cDNA cloning and promoter analysis of rat caspase-9

2001 ◽  
Vol 360 (1) ◽  
pp. 49-56 ◽  
Author(s):  
Junichiro NISHIYAMA ◽  
Xiaolan YI ◽  
Manjeri A. VENKATACHALAM ◽  
Zheng DONG
Keyword(s):  
Critical Role ◽  
Hypoxia Inducible Factor ◽  
Gene Promoter ◽  
Regulatory Elements ◽  
Mitochondrial Pathway ◽  
Genomic Segment ◽  
Caspase 9 ◽  
Promoter Regions ◽  
Genomic Walking ◽  
Flanking Regions

Caspase-9 is the apex caspase of the mitochondrial pathway of apoptosis, which plays a critical role in apoptotic initiation and progression. However, gene regulation of caspase-9 is largely unknown. This is in part due to the lack of information on the gene promoter. Here we have cloned the full-length cDNA of rat caspase-9 and have isolated promoter regions of this gene. The rat caspase-9 cDNA of 2058bp predicts a protein of 454 amino acids, which contains a caspase-recruitment domain (‘CARD’) at the N-terminus and enzymic domains at the C-terminus. The enzyme's active site, with a characteristic motif of QACGG, was also identified. Overall, rat and human caspase-9 have 71% identity. With the cDNA sequence, we subsequently isolated the proximal 5′-flanking regions of rat caspase-9 by the procedure of genomic walking. The 2270bp genomic segment is ‘TATA-less’, but contains several GC boxes. Elements binding known transcription factors such as Sp-1, Pit-1, CCAAT-enhancer-binding protein (C/EBP), glucocorticoid receptor and hypoxia-inducible factor 1 (HIF-1) were also identified. When cloned into reporter gene vectors, the genomic segment showed significant promoter activity, indicating that the 5′-flanking regions isolated by genomic walking contain the gene promoter of rat caspase-9. Of significance is that the cloned promoter segments were activated by severe hypoxia, conditions inducing caspase-9 transcription. Thus, the genomic sequences reported here contain not only the basal promoter of rat caspase-9 but also regulatory elements responsive to pathophysiological stimuli including hypoxia.

scholarly journals The Roles of the Histone Protein Modifier EZH2 in the Uterus and Placenta

Epigenomes ◽  
2020 ◽  
Vol 4 (3) ◽  
pp. 20
Author(s):  
Ana M. Mesa ◽  
Cheryl S. Rosenfeld ◽  
Geetu Tuteja ◽  
Theresa I. Medrano ◽  
Paul S. Cooke
Keyword(s):  
Critical Role ◽  
Histone H3 ◽  
Gene Promoter ◽  
Epigenetic Changes ◽  
Promoter Regions ◽  
Polycomb Repressive Complex 2 ◽  
Gene Sets ◽  
Ezh2 Expression ◽  
And Function ◽  
Transcription Enhancer

Epigenetic modifications regulate normal physiological, as well as pathological processes in various organs, including the uterus and placenta. Both organs undergo dramatic and rapid restructuring that depends upon precise orchestration of events. Epigenetic changes that alter transcription and translation of gene-sets regulate such responses. Histone modifications alter the chromatin structure, thereby affecting transcription factor access to gene promoter regions. Binding of histones to DNA is regulated by addition or removal of subunit methyl and other groups, which can inhibit or stimulate transcription. Enhancer of zeste homolog 2 (EZH2) is the catalytic subunit of polycomb repressive complex 2 (PRC2) that catalyzes tri-methylation of histone H3 at Lys 27 (H3K27me3) and subsequently suppresses transcription of genes bound by such histones. Uterine EZH2 expression exerts a critical role in development and function of this organ with deletion of this gene resulting in uterine hyperplasia and expression of cancer-associated transcripts. Elucidating the roles of EZH2 in uterus and placenta is essential as EZH2 dysregulation is associated with several uterine and placental pathologies. Herein, we discuss EZH2 functions in uterus and placenta, emphasizing its physiological and pathological importance.

scholarly journals Rule-based Clustering for Gene Promoter Structure Discovery

2009 ◽  
Vol 48 (03) ◽  
pp. 229-235
Author(s):  
U. Petrovic ◽  
G. Shaulsky ◽  
B. Zupan ◽  
T. Curk
Keyword(s):  
Gene Expression ◽  
Cellular Response ◽  
Expression Profiles ◽  
Gene Promoter ◽  
Regulatory Elements ◽  
Experiment Planning ◽  
Learning Approaches ◽  
Promoter Regions ◽  
Rule Based ◽  
Gene Regulatory

