Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo development [RNA-seq and mTAIL-seq Human and Drosphila]

ABSTRACT: Eukaryotic mRNAs are subject to multiple types of tailing which critically influence mRNA stability and translatability. To investigate RNA tails at the genomic scale, we previously developed TAIL-seq, but its low sensitivity precluded its application to biological materials of minute quantity. In this study, we report a new version of TAILseq (mRNA TAIL-seq or mTAIL-seq) with enhanced sequencing depth for mRNAs (by ~1000 fold compared to the previous version). The improved method allows us to investigate the regulation of poly(A) tail in Drosophila oocytes and embryos. We find that maternal mRNAs are polyadenylated mainly during late oogenesis, prior to fertilization, and that further modulation occurs upon egg activation. Wispy, a noncanonical poly(A) polymerase, adenylates the vast majority of maternal mRNAs with a few intriguing exceptions such as ribosomal protein transcripts. By comparing mTAILseq data with ribosome profiling data, we find a strong coupling between poly(A) tail length and translational efficiency during egg activation. Our data suggest that regulation of poly(A) tail in oocytes shapes the translatomic landscape of embryos, thereby directing the onset of animal development. By virtue of the high sensitivity, low cost, technical robustness, and broad accessibility, mTAIL-seq will be a potent tool to improve our understanding of mRNA tailing in diverse biological systems. Ten separate sets of TAIL-seq experiments were performed. Two sets of HeLa cells are untransfected normal cells. Eight sets of fly sample include a pair of wild type and mutant.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Jaechul Lim

PROVIDER: E-GEOD-83731 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Global view of mRNA uridylation in Arabidopsis

Project description:To obtain a global view of mRNA uridylation in Arabidopsis, we generated TAIL-seq libraries from WT plants, urt1 and xrn4 single mutants, and urt1 xrn4 double mutant. The TAIL-seq protocol was recently developed to deep-sequence the 3' ends of RNAs (Chang et al., 2014). We generated TAIL-seq libraries from WT plants, urt1 and xrn4 single mutants, and urt1 xrn4 double mutant.

2016-03-11 | E-GEOD-72457 | biostudies-arrayexpress

Poly(A) tail length change of miRNA targets in HeLa cells

Project description:MicroRNA induces deadenylation of its targets according to the current model in the scientific community, but this model is based on the studies of a few individual genes. We tested the model by examining the global effect of miRNA on poly(A) tail of the targets. Synthetic miR-1 mimic was transfected into HeLa cells, and the poly(A) length was measured by TAIL-seq. Deadenylation of miR-1 targets was evident as early as 3 hours post-transfection without a significant change in mRNA level. After 6 or 9 hours, target mRNA level was substantially downregulated. Therefore, although there are some exceptions, our result confirms that, in general, miRNA indeed induces deadenylation. Furthermore, our kinetic global analysis confirms that deadenylation precedes mRNA decay. Four culture dishes of HeLa cells were treated with miR-1 all together, then collected and prepared for sequencing after different time of incubation (0, 3, 6, and 9 hours post-transfection)

2014-02-28 | E-GEOD-54114 | biostudies-arrayexpress

POS-1 protects posterior gut specification by blocking GLD-3/2 polyadenylation of anterior factor neg-1

Project description:The Poly(A)-Tail focused RNA-seq, or PAT-seq approach was utilised to determine the gene expression, poly(A)-site and polyadenylation state of the transcriptome of early C. elegans embryos having been depleated for a series of RNA binding proteins. Namely; pos-1 and mex-5 were independently knocked down using dsRNA expressing E. coli HT115(DE3) fed to ~100,000 starved/synchronized L1 larvae. When half of the population reached adulthood and half were still in the L4 stage, worms were bleached and embryos harvested and stored in Trizol. This ensured an enrichment of early embryos between 1 and 24 cell stage. mex-6(pk440) were synchronized and grown on OP50 until the same time point and embryos harvested in the same manner. Since prolonged gld-3 and gld-2 RNAi result in sterility, starved/synchronized L1 larvae were fed diluted OP50 (200uL of concentrated OP50 diluted in 2mL of M9 and starved L1s) for 16 hours. At that point the OP50 had been mostly consumed by the larvae and concentrated gld-3 or gld-2 dsRNA expressing E. coli were added to the plates. When half of the population reached adulthood and half were still in the L4 stage, worms were bleached and embryos harvested and stored in Trizol. Total RNA was isolated using standard procedures. Analysis of poly(A) dynamics in early C. elegans embryos reponding to depletion of specific RNA binding proteins and adneylation state regulators

2015-05-25 | E-GEOD-57993 | biostudies-arrayexpress

Impact of URT1-mediated uridylation on small RNA tailing in Arabidopsis

Project description:To analyse the impact of URT1-mediated uridylation on miRNA and siRNA tailing, we deep-sequenced small RNA libraries for WT and urt1 duplicate samples at the same developmental stage that was analyzed by TAIL-seq, i.e., two-week-old seedlings. Examination of miRNA and siRNA tailing in WT and urt1 samples.

