scholarly journals Identification of Bovine miRNAs with the Potential to Affect Human Gene Expression

2022 ◽  
Vol 12 ◽  
Author(s):  
Moldir Myrzabekova ◽  
Siegfried Labeit ◽  
Raigul Niyazova ◽  
Aigul Akimniyazova ◽  
Anatoliy Ivashchenko
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Bos Taurus ◽  
Human Gene ◽  
Raw Milk ◽  
Nucleotide Sequences ◽  
Large Mammals ◽  
Human Gene Expression ◽  
Total Length ◽  
Human Genes

Milk and other products from large mammals have emerged during human evolution as an important source of nutrition. Recently, it has been recognized that exogenous miRNAs (mRNA inhibited RNA) contained in milk and other tissues of the mammalian body can enter the human body, which in turn have the ability to potentially regulate human metabolism by affecting gene expression. We studied for exogenous miRNAs from Bos taurus that are potentially contain miRNAs from milk and that could act postprandially as regulators of human gene expression. The interaction of 17,508 human genes with 1025 bta-miRNAs, including 245 raw milk miRNAs was studied. The milk bta-miR-151-5p, bta-miR-151-3p, bta-miRNA-320 each have 11 BSs (binding sites), and bta-miRNA-345-5p, bta-miRNA-614, bta-miRNA-1296b and bta-miRNA-149 has 12, 14, 15 and 26 BSs, respectively. The bta-miR-574-5p from cow’s milk had 209 human genes in mRNAs from one to 25 repeating BSs. We found 15 bta-miRNAs that have 100% complementarity to the mRNA of 13 human target genes. Another 12 miRNAs have BSs in the mRNA of 19 human genes with 98% complementarity. The bta-miR-11975, bta-miR-11976, and bta-miR-2885 BSs are located with the overlap of nucleotide sequences in the mRNA of human genes. Nucleotide sequences of BSs of these miRNAs in 5′UTR mRNA of human genes consisted of GCC repeats with a total length of 18 nucleotides (nt) in 18 genes, 21 nt in 11 genes, 24 nt in 14 genes, and 27–48 nt in nine genes. Nucleotide sequences of BSs of bta-miR-11975, bta-miR-11976, and bta-miR-2885 in CDS mRNA of human genes consisted of GCC repeats with a total length of 18 nt in 33 genes, 21 nt in 13 genes, 24 nt in nine genes, and 27–36 nt in 11 genes. These BSs encoded polyA or polyP peptides. In only one case, the polyR (SLC24A3 gene) was encoded. The possibility of regulating the expression of human genes by exogenous bovine miRNAs is discussed.

scholarly journals Decoding transcriptional regulation via a human gene expression predictor

2020 ◽  
Author(s):  
Yuzhou Wang ◽  
Yu Zhang ◽  
Jiazhen Gong ◽  
Jianqiang Bao ◽  
Shisong Ma
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Stress Response ◽  
Target Gene ◽  
Target Genes ◽  
Human Gene ◽  
Human Gene Expression ◽  
Novel Approach ◽  
Wide Range

ABSTRACTTranscription factors (TF) regulate cellular activities via controlling gene expression, but a predictive model describing how TFs quantitatively modulate human transcriptomes was lacking. We constructed a universal human gene expression predictor and utilized it to decode transcriptional regulation. Using 1613 TFs’ expression, the predictor reconstituted highly accurate transcriptomes for samples derived from a wide range of tissues and conditions. The predictor’s broad applicability indicated it had recapitulated the quantitative relationships between TFs and target genes ubiquitous across tissues. Significant interacting TF-target gene pairs were then extracted from the predictor and enabled downstream inference of TF regulators for diverse pathways involved in development, immunity, metabolism, and stress response. Thus, we present a novel approach to study human transcriptional regulation following the “understanding by modeling” principle.

scholarly journals KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors

2019 ◽  
Vol 48 (D1) ◽  
pp. D93-D100 ◽  
Author(s):  
Chenchen Feng ◽  
Chao Song ◽  
Yuejuan Liu ◽  
Fengcui Qian ◽  
Yu Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Target Genes ◽  
Human Gene ◽  
Biological Effects ◽  
Tissue Cell ◽  
Human Gene Expression ◽  
Network Analyses