Summary Background: The genetic cellular response to internal and external changes is determined by the sequence and structure of gene-regulatory promoter regions. Objectives: Using data on gene-regulatory elements (i.e., either putative or known transcription factor binding sites) and data on gene expression profiles we can discover structural elements in promoter regions and infer the underlying programs of gene regulation. Such hypotheses obtained in silico can greatly assist us in experiment planning. The principal obstacle for such approaches is the combinatorial explosion in different combinations of promoter elements to be examined. Methods: Stemming from several state-ofthe-art machine learning approaches we here propose a heuristic, rule-based clustering method that uses gene expression similarity to guide the search for informative structures in promoters, thus exploring only the most promising parts of the vast and expressively rich rule-space. Results: We present the utility of the method in the analysis of gene expression data on budding yeast S. cerevisiae where cells were induced to proliferate peroxisomes. Conclusions: We demonstrate that the proposed approach is able to infer informative relations uncovering relatively complex structures in gene promoter regions that regulate gene expression.

scholarly journals Folding and Persistence Time of Intramolecular G-Quadruplexes Transiently Embedded in a DNA duplex

2021 ◽  
Author(s):  
Phong Lan Thao Tran ◽  
Martin Rieu ◽  
Samar Hodeib ◽  
Alexandra Joubert ◽  
Jimmy Ouellet ◽  
...  
Keyword(s):  
Single Molecule ◽  
Critical Role ◽  
Genetic Regulation ◽  
Regulatory Elements ◽  
Promoter Regions ◽  
Folding Rate ◽  
Persistence Time ◽  
G4 Dna

ABSTRACTG-quadruplex (G4) DNA structures have emerged as important regulatory elements during DNA replication, transcription or repair. While many in-vitro studies have focused on the kinetics of G4 formation within DNA single-strands, G4 are found in-vivo in double-stranded DNA regions, where their formation is challenged by pairing between the two complementary strands. Since the energy of hybridization of Watson-Crick structures dominates the energy of G4 folding, this competition should play a critical role on the persistence of G4 in vivo. To address this issue, we designed a single molecule assay allowing measuring G4 folding and persistence while the structure is periodically challenged by the complementary strand. We quantified both the folding rate and the persistence time of biologically relevant G4 structures and showed that the dynamics of G4 formation depends strongly on the genomic location. G4 are found much more stable in promoter regions and replication origins than in telomeric regions. In addition, we characterized how G4 dynamics was affected by G4 ligands and showed that both folding rate and persistence increased. Our assay opens new perspectives for the measurement of G4 dynamics, which is critical to understand their role in genetic regulation.

scholarly journals Tissue-specific versus pleiotropic enhancers within the bric-a-brac tandem gene duplicates display differential regulatory activity and evolutionary conservation

2021 ◽  
Author(s):  
Henri-Marc G BOURBON ◽  
Mikhail Benetah ◽  
Emmanuelle Guillou ◽  
Luis Humberto MOJICA VAZQUEZ ◽  
Aissette BAANANNOU ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
De Novo ◽  
Critical Role ◽  
Specific Interaction ◽  
Gene Promoter ◽  
Regulatory Elements ◽  
Specific Expression ◽  
Animal Evolution ◽  
Leg Axis ◽  
Gene Reporter Assay

During animal evolution, de novo emergence and modifications of pre-existing transcriptional enhancers have contributed to biological innovations, by implementing gene regulatory networks. The Drosophila melanogaster bric-a-brac ( bab ) complex, comprising the tandem paralogous genes bab1 - 2 , provides a paradigm to address how enhancers contribute and co-evolve to regulate jointly or differentially duplicated genes. We previously characterized an intergenic enhancer (named LAE) governing bab2 expression in leg and antennal tissues. We show here that LAE activity also regulates bab1 . CRISPR/Cas9-mediated LAE excision reveals its critical role for bab2 -specific expression along the proximo-distal leg axis, likely through paralog-specific interaction with the bab2 gene promoter. Furthermore, LAE appears involved but not strictly required for bab1 - 2 co-expression in leg tissues. Phenotypic rescue experiments, chromatin features and a gene reporter assay reveal a large “pleiotropic” bab1 enhancer (termed BER) including a series of cis -regulatory elements active in the leg, antennal, wing, haltere and gonadal tissues. Phylogenomics analyses indicate that (i) bab2 originates from bab1 duplication within the Muscomorpha sublineage, (ii) LAE and bab1 promoter sequences have been evolutionarily-fixed early on within the Brachycera lineage, while (iii) BER elements have been conserved more recently among muscomorphans. Lastly, we identified conserved binding sites for transcription factors known or prone to regulate directly the paralogous bab genes in diverse developmental contexts. This work provides new insights on enhancers, particularly about their emergence, maintenance and functional diversification during evolution.

