Cis- and trans-regulation of luteovirus gene expression by the 3′ end of the viral genome

Abstract Understanding the persistence of genetic variation within populations has long been a goal of evolutionary biology. One promising route toward achieving this goal is using population genetic approaches to describe how selection acts on the loci associated with trait variation. Gene expression provides a model trait for addressing the challenge of the maintenance of variation because it can be measured genome-wide without information about how gene expression affects traits. Previous work has shown that loci affecting the expression of nearby genes (local or cis-eQTLs) are under negative selection, but we lack a clear understanding of the selective forces acting on variants that affect the expression of genes in trans. Here, we identify loci that affect gene expression in trans using genomic and transcriptomic data from one population of the obligately outcrossing plant, Capsella grandiflora. The allele frequencies of trans-eQTLs are consistent with stronger negative selection acting on trans-eQTLs than cis-eQTLs, and stronger negative selection acting on trans-eQTLs associated with the expression of multiple genes. However, despite this general pattern, we still observe the presence of a trans-eQTL at intermediate frequency that affects the expression of a large number of genes in the same coexpression module. Overall, our work highlights the different selective pressures shaping variation in cis- and trans-regulation.

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RNA-Seq analysis reveals expression regulatory divergence of W-linked genes between two contrasting chicken breeds

10.21203/rs.3.rs-1201051/v1 ◽

2022 ◽

Author(s):

Hongchang Gu ◽

Liang Wang ◽

Xueze Lv ◽

Weifang Yang ◽

Yu Chen ◽

...

Keyword(s):

Gene Expression ◽

Sex Chromosomes ◽

Phenotypic Diversity ◽

Regulation Of Gene Expression ◽

W Chromosome ◽

White Leghorn ◽

Complex Process ◽

Chicken Breeds ◽

Trans Regulation ◽

Cis And Trans

Abstract The regulation of gene expression is a complex process involving organism function and phenotypic diversity, and is caused by cis- and trans- regulation. While prior studies identified the regulatory pattern of the autosome rewiring in hybrids, the role of gene regulation in W sex chromosomes is not clear due to their degradation and sex-limit expression. Here, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, which exhibited broad differences of gender-related traits, and assessed the expression of the genes on W chromosome to disentangle the contribution of cis- and trans-factors to expression divergence. We found that there was not appear to be an association between female fecundity and W chromosome gene expression, that 44% of expressed genes had divergent expression between breeds in both tissues, with only 17% of them showing greater expression in White Leghorn. We observed that the proportion of trans-acting genes in W chromosome was higher than cis-regulatory divergence. There were most parental divergence expression genes in muscle, also more heterosis compared with other two tissues. A strong dominant impact of Cornish alleles in brain, while obvious crosses-specific regulatory patterns appeared in liver. Taken together, this work describes the regulatory divergence of W-linked genes between two contrasting breeds and indicates sex chromosomes have a unique regulation and expression mechanism.

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Comprehensive Analysis of Differential Expression Profiles of Long Non-coding RNAs with Associated Co-expression and Competing Endogenous RNA Networks in the Hippocampus of Patients with Alzheimer's Disease

Current Alzheimer Research ◽

10.2174/1567205018666211202143449 ◽

2021 ◽

Vol 18 ◽

Author(s):

Jian-Jun Zhang ◽

Ze-Xuan-Zhu ◽

Guang-Min-Xu ◽

Peng Su ◽

Qian Lei ◽

...

Keyword(s):

Gene Expression ◽

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Expression Profiles ◽

Gene Expression Omnibus ◽

Competing Endogenous Rna ◽

Pathogenic Genes ◽

Non Coding Rna ◽

Using Data ◽

Trans Regulation

Background: Alzheimer's disease (AD) is still one of the major threats to human health. Although a satisfactory treatment for AD has not yet been discovered, it is necessary to continue to search for novel approaches to deal with this insidious and debilitating disease. Although numerous studies have shown that long non-coding RNA (lncRNA) occupy a significant role in a variety of diseases, their roles in AD remain unclear. Objectives: Using data analysis to explore the role of lncRNA in the course of AD, to further our understanding of AD, and to look forward to finding a new breakthrough for the treatment of AD. Methods: We downloaded and screened expression data of the hippocampal regions of patients with AD from the Gene Expression Omnibus database. We generated lncRNA-miRNA-mRNA networks based on the competing endogenous RNA (ceRNA) hypothesis, and according to gene expression level, we constructed a coding-noncoding co-expression (CNC) network and then executed cis- and trans-regulation analyses. Results: Through comprehensive and systematic analyses, we found that lncRNAs MALAT1, OIP5-AS1, LINC00657, and lnc-NUMB-1 regulated the expression of the key AD pathogenic genes APP, PSEN1, BACE1; and that these lncRNAs may promote the distribution of β-amyloid (Aβ protein) in the brain through exosomes. In addition, lncRNAs were found to adjust viral transcriptional expression, thereby further supporting viral pathogenesis for AD. Conclusions: The lncRNAs MALAT1, OIP5-AS1, LINC00657, and lnc-NUMB-1 that are present in the hippocampus of AD patients exert an important influence on the development of this disease.

