fatvg encodes a new localized RNA that uses a 25-nucleotide element (FVLE1) to localize to the vegetal cortex of Xenopus oocytes

Development ◽  
1999 ◽  
Vol 126 (22) ◽  
pp. 4943-4953 ◽  
Author(s):  
A.P. Chan ◽  
M. Kloc ◽  
L.D. Etkin
Keyword(s):  
Cell Fate ◽  
Xenopus Oocytes ◽  
Single Copy ◽  
Biological Functions ◽  
Embryonic Patterning ◽  
Cis Acting ◽  
Maternal Transcript ◽  
Vegetal Cortex ◽  
Mitochondrial Cloud ◽  
Localization Elements

Vegetally localized transcripts have been implicated in a number of important biological functions, including cell fate determination and embryonic patterning. We have isolated a cDNA, fatvg, which encodes a localized maternal transcript that exhibits a localization pattern reminiscent of Vg1 mRNA. fatvg is the homologue of a mammalian gene expressed in adipose tissues. The fatvg transcript, unlike Vg1 which localizes strictly through the Late pathway, also associates with the mitochondrial cloud that is characteristic of the METRO or Early pathway. This suggests that fatvg mRNA may utilize both the METRO and Late pathways to localize to the vegetal cortex during oogenesis. We have dissected the cis-acting localization elements of fatvg mRNA and compared these elements with Vg1 mRNA. Our results indicate that, like most localized RNAs, in a variety of systems, transcripts of fatvg contain localization elements in the 3′UTR. The 3′UTR of fatvg mRNA contains multiple elements that are able to function independently; however, it functions most efficiently when all of the elements are present. We have defined a short 25-nucleotide element that can direct vegetal localization as a single copy. This element differs in sequence from previously described Vg1 localization elements, suggesting that different localization elements are involved in the localization of RNAs through the Late pathway.

scholarly journals A mRNA localized to the vegetal cortex of Xenopus oocytes encodes a protein with a nanos-like zinc finger domain

Development ◽  
1993 ◽  
Vol 117 (1) ◽  
pp. 377-386 ◽  
Author(s):  
L. Mosquera ◽  
C. Forristall ◽  
Y. Zhou ◽  
M.L. King
Keyword(s):  
Cell Fate ◽  
Zinc Finger ◽  
Regional Differences ◽  
Xenopus Oocytes ◽  
Rna Binding ◽  
Protein Product ◽  
Posterior Pole ◽  
Cortical Region ◽  
Zinc Finger Domain ◽  
Vegetal Cortex

mRNAs concentrated in specific regions of the oocyte have been found to encode determinants that specify cell fate. We show that an intermediate filament fraction isolated from Xenopus stage VI oocytes specifically contains, in addition to Vg1 RNA, a new localized mRNA, Xcat-2. Like Vg1, Xcat-2 is found in the vegetal cortical region, is inherited by the vegetal blasomeres during development, and is degraded very early in development. Sequence analysis suggests that Xcat-2 encodes a protein that belongs to the CCHC RNA-binding family of zinc finger proteins. Interestingly, the closest known relative to Xcat-2 in this family is nanos, an RNA localized to the posterior pole of the Drosophila oocyte whose protein product suppresses the translation of the transcription factor hunchback. The localized and maternally restricted expression of Xcat-2 RNA suggests a role for its protein in setting up regional differences in gene expression that occur early in development.

Two copies of a subelement from the Vg1 RNA localization sequence are sufficient to direct vegetal localization in Xenopus oocytes

Development ◽  
1997 ◽  
Vol 124 (24) ◽  
pp. 5013-5020 ◽  
Author(s):  
D. Gautreau ◽  
C.A. Cote ◽  
K.L. Mowry
Keyword(s):  
Xenopus Oocytes ◽  
Rna Localization ◽  
Sequence Motifs ◽  
Sequence Element ◽  
Cis Acting ◽  
Vegetal Cortex ◽  
Sequence Elements ◽  
Localization Sequence ◽  
Localization Signal ◽  
Localization Element

Localization of mRNA has emerged as a fundamental mechanism for generating polarity during development. In vertebrates, one example of this phenomenon is Vg1 RNA, which is localized to the vegetal cortex of Xenopus oocytes. Vegetal localization of Vg1 RNA is directed by a 340-nt sequence element contained within its 3′ untranslated region. To investigate how such cis-acting elements function in the localization process, we have undertaken a detailed analysis of the precise sequence requirements for vegetal localization within the 340-nt localization element. We present evidence for considerable redundancy within the localization element and demonstrate that critical sequences lie at the ends of the element. Importantly, we show that a subelement from the 5′ end of the Vg1 localization element is, when duplicated, sufficient to direct vegetal localization. We suggest that the Vg1 localization element is composed of smaller, redundant sequence motifs and identify one such 6-nt motif as essential for localization. These results allow insight into what constitutes an RNA localization signal and how RNA sequence elements may act in the localization process.

