scholarly journals Influence of the Bioactive Diet Components on the Gene Expression Regulation

Nutrients ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 3673
Author(s):  
Justyna Mierziak ◽  
Kamil Kostyn ◽  
Aleksandra Boba ◽  
Magdalena Czemplik ◽  
Anna Kulma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Regulation ◽  
Genome Structure ◽  
Good Health ◽  
Bioactive Components ◽  
Modern Approach ◽  
Non Coding Rna ◽  
Activation Of Transcription ◽  
Rna Activation ◽  
Biochemical Mechanisms

Diet bioactive components, in the concept of nutrigenetics and nutrigenomics, consist of food constituents, which can transfer information from the external environment and influence gene expression in the cell and thus the function of the whole organism. It is crucial to regard food not only as the source of energy and basic nutriments, crucial for living and organism development, but also as the factor influencing health/disease, biochemical mechanisms, and activation of biochemical pathways. Bioactive components of the diet regulate gene expression through changes in the chromatin structure (including DNA methylation and histone modification), non-coding RNA, activation of transcription factors by signalling cascades, or direct ligand binding to the nuclear receptors. Analysis of interactions between diet components and human genome structure and gene activity is a modern approach that will help to better understand these relations and will allow designing dietary guidances, which can help maintain good health.

scholarly journals Small-Activating RNA Can Change Nucleosome Positioning in Human Fibroblasts

2016 ◽  
Vol 21 (6) ◽  
pp. 634-642 ◽  
Author(s):  
Bin Wang ◽  
Jing Sun ◽  
Jiandong Shi ◽  
Qing Guo ◽  
Xiangrong Tong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Gene Expression Regulation ◽  
Human Fibroblasts ◽  
Cpg Islands ◽  
Nucleosome Positioning ◽  
Gene Promoters ◽  
Promoter Regions ◽  
Rna Activation ◽  
Gene Expression Studies

RNA activation (RNAa) is a mechanism of positive gene expression regulation mediated by small-activating RNAs (saRNAs), which target gene promoters and have been used as tools to manipulate gene expression. Studies have shown that RNAa is associated with epigenetic modifications at promoter regions; however, it is unclear whether these modifications are the cause or a consequence of RNAa. In this study, we examined changes in nucleosome repositioning and the involvement of RNA polymerase II (RNAPII) in this process. We screened saRNAs for OCT4 ( POU5F1), SOX2, and NANOG, and identified several novel saRNAs. We found that nucleosome positioning was altered after saRNA treatment and that the formation of nucleosome-depleted regions (NDRs) contributed to RNAa at sites of RNAPII binding, such as the TATA box, CpG islands (CGIs), proximal enhancers, and proximal promoters. Moreover, RNAPII appeared to be bound specifically to NDRs. These results suggested that changes in nucleosome positions resulted from RNAa. We thus propose a hypothesis that targeting promoter regions using exogenous saRNAs can induce the formation of NDRs, exposing regulatory binding sites to recruit RNAPII, a key component of preinitiation complex, and leading to increased initiation of transcription.

Understanding non-coding DNA regions in yeast

2013 ◽  
Vol 41 (6) ◽  
pp. 1654-1659 ◽  
Author(s):  
Margarita Schlackow ◽  
Monika Gullerova
Keyword(s):  
Gene Expression ◽  
Fission Yeast ◽  
Rna Sequencing ◽  
Dna Microarrays ◽  
Gene Expression Regulation ◽  
Expression Regulation ◽  
Present Review ◽  
Rna Seq ◽  
Antisense Transcripts ◽  
Non Coding Rna

Non-coding transcripts play an important role in gene expression regulation in all species, including budding and fission yeast. Such regulatory transcripts include intergenic ncRNA (non-coding RNA), 5′ and 3′ UTRs, introns and antisense transcripts. In the present review, we discuss advantages and limitations of recently developed sequencing techniques, such as ESTs, DNA microarrays, RNA-Seq (RNA sequencing), DRS (direct RNA sequencing) and TIF-Seq (transcript isoform sequencing). We provide an overview of methods applied in yeast and how each of them has contributed to our knowledge of gene expression regulation and transcription.

scholarly journals HOXBLINC long non-coding RNA activation promotes leukemogenesis in NPM1-mutant acute myeloid leukemia

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ganqian Zhu ◽  
Huacheng Luo ◽  
Yang Feng ◽  
Olga A. Guryanova ◽  
Jianfeng Xu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Expression Patterns ◽  
Promoter Regions ◽  
Signature Genes ◽  
Non Coding Rna ◽  
Rna Activation ◽  
Long Non Coding Rna ◽  
Acute Myeloid