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Alternative translation and alternative RNA processing mechanism in parvovirus RNA processing

10.32469/10355/45905 ◽

2014 ◽

Author(s):

◽

Olufemi Fasina

Keyword(s):

Gene Expression ◽

Rna Processing ◽

Viral Genome ◽

Transcription Initiation ◽

Alternative Polyadenylation ◽

Open Reading Frames ◽

Genome Replication ◽

University Of Missouri ◽

Diverse Range ◽

Viral Genome Replication

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Viruses as obligate intracellular metabolic parasite require the capacity to orchestrate and modulate the host environment either in the nucleus or cytoplasm for their efficient reproductive life cycle. This warrants the use of diverse range of proteins expressed from the viral genome with the ability of regulating viral genome replication, transcription and translation, in addition antagonizing host factors inhibitory to the virus. Therefore, in order to achieve these goals, viruses utilizes gene expression strategies to expand their coding capacity. Gene expression mechanism such as transcription initiation, capping, splicing and 3ï¿½-end processing afford viruses the opportunities to utilize the eukaryotic metabolic machineries for generating proteome diversity. Parvoviruses and other DNA viruses effectively capitalize on their use of nuclear eukaryotic metabolic machineries to co-opt host cell factors for optimal replication and gene expression. Parvoviruses with small genome size and overlapping open reading frames utilize alternative transcription initiation, alternative splicing and alternative polyadenylation to co-ordinate the expression of its non-structural and structural proteins. In this work, we have characterized how two parvoviruses; Dependovirus AAV5 and Bocavirus Minute virus of canine (MVC) utilize alternative gene expression mechanisms and strategies to optimize expression of viral proteins from their genome.

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Cis- and trans-repression of class I major histocompatibility gene expression in Abelson virus-transformed murine leukemia

Blood ◽

10.1182/blood.v78.2.524.524 ◽

1991 ◽

Vol 78 (2) ◽

pp. 524-532 ◽

Cited By ~ 3

Author(s):

RA Zeff ◽

YF Zhao ◽

R Tatake ◽

H Lachman ◽

F Borriello ◽

...

Keyword(s):

Gene Expression ◽

Cell Line ◽

Mhc Class I ◽

Leukemic Cell ◽

Class I ◽

Leukemic Cell Line ◽

Cis And Trans ◽

I Gene ◽

Murine Leukemia ◽

Mhc Class I Gene

Abstract Numerous tumor cell lines of leukemic origin are known to modulate cell surface expression of major histocompatibility complex (MHC) class I antigens resulting in alterations in their immune detection and tumorigenicity. We have been studying the mechanisms responsible for attenuation of MHC class I gene expression in an H-2 heterozygous (H-2b x H-2d) Abelson-Murine leukemia virus (A-MuLV)-transformed leukemic cell line (designated R8). Here we report that treatment of the R8 cell line with the protein synthesis inhibitor cycloheximide (CHX) increased H-2Kb steady-state messenger RNA (mRNA) levels several fold. The induced H-2Kb mRNA transcripts were functional, as demonstrated by their ability to be translated into immunoprecipitable H-2Kb alloantigen. H-2Kb null variants derived from the R8 cell line were shown to be the product of both cis- and trans-acting mechanisms, insomuch as the treatment of R8-derived H-2Kb non-expressor lines with CHX re-established expression of H-2Kb mRNA to the same extent as transfection of the variant cell line with the wild-type H-2Kb gene. Such findings indicate that downregulation of MHC class I gene expression is constitutive for the R8 leukemic cell line, a phenomenon that may be related to the immature pre-B-cell phenotype of this A-MuLV transformant.

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Landscape and evolution of cis- and trans-regulatory divergence in chicken genome between two contrasted breeds analyzed in three tissues at one day age

10.21203/rs.2.10726/v2 ◽

2019 ◽

Author(s):

Qiong Wang ◽

Yaxiong Jia ◽

Yuan Wang ◽

Zhihua Jiang ◽

Xiang Zhou ◽

...

Keyword(s):

Chicken Genome ◽

Reproductive Traits ◽

Purifying Selection ◽

Population Divergence ◽

Specific Reference ◽

Specific Expression ◽

Allele Specific Expression ◽

Allele Specific ◽

Trans Regulation ◽

Cis And Trans

Abstract Background: Gene expression variation is an important mechanism underlying phenotypic variation, and can occur via cis- and trans-regulation. In order to understand the role of cis- and trans-regulatory variation on population divergence of chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, with major differences in body size and reproductive traits, and used them to identify the degree of cis versus trans variation in brain, liver and muscle of both male and female samples at 1 day age. Results: We provided a landscape about how the transcriptomes are regulated in the hybrid progenies of two contrasted breeds by allele specific expression analysis. Our results showed that compared with the cis-regulatory divergence, trans-acted genes existed more extensively in the chicken genome. Furthermore, a widespread tendency of compensatory regulation exists in chicken genome. Most importantly, we found the evidence of stronger purifying selection on genes regulated by trans variations than the cis elements. Conclusions: We demonstrated a pipeline to explore the allele-specific expression in the hybrid progenies of inbred lines without specific reference genome. Our research performed the first study to describe the regulatory divergence between two contrasted breeds. The results suggested that artificial selection associated with domestication in chicken may have more often acted on trans-regulatory divergence than cis.

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