we performed the chromatin immunoprecipitation sequencing (ChIP-seq) using 35S:FLAG-WRKY33 overexpression transgenic lines (WRKY33-OE) upon 24 hours of submergence treatment.Results: Using ChIP-seq data, we identified a total of 104 WRKY33-binding genes under submergence treatment (WRKY33BGHs). Most of the WRKY33BGHs are involved in the oxidation-reduction process, programmed cell death in response to reactive oxygen species, lipid biosynthesis process, and other processes related to stress responses. Moreover, the major motif identified in the WRKY33BGHs promoters is a new cis-element, TCTCTC (we named it as “TC box”). This cis-element is different from the previously known W box for WRKY33. Further qPCR experiments verified that genes carrying this motif in their promoters could be regulated by WRKY33 upon submergence treatment.Conclusions: Our study has identified a new putative binding motif of WRKY33 and recovered numerous previously unknown target genes of WRKY33 during submergence stress. The WRKY33 gene positively participates in flooding response probably by transcriptional regulation of the downstream hypoxia-related target genes via a “TC box”.

scholarly journals Identification and Analysis of the AP2 Subfamily Transcription Factors in the Pecan (Carya illinoinensis)

2021 ◽  
Vol 22 (24) ◽  
pp. 13568
Author(s):  
Zhengfu Yang ◽  
Hongmiao Jin ◽  
Junhao Chen ◽  
Caiyun Li ◽  
Jiani Wang ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Expression Patterns ◽  
Carya Illinoinensis ◽  
Expression Levels ◽  
Cis Acting ◽  
Similar Expression ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search ◽  
Ethylene Responsive Factor

The AP2 transcriptional factors (TFs) belong to the APETALA2/ ethylene-responsive factor (AP2/ERF) superfamily and regulate various biological processes of plant growth and development, as well as response to biotic and abiotic stresses. However, genome-wide research on the AP2 subfamily TFs in the pecan (Carya illinoinensis) is rarely reported. In this paper, we identify 30 AP2 subfamily genes from pecans through a genome-wide search, and they were unevenly distributed on the pecan chromosomes. Then, a phylogenetic tree, gene structure and conserved motifs were further analyzed. The 30 AP2 genes were divided into euAP2, euANT and basalANT three clades. Moreover, the cis-acting elements analysis showed many light responsive elements, plant hormone-responsive elements and abiotic stress responsive elements are found in CiAP2 promoters. Furthermore, a qPCR analysis showed that genes clustered together usually shared similar expression patterns in euAP2 and basalANT clades, while the expression pattern in the euANT clade varied greatly. In developing pecan fruits, CiAP2-5, CiANT1 and CiANT2 shared similar expression patterns, and their expression levels decreased with fruit development. CiANT5 displayed the highest expression levels in developing fruits. The subcellular localization and transcriptional activation activity assay demonstrated that CiANT5 is located in the nucleus and functions as a transcription factor with transcriptional activation activity. These results help to comprehensively understand the pecan AP2 subfamily TFs and lay the foundation for further functional research on pecan AP2 family genes.

scholarly journals Identification and Functional Analysis of the CLAVATA3/EMBRYO SURROUNDING REGION (CLE) Gene Family in Wheat

2019 ◽  
Vol 20 (17) ◽  
pp. 4319 ◽  
Author(s):  
Li ◽  
Liu ◽  
Xia ◽  
Li ◽  
Niu ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Cell Proliferation And Differentiation ◽  
Genome Wide ◽  
Comprehensive Information ◽  
Cle Peptides ◽  
A Genome ◽  
Cle Peptide ◽  
Proliferation And Differentiation ◽  
Modified Peptides ◽  
Duplication Events

CLAVATA3/EMBRYO SURROUNDING REGION (CLE) peptides are post-translationally cleaved and modified peptides from their corresponding pre-propeptides. Although they are only 12 to 13 amino acids in length, they are important ligands involved in regulating cell proliferation and differentiation in plant shoots, roots, vasculature, and other tissues. They function by interacting with their corresponding receptors. CLE peptides have been studied in many plants, but not in wheat. We identified 104 TaCLE genes in the wheat genome based on a genome-wide scan approach. Most of these genes have homologous copies distributed on sub-genomes A, B, and D. A few genes are derived from tandem duplication and segmental duplication events. Phylogenetic analysis revealed that TaCLE genes can be divided into five different groups. We obtained functional characterization of the peptides based on the evolutionary relationships among the CLE peptide families of wheat, rice, and Arabidopsis, and expression pattern analysis. Using chemically synthesized peptides (TaCLE3p and TaCLE34p), we found that TaCLE3 and TaCLE34 play important roles in regulating wheat and Arabidopsis root development, and wheat stem development. Overexpression analysis of TaCLE3 in Arabidopsis revealed that TaCLE3 not only affects the development of roots and stems, but also affects the development of leaves and fruits. These data represent the first comprehensive information on TaCLE family members.

