Post-transcriptional and translational regulation modulates gene co-expression behavior in more synchronized pace to carry out molecular function in the cell

Wang, Jinzeng; Lv, Qi; Li, Xujuan; Liu, Ya; Kang, Liu; Wang, Haiyun

doi:10.1016/j.gene.2016.04.055

Cited by 2 publications

(2 citation statements)

References 22 publications

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“…Alternatively, more advanced mathematical methods might unravel simultaneous and time‐delayed co‐expression. [ 55 ] Further exploration of these approaches will enhance our understanding of promoter coordination and dynamics.…”

Section: Integration Of Intron‐seqfish Scrna‐seq and Rna Half‐life Da...mentioning

confidence: 99%

Exploring the role of transcriptional and post‐transcriptional processes in mRNA co‐expression

García‐Blay,

Verhagen,

Martin

et al. 2023

BioEssays

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Co‐expression of two or more genes at the single‐cell level is usually associated with functional co‐regulation. While mRNA co‐expression—measured as the correlation in mRNA levels—can be influenced by both transcriptional and post‐transcriptional events, transcriptional regulation is typically considered dominant. We review and connect the literature describing transcriptional and post‐transcriptional regulation of co‐expression. To enhance our understanding, we integrate four datasets spanning single‐cell gene expression data, single‐cell promoter activity data and individual transcript half‐lives. Confirming expectations, we find that positive co‐expression necessitates promoter coordination and similar mRNA half‐lives. Surprisingly, negative co‐expression is favored by differences in mRNA half‐lives, contrary to initial predictions from stochastic simulations. Notably, this association manifests specifically within clusters of genes. We further observe a striking compensation between promoter coordination and mRNA half‐lives, which additional stochastic simulations suggest might give rise to the observed co‐expression patterns. These findings raise intriguing questions about the functional advantages conferred by this compensation between distal kinetic steps.

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Section: Integration Of Intron‐seqfish Scrna‐seq and Rna Half‐life Da...mentioning

confidence: 99%

Exploring the role of transcriptional and post‐transcriptional processes in mRNA co‐expression

García‐Blay,

Verhagen,

Martin

et al. 2023

BioEssays

View full text Add to dashboard Cite

show abstract

“…With the wide application of molecular biology technology in animal genetics and breeding, it is possible to systematically clarify the molecular regulatory mechanisms underlying gene functions (Miao and Qin 2015). Gene regulation is at the core of all biological behaviors and phenotypes, which is a multi-mode spatial and temporal dynamic process and mainly regulated at transcriptional and post-transcriptional levels (Wang et al 2016). Generally, transcriptome refers to the sum of all RNAs transcribed by an organism in a particular environment or physiological state, including mRNA and noncoding RNA (such as rRNA, tRNA, microRNA, siRNA, piRNA, circle RNA, and lncRNA).…”

mentioning

confidence: 99%

Integrated Analysis of miRNA and mRNA Expression Profiles Reveals Functional miRNA-Targets in Development Testes of Small Tail Han Sheep

Bai

Jia

et al. 2019

G3 Genes|Genomes|Genetics

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Small Tail Han Sheep is a highly valued local breed in China because of their precocity, perennial estrus, and high fecundity. The average annual lambing rate of ewes is as high as 180–270%, the semen of ram has characteristics of high yield, high density, and good motility. To reveal the key miRNAs and miRNA-targets underlying testis development and spermatogenesis in male Small Tail Han Sheep, integrated analysis of miRNA and mRNA expression profiles in 2-, 6-, and 12-month-old testes was performed by RNA-seq technology and bioinformatics methods. The results showed that total of 153 known sheep miRNAs and 2712 novel miRNAs were obtained in 2-,6 - and 12-month-old Small Tail Han Sheep testes; 5, 1, and 4 differentially expressed (DE) known sheep miRNAs, and 132, 105, and 24 DE novel miRNAs were identified in 2- vs. 6-, 6- vs. 12-, and 2- vs. 12-month-old testes, respectively. We combined miRNA results of this study and the mRNA results obtained in our previous study to predict the target mRNAs of DE known sheep miRNAs; 131, 10, and 15 target mRNAs of DE known sheep miRNAs and 76, 1, and 11 DE miRNA–targets were identified in the three groups, respectively. GO and KEGG analyses showed that: in 2- vs. 6-month-olds, the target genes of DE known sheep miRNAs were involved in 100 biological processes and 11 signaling pathways; in 6- vs. 12-month-olds, the target genes of DE known sheep miRNAs were involved in 4 biological processes; and in 2- vs. 12-month-olds, the target genes of DE known sheep miRNAs were involved in 17 biological processes and 4 signaling pathways. Three miR–target regulatory networks were constructed based on these DE miRNA–targets. The key miRNA-Targets involved in testis development and spermatogenesis were screened. 6 known sheep miRNAs and 6 novel miRNAs were selected to validate the accuracy of miRNA sequencing data by qRT-PCR. The binding sites of oar-miR-379-5p with WNT8A was validated by a dual luciferase reporter gene detection system.

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Post-transcriptional and translational regulation modulates gene co-expression behavior in more synchronized pace to carry out molecular function in the cell

Cited by 2 publications

References 22 publications

Exploring the role of transcriptional and post‐transcriptional processes in mRNA co‐expression

Exploring the role of transcriptional and post‐transcriptional processes in mRNA co‐expression

Integrated Analysis of miRNA and mRNA Expression Profiles Reveals Functional miRNA-Targets in Development Testes of Small Tail Han Sheep

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