Measuring cis-acting regulatory variants genome-wide: new insights into expression genetics and disease susceptibility

AbstractGenome-wide association studies have identified numerous disease-susceptibility genes. As knowledge of gene–disease associations accumulates, it is becoming increasingly important to translate this knowledge into clinical practice. This challenge involves finding effective drug targets and estimating their potential side effects, which often results in failure of promising clinical trials. Here, we review recent advances and future perspectives in genetics-led drug discovery, with a focus on drug repurposing, Mendelian randomization, and the use of multifaceted omics data.

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Genome-Wide Identification and Expression Analyses of CONSTANS-Like Family Genes in Cucumber (Cucumis sativus L.)

Journal of Plant Growth Regulation ◽

10.1007/s00344-021-10420-4 ◽

2021 ◽

Author(s):

Zhen Tian ◽

Xiaodong Qin ◽

Hui Wang ◽

Ji Li ◽

Jinfeng Chen

Keyword(s):

Floral Induction ◽

Structural Characteristics ◽

Expression Patterns ◽

Evolutionary Relationship ◽

Biological Functions ◽

Promoter Regions ◽

Cucumis Sativus L ◽

Cis Acting ◽

Genome Wide ◽

Induction Process

AbstractThe CONSTANS-like (COL) gene family is one of the plant-specific transcription factor families that play important roles in plant growth and development. However, the knowledge of COLs related in cucumber is limited, and their biological functions, especially in the photoperiod-dependent flowering process, are still unclear. In this study, twelve CsaCOL genes were identified in the cucumber genome. Phylogenetic and conserved motif analyses provided insights into the evolutionary relationship between the CsaCOLs. Further, the comparative genome analysis revealed that COL genes are conserved in different plant species, especially collinearity gene pairs related to CsaCOL5. Ten kinds of cis-acting elements were vividly detected in CsaCOLs promoter regions, including five light-responsive elements, which echo the diurnal rhythm expression patterns of seven CsaCOL genes under SD and LD photoperiod regimes. Combined with the expression data of developmental stage, three CsaCOL genes are involved in the flowering network and play pivotal roles for the floral induction process. Our results provide useful information for further elucidating the structural characteristics, expression patterns, and biological functions of COL family genes in many plants

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Phosphate transporter genes: genome-wide identification and characterization in Camelina sativa

10.1101/2021.02.28.433256 ◽

2021 ◽

Author(s):

Soosan Hasanzadeh ◽

Sahar Faraji ◽

Abdullah ◽

Parviz Heidari

Keyword(s):

Phosphate Transporter ◽

Rna Seq ◽

Specific Expression ◽

Cis Acting ◽

Genome Wide ◽

Sodium Dependent ◽

Intron Number ◽

Response To Stress ◽

Growth Energy ◽

Root Tissues

Phosphorus is known as a key element associated with growth, energy, and cell signaling. In plants, phosphate transporters (PHTs) are responsible for moving and distributing phosphorus in cells and organs. PHT genes have been genome-wide identified and characterized in various plant species, however, these genes have not been widely identified based on available genomic data in Camellia sativa, which is an important oil seed plant. In the present study, we found 66 PHT genes involved in phosphate transporter/translocate in C. sativa. The recognized genes belonged to PHTs1, PHTs2, PHTs4, PHOs1, PHO1 homologs, glycerol-3-PHTs, sodium dependent PHTs, inorganic PHTs, xylulose 5-PHTs, glucose-6-phosphate translocators, and phosphoenolpyruvate translocators. Our finding revealed that PHT proteins are divers based on their physicochemical properties such as Isoelectric point (pI), molecular weight, GRAVY value, and exon-intron number(s). Besides, the expression profile of PHT genes in C. sativa based on RNA-seq data indicate that PHTs are involved in response to abiotic stresses such as cold, drought, salt, and cadmium. The tissue specific expression high expression of PHO1 genes in root tissues of C. sativa. In additions, four PHTs, including a PHT4;5 gene, a sodium dependent PHT gene, and two PHO1 homolog 3 genes were found with an upregulation in response to aforementioned studied stresses. In the current study, we found that PHO1 proteins and their homologs have high potential to post-translation modifications such as N-glycosylation and phosphorylation. Besides, different cis-acting elements associated with response to stress and phytohormone were found in the promoter region of PHT genes. Overall, our results show that PHT genes play various functions in C. Sativa and regulate Camellia responses to external and intracellular stimuli. The results can be used in future studies related to the functional genomics of C. sativa.

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Genome-Wide Identification and Characterization of the RCI2 Gene Family in Allotetraploid Brassica napus Compared with Its Diploid Progenitors

International Journal of Molecular Sciences ◽

10.3390/ijms23020614 ◽

2022 ◽

Vol 23 (2) ◽

pp. 614

Author(s):

Weiqi Sun ◽

Mengdi Li ◽

Jianbo Wang

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Gene Structure ◽

Stress Responses ◽

Stress Protein ◽

Purifying Selection ◽

Cis Acting ◽

Genome Wide ◽

Duplication Events

Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are suitable for studying the problems associated with polyploidization. As an important anti-stress protein, RCI2 proteins widely exist in various tissues of plants, and are crucial to plant growth, development, and stress response. In this study, the RCI2 gene family was comprehensively identified and analyzed, and 9, 9, and 24 RCI2 genes were identified in B. rapa, B. oleracea, and B. napus, respectively. Phylogenetic analysis showed that all of the identified RCI2 genes were divided into two groups, and further divided into three subgroups. Ka/Ks analysis showed that most of the identified RCI2 genes underwent a purifying selection after the duplication events. Moreover, gene structure analysis showed that the structure of RCI2 genes is largely conserved during polyploidization. The promoters of the RCI2 genes in B. napus contained more cis-acting elements, which were mainly involved in plant development and growth, plant hormone response, and stress responses. Thus, B. napus might have potential advantages in some biological aspects. In addition, the changes of RCI2 genes during polyploidization were also discussed from the aspects of gene number, gene structure, gene relative location, and gene expression, which can provide reference for future polyploidization analysis.