The Repetitive Sequence Database and Mining Putative Regulatory Elements in Gene Promoter Regions

2002 ◽  
Vol 9 (4) ◽  
pp. 621-640 ◽  
Author(s):  
Jorng-Tzong Horng ◽  
Hsien-Da Huang ◽  
Ming-Hui Jin ◽  
Li-Cheng Wu ◽  
Shir-Ly Huang
Keyword(s):  
Repetitive Sequence ◽  
Gene Promoter ◽  
Regulatory Elements ◽  
Sequence Database ◽  
Promoter Regions

scholarly journals Genome-wide identification and expression analysis of rice NLR genes responsive to the infections of Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae

2019 ◽  
Author(s):  
Li Ding ◽  
Xiameng Xu ◽  
Weiwen Kong ◽  
Xue Xia ◽  
Shengwei Zhang ◽  
...  
Keyword(s):  
Magnaporthe Oryzae ◽  
Critical Role ◽  
Regulatory Elements ◽  
Xanthomonas Oryzae ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Promoter Regions ◽  
Medium Level ◽  
Rice Disease ◽  
The Veil

Abstract Background Nucleotide-binding site, leucine-rich repeat (NLR) genes play a critical role in rice disease resistance. However, the transcriptional activities of rice NLR genes during pathogen invasions are still unclear.Results To uncover the veil, we identified a total of 430 regular rice NLR genes with both NBS and LRR domains, consisting of 192 CNL and 238 XNL (without a CC motif) members. We performed individual and integrative analyses based on 69 samples from rice microarray after the infections of Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae (Mor). 397 NLR genes were found to be expressed at low/medium level, while 10 NLR genes were observed to show high levels of expression. 400 NLR genes were discovered to be differentially expressed in at least one sample. Further, 46 NLR genes were identified to be differentially expressed in rice response to the two pathogens and 38 of them could be validated by RNA-seq data. Six cis-regulatory elements (MYC, STRE, MYB, ABRE, G-box, and AS-1) were observed to occur frequently in the promoter regions of rice NLR genes. Ten NLR genes were selected for in lab analysis, and qRT-PCR results of seven NLR genes verified the validity of the microarray and RNA-Seq data.Conclusions Our results would shed new light on revealing the roles of NLR genes in rice resistance to Xoo and Mor.

scholarly journals Arabidopsis thaliana Myb59 Gene Is Involved in the Response to Heterodera schachtii Infestation, and Its Overexpression Disturbs Regular Development of Nematode-Induced Syncytia

2021 ◽  
Vol 22 (12) ◽  
pp. 6450
Author(s):  
Anita Wiśniewska ◽  
Kamila Wojszko ◽  
Elżbieta Różańska ◽  
Klaudia Lenarczyk ◽  
Karol Kuczerski ◽  
...  
Keyword(s):  
Cell Metabolism ◽  
Gene Promoter ◽  
Promoter Sequence ◽  
Regulatory Elements ◽  
Heterodera Schachtii ◽  
Myb Transcription Factor ◽  
Parasitic Nematodes ◽  
Regulatory Sequences ◽  
Gene Encoding ◽  
Constitutive Overexpression

Transcription factors are proteins that directly bind to regulatory sequences of genes to modulate and adjust plants’ responses to different stimuli including biotic and abiotic stresses. Sedentary plant parasitic nematodes, such as beet cyst nematode, Heterodera schachtii, have developed molecular tools to reprogram plant cell metabolism via the sophisticated manipulation of genes expression, to allow root invasion and the induction of a sequence of structural and physiological changes in plant tissues, leading to the formation of permanent feeding sites composed of modified plant cells (commonly called a syncytium). Here, we report on the AtMYB59 gene encoding putative MYB transcription factor that is downregulated in syncytia, as confirmed by RT-PCR and a promoter pMyb59::GUS activity assays. The constitutive overexpression of AtMYB59 led to the reduction in A. thaliana susceptibility, as indicated by decreased numbers of developed females, and to the disturbed development of nematode-induced syncytia. In contrast, mutant lines with a silenced expression of AtMYB59 were more susceptible to this parasite. The involvement of ABA in the modulation of AtMYB59 gene transcription appears feasible by several ABA-responsive cis regulatory elements, which were identified in silico in the gene promoter sequence, and experimental assays showed the induction of AtMYB59 transcription after ABA treatment. Based on these results, we suggest that AtMYB59 plays an important role in the successful parasitism of H. schachtii on A. thaliana roots.

