Capture, amplification, and global profiling of microRNAs from low quantities of whole cell lysate

Genome-wide epigenetic changes in plants are being reported during the development and environmental stresses, which are often correlated with gene expression at the transcriptional level. Sum total of the biochemical changes in nuclear DNA, post-translational modifications in histone proteins and variations in the biogenesis of non-coding RNAs in a cell is known as epigenome. These changes are often responsible for variation in expression of the gene without any change in the underlying nucleotide sequence. The changes might also cause variation in chromatin structure resulting into the changes in function/activity of the genome. The epigenomic changes are dynamic with respect to the endogenous and/or environmental stimuli which affect phenotypic plasticity of the organism. Both, the epigenetic changes and variation in gene expression might return to the pre-stress state soon after withdrawal of the stress. However, a part of the epigenetic changes may be retained which is reported to play role in acclimatization, adaptation as well as in the evolutionary processes. Understanding epigenome-engineering for improved stress tolerance in plants has become essential for better utilization of the genetic factors. This review delineates the importance of epigenomics towards possible improvement of plant’s responses to environmental stresses for climate resilient agriculture.

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Study strategies for long non-coding RNAs and their roles in regulating gene expression

Cellular & Molecular Biology Letters ◽

10.1515/cmble-2015-0021 ◽

2015 ◽

Vol 20 (2) ◽

Cited By ~ 3

Author(s):

Dan Qin ◽

Cunshuan Xu

Keyword(s):

Gene Expression ◽

Regulatory Network ◽

Experimental Methods ◽

Study Strategies ◽

Mechanisms Of Action ◽

Cellular Processes ◽

Genome Wide ◽

A Genome ◽

Wide Scale ◽

Non Coding Rnas

AbstractLong non-coding RNAs (lncRNAs) have attracted considerable attention recently due to their involvement in numerous key cellular processes and in the development of various disorders. New high-throughput methods enable their study on a genome-wide scale. Numerous lncRNAs have been identified and characterized as important members of the biological regulatory network, with significant roles in regulating gene expression at the epigenetic, transcriptional and post-transcriptional levels. This paper summarizes the diverse mechanisms of action of these lncRNAs and looks at the study strategies in this field. A major challenge in future study is to establish more effective bioinformatics and experimental methods to explore the functions, detailed mechanisms of action and structures deciding the functional diversity of lncRNAs, since the vast majority remain unresolved.

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Interactions between the MicroRNAs and Microbiota in Cancer Development: Roles and Therapeutic Opportunities

Cancers ◽

10.3390/cancers12040805 ◽

2020 ◽

Vol 12 (4) ◽

pp. 805 ◽

Cited By ~ 10

Author(s):

Alessandro Allegra ◽

Caterina Musolino ◽

Alessandro Tonacci ◽

Giovanni Pioggia ◽

Sebastiano Gangemi

Keyword(s):

Gene Expression ◽

Colon Cancer ◽

Therapeutic Agents ◽

Ovarian Tumour ◽

Cancer Development ◽

Control Gene ◽

Hepatic Carcinoma ◽

Control Gene Expression ◽

The Central Nervous System ◽

Non Coding Rnas

The human microbiota is made up of the fungi, bacteria, protozoa and viruses cohabiting within the human body. An altered microbiota can provoke diseases such as cancer. The mechanisms by which a modified microbiota can intervene in the onset and progression of neoplastic diseases are manifold. For instance, these include the effects on the immune system and the onset of obesity. A different mechanism seems to be constituted by the continuous and bidirectional relationships existing between microbiota and miRNAs. MiRNAs emerged as a novel group of small endogenous non-coding RNAs from that control gene expression. Several works seem to confirm the presence of a close connection between microbiota and miRNAs. Although the main literature data concern the correlations between microbiota, miRNAs and colon cancer, several researches have revealed the presence of connections with other types of tumour, including the ovarian tumour, cervical carcinoma, hepatic carcinoma, neoplastic pathologies of the central nervous system and the possible implication of the microbiota-miRNAs system on the response to the treatment of neoplastic pathologies. In this review, we summarise the physiological and pathological functions of the microbiota on cancer onset by governing miRNA production. A better knowledge of the bidirectional relationships existing between microbiota and miRNAs could provide new markers for the diagnosis, staging and monitoring of cancer and seems to be a promising approach for antagomir-guided approaches as therapeutic agents.

