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| Status |
Public on Jan 17, 2017 |
| Title |
High Throughput Analysis Reveals Novel Maternal Germline RNAs Critical for PGC Preservation and Proper Migration |
| Organism |
Xenopus laevis |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
During oogenesis hundreds of RNAs are selectively localized to either the animal or vegetal cortical region. These maternal RNAs include determinants of both somatic and germline fates. Although microarray analysis has contributed to identifying localized determinants, it is not comprehensive and is limited to known transcripts. Here, we utilized high throughput RNA-sequencing analysis to comprehensively interrogate both animal and vegetal pole RNAs in the fully-grown Xenopus laevis oocyte. We identified 411 enriched RNAs at the vegetal pole, 198 of them annotated transcripts, and 27 RNAs enriched at the animal pole, 15 annotated. Of these, 90 were novel RNAs over 4-fold enriched at the vegetal pole and 6 over 10-fold at the animal pole. Unlike mRNAs, we found that microRNAs were not asymmetrically distributed. Whole mount in situ hybridization revealed all 17 selected RNAs were localized, confirming our data set. Biological function and network analysis of vegetally enriched transcripts identified protein-modifying enzymes, receptors, ligands, RNA binding proteins and 10 transcription factors or co-factors with 5 defining hubs linking 47 genes in a network. Initial functional studies of maternal vegetally-localized RNAs show, for the first time, that sox7 plays an important role in primordial germ cell (PGC) development and efnb1(ephrinB1), known to play important roles in migration/adhesion in the nervous system, is required for proper PGC migration. Based on our findings, we propose potential pathways operating at the vegetal pole that highlight where future investigations might be most fruitful.
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| Overall design |
Examination of animal and vegetal pole samples of stg. VI X. laevis oocyte to determine vegetally enriched genes that may contribute to germ plasm and PGCs.
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| Contributor(s) |
Owens DA, Butler AM, King ML |
| Citation(s) |
28096217 |
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| Submission date |
May 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Mary Lou King |
| E-mail(s) |
[email protected]
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| Phone |
305-243-2457
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| Organization name |
University of Miami: Miller school of Medicine
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| Department |
Cell Biology
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| Street address |
1600 nw 10th ave
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| City |
Miami |
| State/province |
Fl |
| ZIP/Postal code |
33136 |
| Country |
USA |
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| Platforms (1) |
| GPL17682 |
Illumina HiSeq 2000 (Xenopus laevis) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA320214 |
| SRA |
SRP074230 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE80971_RAW.tar |
8.3 Mb |
(http)(custom) |
TAR (of FPKM_TRACKING) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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