The novel allele (3R) of the VNTR polymorphism in the XRCC5 promoter region dramatically decreases the gene expression

2013 ◽  
Vol 430 (2) ◽  
pp. 640-641 ◽  
Author(s):  
Mehrdad Rajaei ◽  
Iraj Saadat ◽  
Mostafa Saadat
Keyword(s):  
Gene Expression ◽  
Promoter Region ◽  
The Novel ◽  
Vntr Polymorphism ◽  
Novel Allele

Sequence‐based typing identification of the novel allele HLA‐A *30:170

HLA ◽  
2021 ◽  
Author(s):  
Xiu‐Min Shi ◽  
Rui‐Ping Hu ◽  
Pei‐Tong Li ◽  
Wei Han ◽  
Su‐Jun Gao
Keyword(s):  
The Novel ◽  
Novel Allele

scholarly journals A novel gene signature based on five immune checkpoint genes predicts the survival of glioma

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Wei Zhang ◽  
You Zhai ◽  
Guanzhang Li ◽  
Tao Jiang
Keyword(s):  
Gene Expression ◽  
Central Nervous System ◽  
Immune Response ◽  
Nervous System ◽  
Cox Regression ◽  
Gene Signature ◽  
Immune Checkpoints ◽  
The Novel ◽  
The Central Nervous System ◽  
Checkpoint Genes

Abstract Background Glioma is the most common and fatal type of nerve neoplasm in the central nervous system. Several biomarkers have been considered for prognosis prediction, which is not accurate enough. We aimed to carry out a gene signature related to the expression of immune checkpoints which was enough for its performance in prediction. Methods Gene expression of immune checkpoints in TGGA database was filtrated. The 5 selected genes underwent verification by COX and Lasso-COX regression. Next, the selected genes were included to build a novel signature for further analysis. Results Patients were sub-grouped into high and low risk according to the novel signature. Immune response, clinicopathologic characters, and survival showed significant differences between those 2 groups. Terms including “naive,” “effector,” and “IL-4” were screened out by GSEA. The results showed strong relevance between the signature and immune response. Conclusions We constructed a gene signature with 5 immune checkpoints. The signature predicted survival effectively. The novel signature performed more functional than previous biomarkers.

scholarly journals Assessing the Genome-Wide Effect of Promoter Region Tandem Repeat Natural Variation on Gene Expression

2012 ◽  
Vol 2 (12) ◽  
pp. 1643-1649 ◽  
Author(s):  
Martha H. Elmore ◽  
John G. Gibbons ◽  
Antonis Rokas
Keyword(s):  
Gene Expression ◽  
Tandem Repeat ◽  
Promoter Region ◽  
Natural Variation ◽  
Genome Wide

scholarly journals Mouse embryonic stem cells can differentiate via multiple paths to the same state

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
James Alexander Briggs ◽  
Victor C Li ◽  
Seungkyu Lee ◽  
Clifford J Woolf ◽  
Allon Klein ◽  
...  
Keyword(s):  
Gene Expression ◽  
Motor Neuron ◽  
Motor Neurons ◽  
Embryonic Stem ◽  
The Novel ◽  
Transitional State ◽  
Single Cell Rna Sequencing ◽  
Intermediate States ◽  
Multiple Paths ◽  
Alternative Routes

In embryonic development, cells differentiate through stereotypical sequences of intermediate states to generate particular mature fates. By contrast, driving differentiation by ectopically expressing terminal transcription factors (direct programming) can generate similar fates by alternative routes. How differentiation in direct programming relates to embryonic differentiation is unclear. We applied single-cell RNA sequencing to compare two motor neuron differentiation protocols: a standard protocol approximating the embryonic lineage, and a direct programming method. Both initially undergo similar early neural commitment. Later, the direct programming path diverges into a novel transitional state rather than following the expected embryonic spinal intermediates. The novel state in direct programming has specific and uncharacteristic gene expression. It forms a loop in gene expression space that converges separately onto the same final motor neuron state as the standard path. Despite their different developmental histories, motor neurons from both protocols structurally, functionally, and transcriptionally resemble motor neurons isolated from embryos.

AVP-induced VIT32 gene expression in collecting duct cells occurs via trans-activation of a CRE in the 5′-flanking region of the VIT32 gene

2004 ◽  
Vol 287 (3) ◽  
pp. F460-F468 ◽  
Author(s):  
Christie P. Thomas ◽  
Randy W. Loftus ◽  
Kang Z. Liu
Keyword(s):  
Gene Expression ◽  
Promoter Region ◽  
Collecting Duct ◽  
Airway Epithelial Cells ◽  
Proximal Promoter ◽  
Xenopus Laevis Oocytes ◽  
Proximal Promoter Region ◽  
Duct Cells ◽  
Collecting Duct Cells ◽  
Flanking Region

VIT32, a vasopressin-induced transcript, inhibits Na+ transport when coexpressed with the epithelial sodium channel in Xenopus laevis oocytes ( EMBO J 21: 5109–5117, 2002). To understand the mechanism of VIT32 gene regulation, we examined the effect of DDAVP and cAMP stimulation on VIT32 expression in M-1 mouse collecting duct cells and in H441 human airway epithelial cells. Elevation of cAMP with forskolin and IBMX increased VIT32 gene expression with a peak effect at 2 h. The increase in gene expression was abolished by H89 and by actinomycin D, suggesting that cAMP stimulates VIT32 mRNA expression by a PKA-mediated increase in gene transcription. An ∼1.5-kb fragment of the 5′-flanking region of VIT32 was cloned and was able to confer cAMP-stimulated reporter gene activity when transfected into M-1 and H441 cells. By deletion analysis and site-directed mutagenesis, a cAMP response element (CRE) was identified within the proximal promoter region that was sufficient to account for the increase in VIT32 gene expression seen with DDAVP and elevation of cAMP. Furthermore, DDAVP-stimulated VIT32 promoter-reporter activity was inhibited by H89 and by a dominant negative CREB construct. Finally, we were able to identify CREB as a nuclear protein that bound to the VIT32 CRE in gel mobility shift assays. In summary, DDAVP stimulates transcription of VIT32 via a CRE within the proximal promoter region of the VIT32 gene.

