scholarly journals Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the AllotetraploidArabidopsis kamchatica

2016 ◽  
Vol 33 (11) ◽  
pp. 2781-2800 ◽  
Author(s):  
Timothy Paape ◽  
Masaomi Hatakeyama ◽  
Rie Shimizu-Inatsugi ◽  
Teo Cereghetti ◽  
Yoshihiko Onda ◽  
...  
Keyword(s):  
Gene Expression ◽  
Parental Gene

Circular RNA as a potential diagnostic and/or therapeutic target for endometriosis

2020 ◽  
Vol 14 (13) ◽  
pp. 1277-1287
Author(s):  
Parisa M Dana ◽  
Mona Taghavipour ◽  
Hamed Mirzaei ◽  
Bahman Yousefi ◽  
Bahram Moazzami ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signaling Pathways ◽  
Therapeutic Target ◽  
Noncoding Rnas ◽  
Circular Rna ◽  
Circular Rnas ◽  
Biological Functions ◽  
Parental Gene

Endometriosis is a pathology form of endometrium that behaves in a similar way to malignancies, such as invasion and resistance to apoptosis. Circular RNAs (CircRNAs) are a class of noncoding RNAs that have several biological functions including, miRNA sponging, sequestering of proteins, enhancing parental gene expression and translation resulting in polypeptides. In this review, we highlighted the roles of circRNAs as potential diagnostic and therapeutic biomarkers in endometriosis. Moreover, we summarized the roles of circRNAs in the pathogenesis of endometriosis via different signaling pathways, such as the miRNA network and apoptosis.

scholarly journals The World of Pseudogenes: New Diagnostic and Therapeutic Targets in Cancers or Still Mystery Molecules?

Life ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1354
Author(s):  
Maciej Stasiak ◽  
Tomasz Kolenda ◽  
Joanna Kozłowska-Masłoń ◽  
Joanna Sobocińska ◽  
Paulina Poter ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Diagnostics ◽  
Antisense Rna ◽  
Biological Fluids ◽  
Detection Methods ◽  
Bioinformatic Tools ◽  
The World ◽  
Parental Gene ◽  
Different Types ◽  
Large Groups

Pseudogenes were once considered as “junk DNA”, due to loss of their functions as a result of the accumulation of mutations, such as frameshift and presence of premature stop-codons and relocation of genes to inactive heterochromatin regions of the genome. Pseudogenes are divided into two large groups, processed and unprocessed, according to their primary structure and origin. Only 10% of all pseudogenes are transcribed into RNAs and participate in the regulation of parental gene expression at both transcriptional and translational levels through senseRNA (sRNA) and antisense RNA (asRNA). In this review, about 150 pseudogenes in the different types of cancers were analyzed. Part of these pseudogenes seem to be useful in molecular diagnostics and can be detected in various types of biological material including tissue as well as biological fluids (liquid biopsy) using different detection methods. The number of pseudogenes, as well as their function in the human genome, is still unknown. However, thanks to the development of various technologies and bioinformatic tools, it was revealed so far that pseudogenes are involved in the development and progression of certain diseases, especially in cancer.

scholarly journals Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Duo Chen ◽  
Peng-Cheng Yan ◽  
Yan-Ping Guo
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Specific Gene ◽  
Differential Adaptation ◽  
Expression Bias ◽  
Parental Gene ◽  
Species Specific ◽  
Go Terms ◽  
Allotetraploid Species