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Genome-wide identification and analysis of the CNGC gene family in maize

PeerJ ◽

10.7717/peerj.5816 ◽

2018 ◽

Vol 6 ◽

pp. e5816 ◽

Cited By ~ 4

Author(s):

Lidong Hao ◽

Xiuli Qiao

Keyword(s):

Gene Family ◽

Expression Profiles ◽

Gene Families ◽

Regulatory Elements ◽

Vital Role ◽

Signal Pathways ◽

Cis Acting ◽

Genome Wide ◽

Gramineous Plant ◽

Gated Channel

As one of the non-selective cation channel gene families, the cyclic nucleotide-gated channel (CNGC) gene family plays a vital role in plant physiological processes that are related to signal pathways, plant development, and environmental stresses. However, genome-wide identification and analysis of the CNGC gene family in maize has not yet been undertaken. In the present study, twelve ZmCNGC genes were identified in the maize genome, which were unevenly distributed on chromosomes 1, 2, 4, 5, 6, 7, and 8. They were classified into five major groups: Groups I, II, III, IVa, and IVb. Phylogenetic analysis showed that gramineous plant CNGC genes expanded unequally during evolution. Group IV CNGC genes emerged first, whereas Groups I and II appeared later. Prediction analysis of cis-acting regulatory elements showed that 137 putative cis-elements were related to hormone-response, abiotic stress, and organ development. Furthermore, 120 protein pairs were predicted to interact with the 12 ZmCNGC proteins and other maize proteins. The expression profiles of the ZmCNGC genes were expressed in tissue-specific patterns. These results provide important information that will increase our understanding of the CNGC gene family in maize and other plants.

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Global analysis of asymmetric RNA enrichment in oocytes reveals low conservation between closely related Xenopus species

Molecular Biology of the Cell ◽

10.1091/mbc.e15-02-0115 ◽

2015 ◽

Vol 26 (21) ◽

pp. 3777-3787 ◽

Cited By ~ 7

Author(s):

Maike Claußen ◽

Thomas Lingner ◽

Claudia Pommerenke ◽

Lennart Opitz ◽

Gabriela Salinas ◽

...

Keyword(s):

Xenopus Laevis ◽

Global Analysis ◽

Primordial Germ Cells ◽

Binding Studies ◽

Closely Related Species ◽

Cis Acting ◽

Genome Wide ◽

Vegetal Cortex ◽

Gain Loss ◽

Germ Layer Patterning

RNAs that localize to the vegetal cortex during Xenopus laevis oogenesis have been reported to function in germ layer patterning, axis determination, and development of the primordial germ cells. Here we report on the genome-wide, comparative analysis of differentially localizing RNAs in Xenopus laevis and Xenopus tropicalis oocytes, revealing a surprisingly weak degree of conservation in respect to the identity of animally as well as vegetally enriched transcripts in these closely related species. Heterologous RNA injections and protein binding studies indicate that the different RNA localization patterns in these two species are due to gain/loss of cis-acting localization signals rather than to differences in the RNA-localizing machinery.

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Genome-Wide Identification of WRKY Genes in Artemisia annua: Characterization of a Putative Ortholog of AtWRKY40

Plants ◽

10.3390/plants9121669 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1669

Author(s):

Angelo De Paolis ◽

Sofia Caretto ◽

Angela Quarta ◽

Gian-Pietro Di Sansebastiano ◽

Irene Sbrocca ◽

...

Keyword(s):

Artemisia Annua ◽

Antimalarial Activity ◽

Regulatory Elements ◽

Promoter Regions ◽

Cis Acting ◽

Protein Motifs ◽

Genome Wide ◽

A Genome ◽

Rapid Amplification

Artemisia annua L. is well-known as the plant source of artemisinin, a sesquiterpene lactone with effective antimalarial activity. Here, a putative ortholog of the Arabidopsis thaliana WRKY40 transcription factor (TF) was isolated via reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends in A. annua and named AaWRKY40. A putative nuclear localization domain was identified in silico and experimentally confirmed by using protoplasts of A. annua transiently transformed with AaWRKY40-GFP. A genome-wide analysis identified 122 WRKY genes in A. annua, and a manually curated database was obtained. The deduced proteins were categorized into the major WRKY groups, with group IIa containing eight WRKY members including AaWRKY40. Protein motifs, gene structure, and promoter regions of group IIa WRKY TFs of A. annua were characterized. The promoter region of AaWRKY group IIa genes contained several abiotic stress cis-acting regulatory elements, among which a highly conserved W-box motif was identified. Expression analysis of AaWRKY40 compared to AaWRKY1 in A. annua cell cultures treated with methyl jasmonate known to enhance artemisinin production, suggested a possible involvement of AaWRKY40 in terpenoid metabolism. Further investigation is necessary to study the role of AaWRKY40 and possible interactions with other TFs in A. annua.

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