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Genome-Wide Analysis of Alternative Splicing and Non-Coding RNAs Reveal Complicated Transcriptional Regulation in Cannabis sativa L.

International Journal of Molecular Sciences ◽

10.3390/ijms222111989 ◽

2021 ◽

Vol 22 (21) ◽

pp. 11989

Author(s):

Bin Wu ◽

Yanni Li ◽

Jishuang Li ◽

Zhenzhen Xie ◽

Mingbao Luan ◽

...

Keyword(s):

Gene Expression ◽

Alternative Splicing ◽

Biosynthetic Pathway ◽

Cannabis Sativa ◽

Transcriptional Level ◽

Gene Expression And Regulation ◽

Structural Genes ◽

Key Enzymes ◽

Genome Wide ◽

Non Coding Rnas

It is of significance to mine the structural genes related to the biosynthetic pathway of fatty acid (FA) and cellulose as well as explore the regulatory mechanism of alternative splicing (AS), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in the biosynthesis of cannabinoids, FA and cellulose, which would enhance the knowledge of gene expression and regulation at post-transcriptional level in Cannabis sativa L. In this study, transcriptome, small RNA and degradome libraries of hemp ‘Yunma No.1’ were established, and comprehensive analysis was performed. As a result, a total of 154, 32 and 331 transcripts encoding key enzymes involved in the biosynthesis of cannabinoids, FA and cellulose were predicted, respectively, among which AS occurred in 368 transcripts. Moreover, 183 conserved miRNAs, 380 C. sativa-specific miRNAs and 7783 lncRNAs were predicted. Among them, 70 miRNAs and 17 lncRNAs potentially targeted 13 and 17 transcripts, respectively, encoding key enzymes or transporters involved in the biosynthesis of cannabinoids, cellulose or FA. Finally, the crosstalk between AS and miRNAs or lncRNAs involved in cannabinoids and cellulose was also predicted. In summary, all these results provided insights into the complicated network of gene expression and regulation in C. sativa.

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Epigenomics of Plant’s Responses to Environmental Stress

10.20944/preprints201710.0185.v3 ◽

2017 ◽

Author(s):

Suresh Kumar

Keyword(s):

Gene Expression ◽

Nuclear Dna ◽

Environmental Stresses ◽

Transcriptional Level ◽

Epigenetic Changes ◽

Post Translational Modifications ◽

Genome Wide ◽

A Cell ◽

Non Coding Rnas ◽

Function Activity

Genome-wide epigenetic changes in plants are being reported during the development and environmental stresses, which are often correlated with gene expression at the transcriptional level. Sum total of the biochemical changes in nuclear DNA, post-translational modifications in histone proteins and variations in the biogenesis of non-coding RNAs in a cell is known as epigenome. These changes are often responsible for variation in expression of the gene without any change in the underlying nucleotide sequence. The changes might also cause variation in chromatin structure resulting into the changes in function/activity of the genome. The epigenomic changes are dynamic with respect to the endogenous and/or environmental stimuli which affect phenotypic plasticity of the organism. Both, the epigenetic changes and variation in gene expression might return to the pre-stress state soon after withdrawal of the stress. However, a part of the epigenetic changes may be retained which is reported to play role in acclimatization, adaptation as well as in the evolutionary processes. Understanding epigenome-engineering for improved stress tolerance in plants has become essential for better utilization of the genetic factors. This review delineates the importance of epigenomics towards possible improvement of plant’s responses to environmental stresses for climate resilient agriculture.