Abstract Background Polyploid species often originate recurrently. While this is well known, there is little information on the extent to which distinct allotetraploid species formed from the same parent species differ in gene expression. The tetraploid yarrow species Achillea alpina and A. wilsoniana arose independently from allopolyploidization between diploid A. acuminata and A. asiatica. The genetics and geography of these origins are clear from previous studies, providing a solid basis for comparing gene expression patterns of sibling allopolyploid species that arose independently. Results We conducted comparative RNA-sequencing analyses on the two Achillea tetraploid species and their diploid progenitors to evaluate: 1) species-specific gene expression and coexpression across the four species; 2) patterns of inheritance of parental gene expression; 3) parental contributions to gene expression in the allotetraploid species, and homeolog expression bias. Diploid A. asiatica showed a higher contribution than diploid A. acuminata to the transcriptomes of both tetraploids and also greater homeolog bias in these transcriptomes, possibly reflecting a maternal effect. Comparing expressed genes in the two allotetraploids, we found expression of ca. 30% genes were species-specific in each, which were most enriched for GO terms pertaining to “defense response”. Despite species-specific and differentially expressed genes between the two allotetraploids, they display similar transcriptome changes in comparison to their diploid progenitors. Conclusion Two independently originated Achillea allotetraploid species exhibited difference in gene expression, some of which must be related to differential adaptation during their post-speciation evolution. On the other hand, they showed similar expression profiles when compared to their progenitors. This similarity might be expected when pairs of merged diploid genomes in tetraploids are similar, as is the case in these two particular allotetraploids.

scholarly journals Parental bias in expression and interaction of genes in the equine placenta

2021 ◽  
Vol 118 (16) ◽  
pp. e2006474118
Author(s):  
Pouya Dini ◽  
Theodore Kalbfleisch ◽  
José M. Uribe-Salazar ◽  
Mariano Carossino ◽  
Hossam El-Sheikh Ali ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Parental Origin ◽  
Minimal Extension ◽  
Specific Expression ◽  
Biallelic Expression ◽  
Fundamental Information ◽  
Parental Gene ◽  
Allele Specific ◽  
Length Of Gestation

Most autosomal genes in the placenta show a biallelic expression pattern. However, some genes exhibit allele-specific transcription depending on the parental origin of the chromosomes on which the copy of the gene resides. Parentally expressed genes are involved in the reciprocal interaction between maternal and paternal genes, coordinating the allocation of resources between fetus and mother. One of the main challenges of studying parental-specific allelic expression (allele-specific expression [ASE]) in the placenta is the maternal cellular remnant at the fetomaternal interface. Horses (Equus caballus) have an epitheliochorial placenta in which both the endometrial epithelium and the epithelium of the chorionic villi are juxtaposed with minimal extension into the uterine mucosa, yet there is no information available on the allelic gene expression of equine chorioallantois (CA). In the current study, we present a dataset of 1,336 genes showing ASE in the equine CA (https://pouya-dini.github.io/equine-gene-db/) along with a workflow for analyzing ASE genes. We further identified 254 potentially imprinted genes among the parentally expressed genes in the equine CA and evaluated the expression pattern of these genes throughout gestation. Our gene ontology analysis implies that maternally expressed genes tend to decrease the length of gestation, while paternally expressed genes extend the length of gestation. This study provides fundamental information regarding parental gene expression during equine pregnancy, a species with a negligible amount of maternal cellular remnant in its placenta. This information will provide the basis for a better understanding of the role of parental gene expression in the placenta during gestation.

scholarly journals Effects of parental genetic divergence on gene expression patterns in interspecific hybrids of Camellia

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Min Zhang ◽  
Yi-Wei Tang ◽  
Ji Qi ◽  
Xin-Kai Liu ◽  
Dan-Feng Yan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Divergence ◽  
Molecular Basis ◽  
Interspecific Hybrids ◽  
Expression Patterns ◽  
Expression Change ◽  
Significant Evidence ◽  
Expression Difference ◽  
Parental Gene ◽  
Over Time

Abstract Background The merging of two divergent genomes during hybridization can result in the remodeling of parental gene expression in hybrids. A molecular basis underling expression change in hybrid is regulatory divergence, which may change with the parental genetic divergence. However, there still no unanimous conclusion for this hypothesis. Results Three species of Camellia with a range of genetic divergence and their F1 hybrids were used to study the effect of parental genetic divergence on gene expression and regulatory patterns in hybrids by RNA-sequencing and allelic expression analysis. We found that though the proportion of differentially expressed genes (DEGs) between the hybrids and their parents did not increase, a greater proportion of DEGs would be non-additively (especially transgressively) expressed in the hybrids as genomes between the parents become more divergent. In addition, the proportion of genes with significant evidence of cis-regulatory divergence increased, whereas with trans-regulatory divergence decreased with parental genetic divergence. Conclusions The discordance within hybrid would intensify as the parents become more divergent, manifesting as more DEGs would be non-additively expressed. Trans-regulatory divergence contributed more to the additively inherited genes than cis, however, its contribution to expression difference would be weakened as cis mutations accumulated over time; and this might be an important reason for that the more divergent the parents are, the greater proportion of DEGs would be non-additively expressed in hybrid.