scholarly journals Identification and characterization of Hoxa9 binding sites in hematopoietic cells

Blood ◽  
2012 ◽  
Vol 119 (2) ◽  
pp. 388-398 ◽  
Author(s):  
Yongsheng Huang ◽  
Kajal Sitwala ◽  
Joel Bronstein ◽  
Daniel Sanders ◽  
Monisha Dandekar ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Binding Sites ◽  
Enhancer Activity ◽  
Transcription Start Sites ◽  
Genome Wide ◽  
A Genome ◽  
Evolutionarily Conserved ◽  
P300 Binding ◽  
Histone H3k4

The clustered homeobox proteins play crucial roles in development, hematopoiesis, and leukemia, yet the targets they regulate and their mechanisms of action are poorly understood. Here, we identified the binding sites for Hoxa9 and the Hox cofactor Meis1 on a genome-wide level and profiled their associated epigenetic modifications and transcriptional targets. Hoxa9 and the Hox cofactor Meis1 cobind at hundreds of highly evolutionarily conserved sites, most of which are distant from transcription start sites. These sites show high levels of histone H3K4 monomethylation and CBP/P300 binding characteristic of enhancers. Furthermore, a subset of these sites shows enhancer activity in transient transfection assays. Many Hoxa9 and Meis1 binding sites are also bound by PU.1 and other lineage-restricted transcription factors previously implicated in establishment of myeloid enhancers. Conditional Hoxa9 activation is associated with CBP/P300 recruitment, histone acetylation, and transcriptional activation of a network of proto-oncogenes, including Erg, Flt3, Lmo2, Myb, and Sox4. Collectively, this work suggests that Hoxa9 regulates transcription by interacting with enhancers of genes important for hematopoiesis and leukemia.

Identification of stress repressive zinc finger gene family and its expression analysis in rice under abiotic constraints

2020 ◽  
Author(s):  
Chao Zhang ◽  
Yanning Tan ◽  
Jemaa Essemine ◽  
Ni Li ◽  
Zhongxiao Hu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Zinc Finger ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Rt Pcr ◽  
Conserved Domains ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Survey

Abstract Background: Stress repressive zinc finger (SRZ) gene family in rice is one of the plant defense gene families that play a pivotal role in plant growth regulation and development, particularly under stressful conditions. However, there is no genome-wide survey regarding SRZ gene family in rice (OsSRZ) till date. Results: We studied, herein, this gene family by performing a genome-wide screening and we identified 25 OsSRZ gene members using Japonica cultivar as an investigating material. Their chromosome localizations, phylogenetic relationships, genomic structures, conserved domains and promoter cis-regulatory elements were analyzed. Besides, their spatio-temporal expression profiles and expression patterns under various hormones and stress treatments were also assessed. Based on the phylogeny and domain constitution, the OsSRZ gene family was classified into five groups (I-V). Conserved domains analysis demonstrates that OsSRZ proteins contain at least one highly conserved SRZ domain. The analysis of expression patterns of the SRZ gene family reveal that OsSRZ genes display tissue-specific expression patterns at various rice developmental stages and exhibit differential responses to both phytohormones and abiotic stresses. Furthermore, q-RT-PCR analysis reveals that Os SRZ genes exhibit different expression patterns under various abiotic stresses. We notice the presence of a single specific gene considerably or strongly up-regulated for each kind of abiotic stress. Over 12 OsSRZ genes analyzed with q-RT-PCR, solely 4 genes (OsSRZ 1, 2, 10 and 11) were found to be substantially or strongly up-regulated following abiotic stress. Notably, OsSRZ 10 and 11 were up-regulated under heat stress by 7 and 5 times, respectively. However, OsSRZ2 was up-regulated by 7 and 3.5 folds under salt and cold stresses, respectively. Interestingly, OsSRZ1 was up-regulated by about 3~11 times in 24 h following artificial oxidative stress application using 1 mM H2O2 . Conclusions: We deduce that some members of OsSRZ gene family function as abiotic stress marker in rice. At the genomic level and expression pattern, our genome-wide survey could provide promising and valuable insights to widen and strengthen further future investigation by leading a cutting edge research regarding the biological and molecular functions of this gene family.

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