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Stem cell transcriptional profiles from mouse subspecies reveal cis-regulatory evolution at translation genes

ABSTRACT: Stem cell transcriptional profiles from mouse subspecies reveal cis-regulatory evolution at translation genes

PROVIDER: PRJNA982866 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24900476_1.fastq.gz	Fastqsanger.gz
	SRR24900476_2.fastq.gz	Fastqsanger.gz
	SRR24900477_1.fastq.gz	Fastqsanger.gz
	SRR24900477_2.fastq.gz	Fastqsanger.gz
	SRR27372600_1.fastq.gz	Fastqsanger.gz

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Stem cell transcriptional profiles from mouse subspecies reveal cis-regulatory evolution at translation genes

Project description:A key goal of evolutionary genomics is to harness molecular data to draw inferences about selective forces that have acted on genomes. The field progresses in large part through the development of advanced molecular-evolution analysis methods. Here we explored the intersection between classical sequence-based tests for selection and an empirical expression-based approach, using stem cells from Mus musculus subspecies as a model. Using a test of directional, cis-regulatory evolution across genes in pathways, we discovered a unique program of induction of translation genes in stem cells of the Southeast Asian mouse M. m. castaneus relative to its sister taxa. We then mined population-genomic sequences to pursue underlying regulatory mechanisms for this expression divergence, finding robust evidence for alleles unique to M. m. castaneus at the upstream regions of the translation genes. We interpret our data under a model of changes in lineage-specific pressures across Mus musculus in stem cells with high translational capacity. Our findings underscore the rigor of integrating expression and sequence-based methods to generate hypotheses about evolutionary events from long ago.

2024-11-06 | GSE234761 | GEO

Stem cell transcriptional profiles from mouse subspecies reveal cis-regulatory evolution at translation genes.

| S-EPMC11527988 | biostudies-literature

Stem cell transcriptional profiles from mouse subspecies reveal <i>cis</i>-regulatory evolution at ribosomal large-subunit genes.

Project description:A key goal of evolutionary genomics is to harness molecular data to draw inferences about selective forces that have acted on genomes. The field progresses in large part through the development and benchmarking of advanced molecular-evolution analysis methods. Here we evaluated the rigor and performance of a test of directional, cis-regulatory evolution across genes in pathways, using stem cells from Mus musculus subspecies as a model. We discovered a unique program of induction of ribosomal large-subunit genes in stem cells of the Southeast Asian mouse M. m. castaneus relative to its sister taxa, driven in part by cis-regulatory variation. As a complement, we used sequence analyses to find population- and comparative-genomic signatures of selection in M. m. castaneus, at the upstream regions of the ribosomal gene cohort. The unique high-expression program for these loci in M. m. castaneus was recapitulated in stem cell-derived neurons. We interpret our data under a model of changes in lineage-specific pressures across Mus musculus in stem cells with high translational capacity. Together, our findings underscore the rigor of integrating expression and sequence-based methods to generate hypotheses about evolutionary events from long ago.

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Project description:We studied the evolution of alternative splicing in the early stages of species divergence in the house mouse. We sequenced the testis transcriptomes of three Mus musculus subspecies and Mus spretus using Illumina technology. On the basis of a genome-wide analysis of read coverage differences among subspecies, we identified several hundred candidate alternatively spliced regions.

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Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

Project description:Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

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Multi-task learning uncovers robust translation cis-regulatory features

Project description:Multi-task learning uncovers robust translation cis-regulatory features

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Genome-wide identification of putative translation regulator cis-Natural Antisense Transcripts in Arabidopsis thaliana

Project description:The development of high-throughput genomic technologies has revealed that a large fraction of the genomes of eukaryotes is associated with the expression of noncoding RNAs. One class of noncoding RNA, the cis-natural antisense transcripts (cis-NATs), are particularly interesting as they are at least partially complementary to the protein-coding mRNAs. Although most studies described cis-NATs involved in the regulation of transcription, a few reports have shown recently that cis-NATs can also regulate translation of the cognate sense coding genes in plants and mammals. In order to identify novel examples of translation regulator cis-NATs in Arabidopsis thaliana, we designed a high-throughput experiment based on polysome profiling and RNA-sequencing. Expression of cis-NATs and translation efficiency of the cognate coding mRNAs were measured in roots and shoots in response to various conditions, including phosphate deficiency and treatment with phytohormones. We identified several promising candidates, and validated a few of them experimentally, in Arabidopsis thaliana transgenic lines over-expressing in trans the translation regulator candidate cis-NATs.

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Ribosome collisions trigger cis-acting feedback inhibition of translation initiation

Project description:Translation of aberrant mRNAs can cause ribosomes to stall, leading to collisions with trailing ribosomes. Collided ribosomes are specifically recognized by ZNF598 to initiate protein and mRNA quality control pathways. Here we found using quantitative proteomics of collided ribosomes that EDF1 is a ZNF598-independent sensor of ribosome collisions. EDF1 recruits and stabilizes GIGYF2 at collisions to inhibit translation initiation in cis via 4EHP. The GIGYF2 axis acts independently of the ZNF598 axis, but each pathway’s output is more pronounced without the other. We propose that the widely conserved and highly abundant EDF1 monitors the transcriptome for excessive ribosome density, then triggers a GIGYF2-mediated response to locally and temporarily reduce ribosome loading. Only when collisions persist is translation abandoned to initiate ZNF598-dependent quality control. This tiered response to ribosome collisions would allow cells to dynamically tune translation rates while ensuring fidelity of the resulting protein products.

2020-07-14 | PXD020239 | Pride

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Genetic selection shaped the gene expression patterns of mRNA and protein in rice subspecies

Project description:Eukaryotes gene expression of mRNA and protein is a basic cellular activity and regulated by multiple process, yet the expression patterns at these two levels and their genetic and evolutionary determinants remain undefined in plants. Here, using RNA-sequencing and TMT labeled LC-MS/MS analysis, we investigated the genome-wide variation of mRNA and protein expression in rice subspecies japonica C92, indica MH63 and their F1 hybrid. Different expression patterns of mRNA and protein between C92 and MH63 were linked to distinct functional categories. Genes with consistent divergence of mRNA and protein expression between subspecies tend to be regulated by cis effect and had higher sequence variation in nonsynonymous sites. Population differentiation (FST) analysis showed that genes with conserved expression of either mRNA or protein in C92 and MH63 were more likely to be under purify selection, while genes with consistent divergence in mRNA or protein expression were more likely to be under positive selection, especially in their nonsynonymous site have high frequency of positive selected genes that changed their protein sequence by nonsynonymous mutation. Furthermore, oxidative stress response genes were enriched in genes with consistent divergence of expression, and showed higher sequence variation in nonsynonymous sites and are more likely to be positive selected in evolution. These results suggested that cis-regulation with high nonsynonymous-variation was evolutionarily important feature to shape divergent expression patterns of mRNA and protein and may contribute to diversity in oxidative stress response between rice subspecies.

2023-12-27 | GSE142770 | GEO

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