Abstract Transcription factors (TFs) and their target genes have important functions in human diseases and biological processes. Gene expression profile analysis before and after knockdown or knockout is one of the most important strategies for obtaining target genes of TFs and exploring TF functions. Human gene expression profile datasets with TF knockdown and knockout are accumulating rapidly. Based on the urgent need to comprehensively and effectively collect and process these data, we developed KnockTF (http://www.licpathway.net/KnockTF/index.html), a comprehensive human gene expression profile database of TF knockdown and knockout. KnockTF provides a number of resources for human gene expression profile datasets associated with TF knockdown and knockout and annotates TFs and their target genes in a tissue/cell type-specific manner. The current version of KnockTF has 570 manually curated RNA-seq and microarray datasets associated with 308 TFs disrupted by different knockdown and knockout techniques and across multiple tissue/cell types. KnockTF collects upstream pathway information of TFs and functional annotation results of downstream target genes. It provides details about TFs binding to promoters, super-enhancers and typical enhancers of target genes. KnockTF constructs a TF-differentially expressed gene network and performs network analyses for genes of interest. KnockTF will help elucidate TF-related functions and potential biological effects.

scholarly journals Genetic analysis of radiation-induced changes in human gene expression

Nature ◽  
2009 ◽  
Vol 459 (7246) ◽  
pp. 587-591 ◽  
Author(s):  
Denis A. Smirnov ◽  
Michael Morley ◽  
Eunice Shin ◽  
Richard S. Spielman ◽  
Vivian G. Cheung
Keyword(s):  
Gene Expression ◽  
Genetic Analysis ◽  
Human Gene ◽  
Human Gene Expression ◽  
Radiation Induced ◽  
Induced Changes

scholarly journals Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression

PLoS ONE ◽  
2016 ◽  
Vol 11 (6) ◽  
pp. e0157484 ◽  
Author(s):  
Aurora Torrente ◽  
Margus Lukk ◽  
Vincent Xue ◽  
Helen Parkinson ◽  
Johan Rung ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Gene ◽  
Human Gene Expression

Time series analysis of gene changes and processes after burn with human gene expression profiles

Burns ◽  
2019 ◽  
Vol 45 (2) ◽  
pp. 387-397
Author(s):  
Dan Wu ◽  
Ming Zhou ◽  
Liang Li ◽  
Xiangfeng Leng ◽  
Zheng Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Series ◽  
Time Series Analysis ◽  
Human Gene ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Human Gene Expression ◽  
Series Analysis

scholarly journals VExD: A curated resource for human gene expression following viral infection

2021 ◽  
Author(s):  
Phillip J Dexheimer ◽  
Mario Pujato ◽  
Krishna Roskin ◽  
Matthew T Weirauch
Keyword(s):  
Gene Expression ◽  
Viral Infection ◽  
Human Gene ◽  
Application Programming Interface ◽  
Gene Expression Response ◽  
Human Gene Expression ◽  
Link Type ◽  
Uniform Manner ◽  
Expression Response ◽  
Virus Expression

AbstractMotivationHuman viruses cause significant mortality, morbidity, and economic disruption worldwide. The human gene expression response to viral infection can yield important insights into the detrimental effects to the host. To date, hundreds of studies have performed genome-scale profiling of the effect of viral infection on human gene expression. However, no resource exists that aggregates human expression results across multiple studies, viruses, and tissue types.ResultsWe developed the Virus Expression Database (VExD), a comprehensive curated resource of transcriptomic studies of viral infection in human cells. We have processed all studies within VExD in a uniform manner, allowing users to easily compare human gene expression changes across conditions.Availability and ImplementationVExD is freely accessible at https://vexd.cchmc.org for all modern web browsers. An Application Programming Interface (API) for VExD is also available. The source code is available at https://github.com/pdexheimer/[email protected], [email protected]

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