AbstractNucleophosmin (NPM1) is the most commonly mutated gene in acute myeloid leukemia (AML) resulting in aberrant cytoplasmic translocation of the encoded nucleolar protein (NPM1c+). NPM1c+ maintains a unique leukemic gene expression program, characterized by activation of HOXA/B clusters and MEIS1 oncogene to facilitate leukemogenesis. However, the mechanisms by which NPM1c+ controls such gene expression patterns to promote leukemogenesis remain largely unknown. Here, we show that the activation of HOXBLINC, a HOXB locus-associated long non-coding RNA (lncRNA), is a critical downstream mediator of NPM1c+-associated leukemic transcription program and leukemogenesis. HOXBLINC loss attenuates NPM1c+-driven leukemogenesis by rectifying the signature of NPM1c+ leukemic transcription programs. Furthermore, overexpression of HoxBlinc (HoxBlincTg) in mice enhances HSC self-renewal and expands myelopoiesis, leading to the development of AML-like disease, reminiscent of the phenotypes seen in the Npm1 mutant knock-in (Npm1c/+) mice. HoxBlincTg and Npm1c/+ HSPCs share significantly overlapped transcriptome and chromatin structure. Mechanistically, HoxBlinc binds to the promoter regions of NPM1c+ signature genes to control their activation in HoxBlincTg HSPCs, via MLL1 recruitment and promoter H3K4me3 modification. Our study reveals that HOXBLINC lncRNA activation plays an essential oncogenic role in NPM1c+ leukemia. HOXBLINC and its partner MLL1 are potential therapeutic targets for NPM1c+ AML.

scholarly journals The Biomarker and Therapeutic Potential of Circular Rnas in Schizophrenia

Cells ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 2238
Author(s):  
Artem Nedoluzhko ◽  
Natalia Gruzdeva ◽  
Fedor Sharko ◽  
Sergey Rastorguev ◽  
Natalia Zakharova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Binding ◽  
Gene Expression Regulation ◽  
Rna Binding Proteins ◽  
Therapeutic Potential ◽  
Expression Patterns ◽  
Circular Rna ◽  
Circular Rnas ◽  
Cellular Processes ◽  
Non Coding Rna

Circular RNAs (circRNAs) are endogenous, single-stranded, most frequently non-coding RNA (ncRNA) molecules that play a significant role in gene expression regulation. Circular RNAs can affect microRNA functionality, interact with RNA-binding proteins (RBPs), translate proteins by themselves, and directly or indirectly modulate gene expression during different cellular processes. The affected expression of circRNAs, as well as their targets, can trigger a cascade of events in the genetic regulatory network causing pathological conditions. Recent studies have shown that altered circular RNA expression patterns could be used as biomarkers in psychiatric diseases, including schizophrenia (SZ); moreover, circular RNAs together with other cell molecules could provide new insight into mechanisms of this disorder. In this review, we focus on the role of circular RNAs in the pathogenesis of SZ and analyze their biomarker and therapeutic potential in this disorder.

scholarly journals Structural Variations of the 3D Genome Architecture in Cervical Cancer Development

2021 ◽  
Vol 9 ◽  
Author(s):  
Muhammad Muzammal Adeel ◽  
Hao Jiang ◽  
Yibeltal Arega ◽  
Kai Cao ◽  
Da Lin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cervical Cancer ◽  
Gene Expression Regulation ◽  
Genome Structure ◽  
Cancer Development ◽  
Genome Architecture ◽  
Structural Variations ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Cervical Cancer Development

Human papillomavirus (HPV) integration is the major contributor to cervical cancer (CC) development by inducing structural variations (SVs) in the human genome. SVs are directly associated with the three-dimensional (3D) genome structure leading to cancer development. The detection of SVs is not a trivial task, and several genome-wide techniques have greatly helped in the identification of SVs in the cancerous genome. However, in cervical cancer, precise prediction of SVs mainly translocations and their effects on 3D-genome and gene expression still need to be explored. Here, we have used high-throughput chromosome conformation capture (Hi-C) data of cervical cancer to detect the SVs, especially the translocations, and validated it through whole-genome sequencing (WGS) data. We found that the cervical cancer 3D-genome architecture rearranges itself as compared to that in the normal tissue, and 24% of the total genome switches their A/B compartments. Moreover, translocation detection from Hi-C data showed the presence of high-resolution t(4;7) (q13.1; q31.32) and t(1;16) (q21.2; q22.1) translocations, which disrupted the expression of the genes located at and nearby positions. Enrichment analysis suggested that the disrupted genes were mainly involved in controlling cervical cancer-related pathways. In summary, we detect the novel SVs through Hi-C data and unfold the association among genome-reorganization, translocations, and gene expression regulation. The results help understand the underlying pathogenicity mechanism of SVs in cervical cancer development and identify the targeted therapeutics against cervical cancer.