Two distinct pathways for the localization of RNAs at the vegetal cortex in Xenopus oocytes

Development ◽  
1995 ◽  
Vol 121 (2) ◽  
pp. 287-297 ◽  
Author(s):  
M. Kloc ◽  
L.D. Etkin
Keyword(s):  
Xenopus Laevis ◽  
Xenopus Oocytes ◽  
Spatial Localization ◽  
Distinct Pattern ◽  
Body Axis ◽  
The Other ◽  
Actin Microfilaments ◽  
Vegetal Cortex ◽  
Oocyte Cytoplasm ◽  
Mitochondrial Cloud

We found that there are two major pathways by which RNAs are localized at the vegetal cortex during oogenesis of Xenopus laevis. One of these, through which Xlsirts, Xcat2 and Xwnt11 are localized, involves transport during stages 1 and 2 of oogenesis via a region of the mitochondrial cloud that we call the message transport organizer or METRO. This pathway involved three steps, transport of RNA from the GV to the mitochondrial cloud, sorting of the RNAs to specific regions of the METRO, and translocation to and anchoring at the vegetal cortex. These three RNAs exhibit a distinct pattern of spatial localization within the METRO when they approach the vegetal cortex. The other pathway is used by Vg1. We detected Vg1 throughout the oocyte cytoplasm during stages 1 and 2. During stage 3 it was translocated to the vegetal cortex and associated with the cortex overlapping the region at which the Xlsirt, Xcat2, and Xwnt11 RNAs are anchored. Our results also showed that anchoring of these RNAs was dependent in part on actin microfilaments, but was independent of microtubules. These results demonstrate a novel mechanism of translocation and RNA sorting used by RNAs several of which may be involved in the establishment of the embryonic body axis.

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

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

scholarly journals A Sponge-like Structure Involved in the Association and Transport of Maternal Products during Drosophila Oogenesis

1997 ◽  
Vol 139 (3) ◽  
pp. 817-829 ◽  
Author(s):  
Michaela Wilsch-Bräuninger ◽  
Heinz Schwarz ◽  
Christiane Nüsslein-Volhard
Keyword(s):  
Xenopus Oocytes ◽  
Polar Granule ◽  
Rna Localization ◽  
Drosophila Embryo ◽  
Fibrillar Structure ◽  
Subcellular Structure ◽  
Cytoplasmic Bridges ◽  
Dense Mass ◽  
Mitochondrial Cloud ◽  
Surrounding Membrane

Localization of maternally provided RNAs during oogenesis is required for formation of the antero–posterior axis of the Drosophila embryo. Here we describe a subcellular structure in nurse cells and oocytes which may function as an intracellular compartment for assembly and transport of maternal products involved in RNA localization. This structure, which we have termed “sponge body,” consists of ER-like cisternae, embedded in an amorphous electron-dense mass. It lacks a surrounding membrane and is frequently associated with mitochondria. The sponge bodies are not identical to the Golgi complexes. We suggest that the sponge bodies are homologous to the mitochondrial cloud in Xenopus oocytes, a granulo-fibrillar structure that contains RNAs involved in patterning of the embryo. Exuperantia protein, the earliest factor known to be required for the localization of bicoid mRNA to the anterior pole of the Drosophila oocyte, is highly enriched in the sponge bodies but not an essential structural component of these. RNA staining indicates that sponge bodies contain RNA. However, neither the intensity of this staining nor the accumulation of Exuperantia in the sponge bodies is dependent on the amount of bicoid mRNA present in the ovaries. Sponge bodies surround nuage, a possible polar granule precursor. Microtubules and microfilaments are not present in sponge bodies, although transport of the sponge bodies through the cells is implied by their presence in cytoplasmic bridges. We propose that the sponge bodies are structures that, by assembly and transport of included molecules or associated structures, are involved in localization of mRNAs in Drosophila oocytes.

scholarly journals m5CPred-SVM:  A Novel Method for Predicting m5C Sites of RNA

2020 ◽  
Author(s):  
Xiao Chen ◽  
Yi Xiong ◽  
Yinbo Liu ◽  
Yuqing Chen ◽  
Shoudong Bi ◽  
...  
Keyword(s):  
Cell Fate ◽  
Prediction Accuracy ◽  
Cytosine Methylation ◽  
Low Cost ◽  
Computational Method ◽  
Selection Strategy ◽  
Support Vector ◽  
Feature Subset ◽  
Biological Functions ◽  
Accurate Identification

Abstract Background: As one of the most common post-transcriptional modifications (PTCM) in RNA, 5-cytosine-methylation plays important roles in many biological functions such as RNA metabolism and cell fate decision. Through accurate identification of 5-methylcytosine (m5C) sites on RNA, researchers can better understand the exact role of 5-cytosine-methylation in these biological functions. In recent years, computational methods of predicting m5C sites have attracted lots of interests because of its efficiency and low-cost. However, both the accuracy and efficiency of these methods are not satisfactory yet and need further improvement. Results: In this work, we have developed a new computational method, m5CPred-SVM, to identify m5C sites in three species, H. sapiens, M. musculus and A. thaliana. To build this model, we first collected benchmark datasets following three recently published methods. Then, six types of sequence-based features were generated based on RNA segments and the sequential forward feature selection strategy was used to obtain the optimal feature subset. After that, the performance of models based on different learning algorithms were compared, and the model based on the support vector machine provided the highest prediction accuracy. Finally, our proposed method, m5CPred-SVM was compared with several existing methods, and the result showed that m5CPred-SVM offered substantially higher prediction accuracy than previously published methods. It is expected that our method, m5CPred-SVM, can become a useful tool for accurate identification of m5C sites.Conclusion: In this study, by introducing position-specific propensity related features, we built a new model, m5CPred-SVM, to predict RNA m5C sites of three different species. The result shows that our model outperformed the existing state-of-art models. Our model is available for users through a web server at http://zhulab.ahu.edu.cn/m5CPred-SVM.

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