scholarly journals Prrx1 promotes stemness and angiogenesis via activating TGF-β/smad pathway and upregulating proangiogenic factors in glioma

2021 ◽  
Vol 12 (6) ◽  
Author(s):  
Zetao Chen ◽  
Yihong Chen ◽  
Yan Li ◽  
Weidong Lian ◽  
Kehong Zheng ◽  
...  
Keyword(s):  
Stem Cells ◽  
Therapeutic Strategy ◽  
Critical Role ◽  
Glioma Stem Cells ◽  
Promoter Regions ◽  
Aberrant Expression ◽  
Smad Pathway ◽  
Tgf Β1

AbstractGlioma is one of the most lethal cancers with highly vascularized networks and growing evidences have identified glioma stem cells (GSCs) to account for excessive angiogenesis in glioma. Aberrant expression of paired-related homeobox1 (Prrx1) has been functionally associated with cancer stem cells including GSCs. In this study, Prrx1 was found to be markedly upregulated in glioma specimens and elevated Prrx1 expression was inversely correlated with prognosis of glioma patients. Prrx1 potentiated stemness acquisition in non-stem tumor cells (NSTCs) and stemness maintenance in GSCs, accompanied with increased expression of stemness markers such as SOX2. Prrx1 also promoted glioma angiogenesis by upregulating proangiogenic factors such as VEGF. Consistently, silencing Prrx1 markedly inhibited glioma proliferation, stemness, and angiogenesis in vivo. Using a combination of subcellular proteomics and in vitro analyses, we revealed that Prrx1 directly bound to the promoter regions of TGF-β1 gene, upregulated TGF-β1 expression, and ultimately activated the TGF-β/smad pathway. Silencing TGF-β1 mitigated the malignant behaviors induced by Prrx1. Activation of this pathway cooperates with Prrx1 to upregulate the expression of stemness-related genes and proangiogenic factors. In summary, our findings revealed that Prrx1/TGF-β/smad signal axis exerted a critical role in glioma stemness and angiogeneis. Disrupting the function of this signal axis might represent a new therapeutic strategy in glioma patients.

scholarly journals Self-Assembling Polypeptide Hydrogels as a Platform to Recapitulate the Tumor Microenvironment

Cancers ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 3286
Author(s):  
Dariusz Lachowski ◽  
Carlos Matellan ◽  
Ernesto Cortes ◽  
Alberto Saiani ◽  
Aline F. Miller ◽  
...  
Keyword(s):  
Cell Culture ◽  
Tumor Microenvironment ◽  
Cancer Cell ◽  
Critical Role ◽  
Hypoxia Inducible Factor ◽  
Pancreatic Cancer Cell Line ◽  
Cancer Cell Line ◽  
Culture Systems ◽  
A Cell

The tumor microenvironment plays a critical role in modulating cancer cell migration, metabolism, and malignancy, thus, highlighting the need to develop in vitro culture systems that can recapitulate its abnormal properties. While a variety of stiffness-tunable biomaterials, reviewed here, have been developed to mimic the rigidity of the tumor extracellular matrix, culture systems that can recapitulate the broader extracellular context of the tumor microenvironment (including pH and temperature) remain comparably unexplored, partially due to the difficulty in independently tuning these parameters. Here, we investigate a self-assembled polypeptide network hydrogel as a cell culture platform and demonstrate that the culture parameters, including the substrate stiffness, extracellular pH and temperature, can be independently controlled. We then use this biomaterial as a cell culture substrate to assess the effect of stiffness, pH and temperature on Suit2 cells, a pancreatic cancer cell line, and demonstrate that these microenvironmental factors can regulate two critical transcription factors in cancer: yes-associated protein 1 (YAP) and hypoxia inducible factor (HIF-1A).

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