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High-resolution Ribosome Profiling Reveals Translational Selectivity in Bovine Preimplantation Embryo Development

ABSTRACT: High-resolution Ribosome Profiling Reveals Translational Selectivity in Bovine Preimplantation Embryo Development

PROVIDER: PRJNA805180 | ENA |

REPOSITORIES: ENA

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High-resolution Ribosome Profiling Reveals Translational Selectivity in Bovine Preimplantation Embryo Development

Project description:High resolution polysome fractionation and low-input ribosome profiling of bovine oocytes and preimplantation embryos has enabled us to define the translational landscape of early embryo development at an unprecedented level. We systematically and comparatively analyzed the transcriptome, polysome- and nonpolysome-bound RNA profiles of bovine oocytes and early embryos at 2-, 8-cell, morula, and blastocyst stage, and defined four modes of translational selectivity in bovine preimplantation embryo development: i. selective translation of non-abundant mRNAs, ii. active translating highly expressed mRNAs, iii. Translationally suppressed abundant mRNAs, and iv. Monosomaly occupied mRNAs. A strong selection towards genes involved in mitochondrial function and metabolic pathways was found throughout bovine preimplantation development. We found translatome largely follows transcriptome at oocytes, followed by a marked translational control at 8-cell embryos, which is gradually synchronized at the morula and blastocyst stage. We identified important novel cellular/embryonic functional regulators that being utilized and prioritized for translation at each developmental stage, that accompanies little-known bovine embryonic developmental programming. Together, these data reveal a unique spatiotemporal translational regulation that accompanies bovine preimplantation development.

2022-10-01 | GSE196484 | GEO

High-resolution ribosome profiling reveals translational selectivity for transcripts in bovine preimplantation embryo development.

Project description:High-resolution ribosome fractionation and low-input ribosome profiling of bovine oocytes and preimplantation embryos has enabled us to define the translational landscapes of early embryo development at an unprecedented level. We analyzed the transcriptome and the polysome- and non-polysome-bound RNA profiles of bovine oocytes (germinal vesicle and metaphase II stages) and early embryos at the two-cell, eight-cell, morula and blastocyst stages, and revealed four modes of translational selectivity: (1) selective translation of non-abundant mRNAs; (2) active, but modest translation of a selection of highly expressed mRNAs; (3) translationally suppressed abundant to moderately abundant mRNAs; and (4) mRNAs associated specifically with monosomes. A strong translational selection of low-abundance transcripts involved in metabolic pathways and lysosomes was found throughout bovine embryonic development. Notably, genes involved in mitochondrial function were prioritized for translation. We found that translation largely reflected transcription in oocytes and two-cell embryos, but observed a marked shift in the translational control in eight-cell embryos that was associated with the main phase of embryonic genome activation. Subsequently, transcription and translation become more synchronized in morulae and blastocysts. Taken together, these data reveal a unique spatiotemporal translational regulation that accompanies bovine preimplantation development.

| S-EPMC9687001 | biostudies-literature

Rules governing translation selectivity under limiting ribosome availability

Project description:Ribosomopathies are cell-type-specific pathologies related to a ribosomal protein (RP) gene insult. The 5q- syndrome is a somatic ribosomopathy linked to RPS14 gene haploinsufficiency and characterized by a prominent erythroid hypoplasia. Using quantitative proteomic, we show that GATA1 protein expression is low in shRPS14 cells in which ribosome quantities are diminished. Here, we investigated the cause of low GATA1 protein expression in limiting ribosome availability. A global analysis of translation in RPs deficiencies highlights the rules that drive translation selectivity. We demonstrate that in addition of the transcript length, a high codon adaptation index (CAI) and a highly structured 3’UTR are the key characteristics for a selective translation. An integrated analysis of transcriptome and proteome confirms that the post-transcriptional regulations of gene expression are directly linked to the criteria governing the translational selectivity. In particular, these criteria explain GATA1 translation default with unprecedented precision. More generally, the proteins that accumulate along normal erythropoiesis share the determinants of translation selectivity revealed by the conditions of limiting ribosome availability. We performed translatome expression profiling of cells infected with shRPS14 or shSCR

2020-04-28 | GSE124800 | GEO

Preimplantation mouse embryo development MOE430B

Project description:Preimplantation mouse embryo development on Affymetrix MOE430B. Zeng et al (2004) Dev Biol 272:483-496. Keywords: other

2004-09-10 | GSE1745 | GEO

Preimplantation mouse embryo development MOE430A

Project description:Preimplantation mouse embryo development study on Affymetrix MOE430A. Zeng et al (2004) Dev Biol 272:483-496. Keywords: other

2004-09-10 | GSE1744 | GEO

Preimplantation mouse embryo development U74Av2

Project description:Preimplantation mouse embryo development study on Affymetrix U74Av2. Zeng et al Dev Biol (2004) 272:483-496. Keywords: other

2004-07-06 | GSE1391 | GEO

Transcription profiling of preimplantation mouse embryo development

Project description:Preimplantation mouse embryo development study on Affymetrix MOE430A. Zeng et al (2004) Dev Biol 272:483-496.

2008-06-11 | E-GEOD-1744 | biostudies-arrayexpress

Rules governing translation selectivity under limiting ribosome availability

Project description:Rules governing translation selectivity under limiting ribosome availability

| PRJNA513511 | ENA

Tau drives translational selectivity by interacting with ribosomal proteins

Project description:Tau drives translational selectivity by interacting with ribosomal proteins

| PRJNA496504 | ENA

Isoform-resolved transcriptome of the human preimplantation embryo [PacBio]

Project description:Human preimplantation development is a complex process involving extensive remodeling of gene expression. However, the preimplantation embryo transcriptome has only been annotated using short-read sequencing, which fails to capture full-length mRNAs and associated isoform diversity. We present a novel human embryo transcriptome using integrated long- and short-read RNA sequencing data. Our analysis reveals a total of 110,212 novel isoforms transcribed from known genes containing either a novel combination of known splice sites or at least one novel splice site, and 17,964 isoforms transcribed from completely novel genes located either in antisense direction of known genes or in intergenic space.

2023-09-26 | GSE190547 | GEO

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