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Long Noncoding RNA 00472: A Novel Biomarker in Human Diseases

Frontiers in Pharmacology ◽

10.3389/fphar.2021.726908 ◽

2021 ◽

Vol 12 ◽

Author(s):

Dan-yang Ren ◽

Xin-rong Yuan ◽

Cai-xia Tu ◽

Jian-ling Shen ◽

Yun-wei Li ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Therapeutic Target ◽

Noncoding Rna ◽

Human Diseases ◽

Biological Processes ◽

Control Gene ◽

Control Gene Expression ◽

Non Coding Rnas ◽

Gene Expression Levels

Long non-coding RNAs (lncRNAs) play important roles in human diseases. They control gene expression levels and influence various biological processes through multiple mechanisms. Functional abnormalities in lncRNAs are strongly associated with occurrence and development of various diseases. LINC00472, which is located on chromosome 6q13, is involved in several human diseases, particularly cancers of the breast, lung, liver, osteosarcoma, bladder, colorectal, ovarian, pancreatic and stomach. Importantly, LINC00472 can be used as a biomarker for breast cancer cell sensitivity to chemotherapeutic regimens, including doxorubicin. LINC00472 is regulated by microRNAs and several signaling pathways. However, the significance of LINC00472 in human diseases has not been clearly established. In this review, we elucidate on the significance of LINC00472 in various human diseases, indicating that LINC00472 may be a diagnostic, prognostic as well as therapeutic target for these diseases.

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Genome-wide profiling reveals a role for T-cell intracellular antigens TIA1 and TIAR in the control of translational specificity in HeLa cells

Biochemical Journal ◽

10.1042/bj20140227 ◽

2014 ◽

Vol 461 (1) ◽

pp. 43-50 ◽

Cited By ~ 8

Author(s):

Isabel Carrascoso ◽

Carmen Sánchez-Jiménez ◽

José M. Izquierdo

Keyword(s):

Gene Expression ◽

Hela Cells ◽

Rna Binding ◽

Rna Binding Proteins ◽

Control Gene ◽

Control Of Gene Expression ◽

Regulatory Changes ◽

Control Gene Expression ◽

Genome Wide ◽

Multiple Levels

The present study is focused on aspects related to the control of gene expression mediated by the DNA/RNA-binding proteins TIA1 and TIAR. These proteins control gene expression globally at multiple levels in response to dynamic regulatory changes and environmental stresses.

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Epigenomics of Plant’s Responses to Environmental Stress

10.20944/preprints201710.0185.v1 ◽

2017 ◽

Author(s):

Suresh Kumar

Keyword(s):

Gene Expression ◽

Nuclear Dna ◽

Environmental Stresses ◽

Transcriptional Level ◽

Epigenetic Changes ◽

Post Translational Modifications ◽

Genome Wide ◽

A Cell ◽

Non Coding Rnas ◽

Function Activity

Genome-wide epigenetic changes in plants are being reported during the development and environmental stresses, which are often correlated with gene expression at the transcriptional level. Sum total of the biochemical changes in nuclear DNA, post-translational modifications in histone proteins and variations in the biogenesis of small non-coding RNAs in a cell is known as epigenome. These changes are often responsible for variation in expression of the gene without any change in the underlying nucleotide sequence. The changes might also cause variation in chromatin structure resulting into the changes in function/activity of the genome. The epigenomic changes are dynamic with respect to the endogenous and/or environmental stimuli which affect phenotypic plasticity of the organism. Both, the epigenetic changes and variation in gene expression might return to the pre-stress state soon after withdrawal of the stress. However, a part of the epigenetic changes may be retained which is reported to play role in acclimatization, adaptation as well as in the evolutionary processes. Understanding epigenome-engineering for improved stress tolerance in plants has become essential for better utilization of the genetic factors. This review delineates the importance of epigenomics towards possible improvement of plant’s responses to environmental stresses for climate resilient agriculture.

Download Full-text