scholarly journals Insight into m 6 A methylation from occurrence to functions

Open Biology ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 200091
Author(s):  
Wenxiu Ru ◽  
Xiaoyan Zhang ◽  
Binglin Yue ◽  
Ao Qi ◽  
Xuemei Shen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Regulation ◽  
Expression Regulation ◽  
Cancer Development ◽  
Regulatory Effect ◽  
Non Coding Rna ◽  
Reversible Modification ◽  
Regulatory Functions ◽  
Insight Into

RNA m 6 A methylation is a post-transcriptional modification that occurs at the nitrogen-6 position of adenine. This dynamically reversible modification is installed, removed and recognized by methyltransferases, demethylases and readers, respectively. This modification has been found in most eukaryotic mRNA, tRNA, rRNA and other non-coding RNA. Recent studies have revealed important regulatory functions of the m 6 A including effects on gene expression regulation, organism development and cancer development. In this review, we summarize the discovery and features of m 6 A, and briefly introduce the mammalian m 6 A writers, erasers and readers. Finally, we discuss progress in identifying additional functions of m 6 A and the outstanding questions about the regulatory effect of this widespread modification.

scholarly journals Dynamic Signature of tRNA-Derived small RNAs in Cancer Pathogenesis as a Promising Valuable Approach

2020 ◽  
Author(s):  
Somayeh Vafaei ◽  
Fahimeh Fattahi ◽  
Maryam Sahlolbei ◽  
Zahra Madjd ◽  
Ayna Yazdanpanah ◽  
...  
Keyword(s):  
Gene Expression ◽  
Small Rnas ◽  
Gene Expression Regulation ◽  
Transfer Rnas ◽  
Physiological Processes ◽  
Cancer Pathogenesis ◽  
Non Coding Rna ◽  
Cancer Field ◽  
Cancer Types ◽  
Dynamic Signature

Abstract Background: Non-coding RNAs are a cluster of RNAs that do not encode functional proteins, and involve infrastructural and regulatory types, which transfer RNAs (tRNAs) belong to former and small RNAs (sRNA) to the latter one. Recently, tRNA-derived small RNAs (tDRs) were discovered among small non-coding RNA, as the newly discovered regulatory small RNA. It plays a role in pathological and physiological processes, which is frequently dysregulated in gene expression regulation. tsRNAs can be bounded to argonaute proteins and piwi proteins such as miRNAs and piRNAs sequentially. In addition, it can interact with DNA and histone methylation machinery Results: In initial searching, 2744 unique articles were identified by bio electronically search of following databases: PubMed, Embase, Web of Science, Scopus, and google scholar up to 25 February 2020. Finally, after Full-text assessment 48 related article to gene expression profiling tsRNA in cancer were achieved. Conclusions: In this systematic review, we summarized the most recent findings related to the expression of tsRNAs in 17 cancer types. We suggested that tsRNA in cancer field attracted the researchers' focus and effectively facilitated diagnostic and therapy approaches.

Placental Therapy as Panacea: An Insight to Its Therapeutic Potential

2020 ◽  
Vol 06 ◽  
Author(s):  
Sayed Md Mumtaz ◽  
Madhu Gupta ◽  
Ramesh K. Goyal
Keyword(s):  
Tissue Regeneration ◽  
Therapeutic Potential ◽  
Biologically Active ◽  
Bioactive Components ◽  
Biochemical Mechanisms ◽  
Clinically Significant ◽  
Available Information ◽  
Clinical Potential ◽  
Placental Extract

Abstract:: The placenta that maintains and regulates the growth of fetus, consists of various biological treasures nutrients such as cytomedines, vitamins, trace elements, amino acids, peptides, growth factors and other biologically active constituents. Their therapeutic usefulness can well define in the terms of biochemical mechanisms of various components present in it. Biomedical waste derived extract is also a panacea for treatment of various diseases. Placental therapy has been reported specifically to have potent action on recovery of diseases and tissue regeneration. Placental bioactive components and their multi targeting identity prompted us to compile the précised information on placental extract products. However, some findings are needed to be explored by scientific community to prove their clinical potential with clinically significant statistical conclusions. In the light of available information and the usefulness of the placental extract, it is necessary for the development of various formulations for various unmet meet for the treatment as well as access their adverse effects as well as contradictions and precisely evaluated in the short and in the long-term periods.

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