2016-03-11 | E-GEOD-72456 | biostudies-arrayexpress

Poly(A)-tail profiling reveals an embryonic switch in translational control

Project description:Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths have impeded greater understanding of poly(A)-tail function. Here we describe poly(A)-tail length profiling by sequencing (PAL-seq) and apply it to measure tail lengths of millions of individual RNAs isolated from yeasts, cell lines, Arabidopsis thaliana leaves, mouse liver, and zebrafish and frog embryos. Poly(A)-tail lengths were conserved between orthologous mRNAs, with mRNAs encoding ribosomal proteins and other 'housekeeping' proteins tending to have shorter tails. As expected, tail lengths were coupled to translational efficiencies in early zebrafish and frog embryos. However, this strong coupling diminished at gastrulation and was absent in non-embryonic samples, indicating a rapid developmental switch in the nature of translational control. This switch complements an earlier switch to zygotic transcriptional control and explains why the predominant effect of microRNA mediated deadenylation concurrently shifts from translational repression to mRNA destabilization. 64 samples from a variety of species

2014-01-29 | E-GEOD-52809 | biostudies-arrayexpress

mRNA Poly(A)-tail Changes Specified by Deadenylation Broadly Reshape Translation in Drosophila Oocytes and Early Embryos

Project description:Because maturing oocytes and early embryos lack transcription, posttranscriptional regulatory processes must control their development. To better understand this control, we profiled translational efficiencies and poly(A)-tail lengths throughout Drosophila oocyte maturation and early embryonic development. The correspondence between translational-efficiency changes and tail-length changes indicated that tail-length changes broadly reshape translational activity until gastrulation, when this coupling disappears. Relative changes were largely retained in the absence of poly(A)-tail lengthening, which indicated that selective poly(A)-tail shortening primarily specifies the changes. Many translational changes depended on PAN GU and Smaug, and both acted primarily through tail-length changes. Our results also revealed tail-lengthâindependent mechanisms of translational control that repressed translation regardless of tail-length changes during oocyte maturation, maintained translation despite tail-length shortening during oocyte maturation, and prevented detectable translation of bicoid and several other mRNAs before egg activation. In addition to these fundamental insights, our results provide valuable resources for future studies. 42 samples analyzed using RNA-seq, ribosome footprint profiling, and PAL-seq.

2016-08-08 | E-GEOD-83616 | biostudies-arrayexpress

PAPERCLIP identifies novel microRNA targets and provides insights into mRNA alternative polyadenylation

Project description:Accurate and precise annotation of the 3â² untranslated regions (3â² UTRs) is critical in understanding how mRNA stability, localization and translational efficiency are regulated by microRNAs (miRNAs) and RNA-binding proteins (RBPs). Here we describe a novel method, PAPERCLIP (Poly(A) binding Protein-mediated mRNA 3Â´End Retrieval by CrossLinking ImmunoPrecipitation), which shows high specificity for the mRNA 3â² ends and compares favorably to existing 3â² end mapping methods including direct RNA sequencing in performance. PAPERCLIP protocol and RNA-Seq on human cell lines and mouse whole brain cortex.

2016-02-19 | E-GEOD-66092 | biostudies-arrayexpress

Extensive alternative polyadenylation during zebrafish development

Project description:The post-transcriptional fate of messenger RNAs (mRNAs) is largely dictated by their 3' untranslated regions (3'UTRs), which are defined by cleavage and polyadenylation (CPA) of pre-mRNAs. We used poly(A)-position profiling by sequencing (3P-Seq) to map poly(A) sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P-Seq reads substantially increased and improved existing 3'UTR annotations, resulting in confidently identified 3'UTRs for more than 78.79% of the annotated protein-coding genes in zebrafish. Most zebrafish genes undergo alternative CPA with more than a thousand genes using different dominant 3'UTRs at different stages. 3'UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest 3'UTRs are highly expressed in the ovary yet absent in the maternally contributed RNAs of the embryo, perhaps because their 3'UTRs are too short to accommodate a uridine-rich motif required for stability of the maternal mRNA. At two hours post-fertilization, thousands of unique poly(A) sites appear at locations lacking a typical polyadenylation signal, which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities, formation, and evolution of zebrafish 3'UTRs provide a resource for studying gene regulation during vertebrate development. 3P-Seq was used to map the 3' ends of protein-coding genes in the zebrafish genome

2012-06-17 | E-GEOD-37453 | biostudies-arrayexpress

MicroRNA expression in chicken cecum following Campylobacter jejuni infection

Project description:SPF leghorn chickens were infected with C. jejuni. The cecum were collected at 8h post infection for total RNA isolation. The significantly expressed microRNAs between infected and non-infected chickens were identified through Solexa sequencing technology. Two libraries were made from each group, in total, four libraries were used for Solexa sequencing.

2016-07-25 | E-GEOD-58767 | biostudies-arrayexpress

mTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo development [RNA-seq Drosophila oocyte stages]

Project description:Eukaryotic mRNAs are subject to multiple types of tailing which critically influence mRNA stability and translatability. To investigate RNA tails at the genomic scale, we previously developed TAIL-seq, but its low sensitivity precluded its application to biological materials of minute quantity. In this study, we report a new version of TAILseq (mRNA TAIL-seq or mTAIL-seq) with enhanced sequencing depth for mRNAs (by ~1000 fold compared to the previous version). The improved method allows us to investigate the regulation of poly(A) tail in Drosophila oocytes and embryos. We find that maternal mRNAs are polyadenylated mainly during late oogenesis, prior to fertilization, and that further modulation occurs upon egg activation. Wispy, a noncanonical poly(A) polymerase, adenylates the vast majority of maternal mRNAs with a few intriguing exceptions such as ribosomal protein transcripts. By comparing mTAILseq data with ribosome profiling data, we find a strong coupling between poly(A) tail length and translational efficiency during egg activation. Our data suggest that regulation of poly(A) tail in oocytes shapes the translatomic landscape of embryos, thereby directing the onset of animal development. By virtue of the high sensitivity, low cost, technical robustness, and broad accessibility, mTAIL-seq will be a potent tool to improve our understanding of mRNA tailing in diverse biological systems. Two sets of RNA-seq on 3 developmental stages (immature oocyte, mature oocyte, and activated egg) of wild type and wispy mutant of Drosophila melanogaster.

2016-08-01 | E-GEOD-83730 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data