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 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 Genome-Wide Identification of CsATGs in Tea Plant and the Involvement of CsATG8e in Nitrogen Utilization

2020 ◽  
Vol 21 (19) ◽  
pp. 7043
Author(s):  
Wei Huang ◽  
Dan-Ni Ma ◽  
Hong-Ling Liu ◽  
Jie Luo ◽  
Pu Wang ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Woody Species ◽  
Nutrient Utilization ◽  
Tea Plant ◽  
Plant Genome ◽  
Wild Type ◽  
Genome Wide ◽  
A Genome ◽  
Phosphorus And Potassium ◽  
Stage 1

Nitrogen (N) is a macroelement with an indispensable role in the growth and development of plants, and tea plant (Camellia sinensis) is an evergreen perennial woody species with young shoots for harvest. During senescence or upon N stress, autophagy has been shown to be induced in leaves, involving a variety of autophagy-related genes (ATGs), which have not been characterized in tea plant yet. In this study, a genome-wide survey in tea plant genome identified a total of 80 Camellia Sinensis autophagy-related genes, CsATGs. The expression of CsATG8s in the tea plant showed an obvious increase from S1 (stage 1) to S4 (stage 4), especially for CsATG8e. The expression levels of AtATGs (Arabidopsis thaliana) and genes involved in N transport and assimilation were greatly improved in CsATG8e-overexpressed Arabidopsis. Compared with wild type, the overexpression plants showed earlier bolting, an increase in amino N content, as well as a decrease in biomass and the levels of N, phosphorus and potassium. However, the N level was found significantly higher in APER (aerial part excluding rosette) in the overexpression plants relative to wild type. All these results demonstrated a convincing function of CsATG8e in N remobilization and plant development, indicating CsATG8e as a potential gene for modifying plant nutrient utilization.

scholarly journals Pooled genome-wide CRISPR screening for basal and context-specific fitness gene essentiality in Drosophila cells

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Raghuvir Viswanatha ◽  
Zhongchi Li ◽  
Yanhui Hu ◽  
Norbert Perrimon
Keyword(s):  
Cultured Cells ◽  
Growth Conditions ◽  
Vertebrate Lineage ◽  
Site Specific Integration ◽  
Genome Wide ◽  
Dna Libraries ◽  
A Genome ◽  
Context Specific ◽  
A Site ◽  
Drosophila Cells

Genome-wide screens in Drosophila cells have offered numerous insights into gene function, yet a major limitation has been the inability to stably deliver large multiplexed DNA libraries to cultured cells allowing barcoded pooled screens. Here, we developed a site-specific integration strategy for library delivery and performed a genome-wide CRISPR knockout screen in Drosophila S2R+ cells. Under basal growth conditions, 1235 genes were essential for cell fitness at a false-discovery rate of 5%, representing the highest-resolution fitness gene set yet assembled for Drosophila, including 407 genes which likely duplicated along the vertebrate lineage and whose orthologs were underrepresented in human CRISPR screens. We additionally performed context-specific fitness screens for resistance to or synergy with trametinib, a Ras/ERK/ETS inhibitor, or rapamycin, an mTOR inhibitor, and identified key regulators of each pathway. The results present a novel, scalable, and versatile platform for functional genomic screens in invertebrate cells.

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 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.

A Genome-Wide Retroviral Insertional Mutagenesis Screen for Genes Cooperating with Truncated, Oncogenic GATA1s.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2990-2990 ◽  
Author(s):  
Zhe Li ◽  
Jan-Henning Klusmann ◽  
Frank J. Godinho ◽  
Hee-Won Lee ◽  
Dirk Reinhardt ◽  
...  
Keyword(s):  
Cell Lines ◽  
Insertional Mutagenesis ◽  
Fetal Liver ◽  
Myeloproliferative Disorder ◽  
Mutagenesis Screen ◽  
Retroviral Integration ◽  
Genome Wide ◽  
A Genome ◽  
Integration Sites ◽  
Insertional Mutagenesis Screen