scholarly journals Unraveling the functional role of DNA methylation using targeted DNA demethylation by steric blockage of DNA methyltransferase with CRISPR/dCas9

2020 ◽  
Author(s):  
Daniel M. Sapozhnikov ◽  
Moshe Szyf
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Promoter Region ◽  
Dna Methyltransferase ◽  
Dna Demethylation ◽  
New Method ◽  
Inducible Promoters ◽  
Specific Targeting ◽  
Main Effect

AbstractAlthough associations between DNA methylation and gene expression were established four decades ago, the causal role of DNA methylation in gene expression remains unresolved. Different strategies to address this question were developed; however, all are confounded and fail to disentangle cause and effect. We developed here a highly effective new method using only deltaCas9(dCas9):gRNA site-specific targeting to physically block DNA methylation at specific targets in the absence of a confounding flexibly-tethered enzymatic activity, enabling examination of the role of DNA methylation per se in living cells. We show that the extensive induction of gene expression achieved by TET/dCas9-based targeting vectors is confounded by DNA methylation-independent activities, inflating the role of DNA methylation in the promoter region. Using our new method, we show that in several inducible promoters, the main effect of DNA methylation is silencing basal promoter activity. Thus, the effect of demethylation of the promoter region in these genes is small, while induction of gene expression by different inducers is large and DNA methylation independent. In contrast, targeting demethylation to the pathologically silenced FMR1 gene targets robust induction of gene expression. We also found that standard CRISPR/Cas9 knockout generates a broad unmethylated region around the deletion, which might confound interpretation of CRISPR/Cas9 gene depletion studies. In summary, this new method could be used to reveal the true extent, nature, and diverse contribution to gene regulation of DNA methylation at different regions.

scholarly journals Maturation of Human Long-lived Plasma Cells Results in Resistance to Apoptosis by Transcriptional and Epigenetic Regulation

2021 ◽  
Author(s):  
Chester J Joyner ◽  
Ariel Ley ◽  
Doan Nguyen ◽  
Muhammad Ali ◽  
Alessia Corrado ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plasma Cells ◽  
The Novel ◽  
Epigenetic Changes ◽  
Apoptosis Pathway ◽  
Apoptotic Gene ◽  
Survival Gene ◽  
Distinct Morphology ◽  
Antibody Secreting Cells

Antibody secreting cells (ASC) circulate after vaccination and migrate to the bone marrow (BM) where a subset known as long-lived plasma cells (LLPC) persist and secrete antibodies for a lifetime. The mechanisms of how circulating ASC become LLPC are not well elucidated. Here, we show that human blood ASCs have distinct morphology, transcriptomes, and epigenetics compared to BM LLPC. LLPC acquire transcriptional and epigenetic changes in the apoptosis pathway to support their survival. Upregulation of pro-survival gene expression accompanies downregulation of pro-apoptotic gene expression in LLPC. While pro-apoptotic gene loci are less accessible, pro-survival gene loci are not always accompanied by accessibility changes. Importantly, we show similar LLPC morphological and transcriptional maturation of blood ASC in response to the novel in vitro BM mimetic. In all, our study demonstrates that blood ASC in the BM microniche must undergo morphological and molecular changes to mature into apoptotic-resistant LLPC.

scholarly journals Identification and evaluation of the novel genes for transcript normalization during female gametophyte development in sugarcane

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12298
Author(s):  
Maokai Yan ◽  
Xingyue Jin ◽  
Yanhui Liu ◽  
Huihuang Chen ◽  
Tao Ye ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sexual Reproduction ◽  
Reference Genes ◽  
Female Gametophyte ◽  
Developmental Stages ◽  
Reproductive Organs ◽  
The Novel ◽  
Biofuel Feedstock ◽  
Gametophyte Development ◽  
Female Gametophyte Development

Background Sugarcane (Saccharum spontaneum L.), the major sugar and biofuel feedstock crop, is cultivated mainly by vegetative propagation worldwide due to the infertility of female reproductive organs resulting in the reduction of quality and output of sugar. Deciphering the gene expression profile during ovule development will improve our understanding of the complications underlying sexual reproduction in sugarcane. Optimal reference genes are essential for elucidating the expression pattern of a given gene by quantitative real-time PCR (qRT-PCR). Method In this study, based on transcriptome data obtained from sugarcane ovule, eighteen candidate reference genes were identified, cloned, and their expression levels were evaluated across five developmental stages ovule (AC, MMC, Meiosis, Mitosis, and Mature). Results Our results indicated that FAB2 and MOR1 were the most stably expressed genes during sugarcane female gametophyte development. Moreover, two genes, cell cycle-related genes REC8 and CDK, were selected, and their feasibility was validated. This study provides important insights into the female gametophyte development of sugarcane and reports novel reference genes for gene expression research on sugarcane sexual reproduction.

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