scholarly journals Effects of parental genetic divergence on gene expression patterns in interspecific hybrids of Camellia

2019 ◽  
Author(s):  
Min Zhang ◽  
Yi-Wei Tang ◽  
Ji Qi ◽  
Xin-Kai Liu ◽  
Dan-Feng Yan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Divergence ◽  
Molecular Basis ◽  
Gene Expression Analysis ◽  
Expression Patterns ◽  
Specific Gene ◽  
Expression Change ◽  
Expression Difference ◽  
Parental Gene ◽  
Allele Specific

Abstract Background: The merging of two divergent genomes during hybridization can result in the remodeling of parental gene expression in hybrids. A molecular basis underling expression change in hybrid is regulatory divergence, which may change with the parental genetic divergence. However, there still no unanimous conclusion for this hypothesis. Results : Three species of Camellia with a range of genetic divergence and their F 1 hybrids were used to study the effect of parental genetic divergence on gene expression and regulatory patterns in hybrids by RNA-sequencing and allele-specific gene expression analysis. We found that though the proportion of differentially expressed genes (DEGs) between the hybrids and their parents did not increase, a greater proportion of DEGs would be non-additively (especially transgressively) expressed in the hybrids as genomes between the parents become more divergent . In addition, the proportion of genes with significant evidence of cis -regulatory divergence increased , whereas with trans -regulatory divergence decreased with parental genetic divergence. Conclusions : The discordance within hybrid would intensify as the parents become more divergent, manifesting as more DEGs would be non-additively expressed. Trans -regulatory divergence contributed more to the additively inherited genes than cis , however, its contribution to expression difference would be weakened as cis mutations accumulated over time; and this might be an important reason for that the more divergent the parents are, the greater proportion of DEGs would be non-additively expressed in hybrid.

scholarly journals Effects of parental genetic divergence on gene expression patterns in interspecific hybrids of Camellia

2019 ◽  
Author(s):  
Min Zhang ◽  
Yi-Wei Tang ◽  
Ji Qi ◽  
Xin-Kai Liu ◽  
Dan-Feng Yan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Divergence ◽  
Molecular Basis ◽  
Interspecific Hybrids ◽  
Expression Patterns ◽  
Expression Change ◽  
Significant Evidence ◽  
Expression Difference ◽  
Parental Gene ◽  
Over Time

Abstract Background: The merging of two divergent genomes during hybridization can result in the remodeling of parental gene expression in hybrids. A molecular basis underling expression change in hybrid is regulatory divergence, which may change with the parental genetic divergence. However, there still no unanimous conclusion for this hypothesis. Results : Three species of Camellia with a range of genetic divergence and their F 1 hybrids were used to study the effect of parental genetic divergence on gene expression and regulatory patterns in hybrids by RNA-sequencing and allelic expression analysis. We found that though the proportion of differentially expressed genes (DEGs) between the hybrids and their parents did not increase, a greater proportion of DEGs would be non-additively (especially transgressively) expressed in the hybrids as genomes between the parents become more divergent . In addition, the proportion of genes with significant evidence of cis -regulatory divergence increased , whereas with trans -regulatory divergence decreased with parental genetic divergence. Conclusions : The discordance within hybrid would intensify as the parents become more divergent, manifesting as more DEGs would be non-additively expressed. Trans -regulatory divergence contributed more to the additively inherited genes than cis , however, its contribution to expression difference would be weakened as cis mutations accumulated over time; and this might be an important reason for that the more divergent the parents are, the greater proportion of DEGs would be non-additively expressed in hybrid.

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