Abstract Somatic mutations in the hematopoietic transcription factor GATA1 are found in megakaryoblasts of Down Syndrome (DS) patients with transient myeloproliferative disorder (TMD, or transient leukemia or TL) and the related acute megakaryoblastic leukemia (DS-AMKL, or DS- AML M7). These mutations lead to production of a GATA1 variant (GATA1s) lacking its N-terminal domain. Mice carrying GATA1s mutation have normal adult hematopoiesis. However, during embryonic/fetal development, we have identified a transient population of abnormal yolk sac/fetal liver megakaryocytic progenitors in mutant mice. We proposed that these progenitor cells are the target for transformation in DS-AMKL/TMD. GATA1s mice (either during development or as adults) do not develop myeloproliferative disorder or leukemia. To recapitulate human DS TMD in mice, we bred GATA1s mice to mouse DS models (Ts65Dn and Ts1Cje) and generated GATA1s/DS double mutants. The phenotype of GATA1s/DS mice is not different from that of GATA1s mice, suggesting that these mouse DS models (representing ~166 and 112 trisomic genes on human chromosome 21, respectively, including Runx1, Ets2, and Erg) do not accurately recapitulate the effects of trisomy in DS. To search for genes that cooperate with GATA1s in an unbiased fashion, we established a genome-wide retroviral insertional mutagenesis screen. GATA1s mutant fetal liver progenitors proliferate in culture in the presence of thrombopoietin (Tpo) for about 4–5 weeks. We infected mutant fetal progenitors with MSCV retrovirus and selected in vitro in the presence of Tpo for immortalized cell lines. Retroviral integration sites in these cell lines were determined by Splinkerette PCR, and confirmed by genomic PCR. Genes that were affected by retroviral integration were confirmed by real-time PCR for their elevated expression or knock-down. From the genetic screen performed thus far, we identified two common retroviral integration sites, Evi1 and Prdm16 (PR domain containing 16). Interestingly, Evi1 is also overexpressed in M7 leukemias, though its expression in non-DS M7 leukemia is higher than in DS M7 leukemia. By retroviral overexpression, we have confirmed that ectopic expression of Evi1 in GATA1s mutant fetal progenitors further enhanced proliferation. Currently we are testing the in vivo leukemogenic abilities of these cell lines by transplantation. By this approach, we will identify genes that cooperate with GATA1s in cellular transformation and, thereby, gain insights into the mechanism of leukemogenesis in DS-AMKL/TMD.

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.

scholarly journals Computational and Experimental Tools to Monitor the Changes in Translation Efficiency of Plant mRNA on a Genome-Wide Scale: Advantages, Limitations, and Solutions

2018 ◽  
Vol 20 (1) ◽  
pp. 33 ◽  
Author(s):  
Irina Goldenkova-Pavlova ◽  
Olga Pavlenko ◽  
Orkhan Mustafaev ◽  
Igor Deyneko ◽  
Ksenya Kabardaeva ◽  
...  
Keyword(s):  
Translational Control ◽  
Gene Expression Regulation ◽  
Plant Genome ◽  
Computational Algorithms ◽  
Translation Efficiency ◽  
Translation Control ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Experimental Approaches

The control of translation in the course of gene expression regulation plays a crucial role in plants’ cellular events and, particularly, in responses to environmental factors. The paradox of the great variance between levels of mRNAs and their protein products in eukaryotic cells, including plants, requires thorough investigation of the regulatory mechanisms of translation. A wide and amazingly complex network of mechanisms decoding the plant genome into proteome challenges researchers to design new methods for genome-wide analysis of translational control, develop computational algorithms detecting regulatory mRNA contexts, and to establish rules underlying differential translation. The aims of this review are to (i) describe the experimental approaches for investigation of differential translation in plants on a genome-wide scale; (ii) summarize the current data on computational algorithms for detection of specific structure–function features and key determinants in plant mRNAs and their correlation with translation efficiency; (iii) highlight the methods for experimental verification of existed and theoretically predicted features within plant mRNAs important for their differential translation; and finally (iv) to discuss the perspectives of discovering the specific structural features of plant mRNA that mediate differential translation control by the combination of computational and experimental approaches.

scholarly journals Genome-Wide Association of Mediator and RNA Polymerase II in Wild-Type and Mediator Mutant Yeast

2014 ◽  
Vol 35 (1) ◽  
pp. 331-342 ◽  
Author(s):  
Emily Paul ◽  
Z. Iris Zhu ◽  
David Landsman ◽  
Randall H. Morse
Keyword(s):  
Rna Polymerase Ii ◽  
Transcriptional Activation ◽  
Open Reading Frames ◽  
Temperature Sensitive ◽  
Gene Promoters ◽  
Content Type ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range

Mediator is a large, multisubunit complex that is required for essentially all mRNA transcription in eukaryotes. In spite of the importance of Mediator, the range of its targets and how it is recruited to these is not well understood. Previous work showed that inSaccharomyces cerevisiae, Mediator contributes to transcriptional activation by two distinct mechanisms, one depending on the tail module triad and favoring SAGA-regulated genes, and the second occurring independently of the tail module and favoring TFIID-regulated genes. Here, we use chromatin immunoprecipitation sequencing (ChIP-seq) to show that dependence on tail module subunits for Mediator recruitment and polymerase II (Pol II) association occurs preferentially at SAGA-regulated over TFIID-regulated genes on a genome-wide scale. We also show that recruitment of tail module subunits to active gene promoters continues genome-wide when Mediator integrity is compromised inmed17temperature-sensitive (ts) yeast, demonstrating the modular nature of the Mediator complexin vivo. In addition, our data indicate that promoters exhibiting strong and stable occupancy by Mediator have a wide range of activity and are enriched for targets of the Tup1-Cyc8 repressor complex. We also identify a number of strong Mediator occupancy peaks that overlap dubious open reading frames (ORFs) and are likely to include previously unrecognized upstream activator sequences.

Sign in / Sign up

Export Citation Format

Share Document