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Single-cell transcriptomic atlas reveals the evolution of immune cells and molecules across multiple vertebrate species

ABSTRACT: Single-cell transcriptomic atlas reveals the evolution of immune cells and molecules across multiple vertebrate species

PROVIDER: PRJNA772751 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16490731_1.fastq.gz	Fastqsanger.gz
	SRR16490731_2.fastq.gz	Fastqsanger.gz
	SRR16490732_1.fastq.gz	Fastqsanger.gz
	SRR16490732_2.fastq.gz	Fastqsanger.gz
	SRR16490733_1.fastq.gz	Fastqsanger.gz

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Single-cell transcriptomic atlas reveals the evolution of immune cells and molecules across multiple vertebrate species

Project description:We utilized single-cell RNA sequencing (scRNA-seq) to carry out comparative transcriptome analysis in various immune cells from the spleens across seven vertebrate species.

2023-01-30 | GSE186158 | GEO

Single-cell sequencing reveals the evolution of immune molecules across multiple vertebrate species.

Project description:IntroductionBoth innate and adaptive immune system undergo evolution from low to high vertebrates. Due to the limitation of conventional approaches in identifying broader spectrum of immune cells and molecules from various vertebrates, it remains unclear how immune molecules evolve among vertebrates.ObjectivesHere, we utilized carry out comparative transcriptome analysis in various immune cells across seven vertebrate species.MethodsSingle-cell RNA sequencing (scRNA-seq).ResultsWe uncovered both conserved and species-specific profiling of gene expression in innate and adaptive immunity. Macrophages exhibited highly-diversified genes and developed sophisticated molecular signaling networks along with evolution, indicating effective and versatile functions in higher species. In contrast, B cells conservatively evolved with less differentially-expressed genes in analyzed species. Interestingly, T cells represented a dominant immune cell populations in all species and unique T cell populations were identified in zebrafish and pig. We also revealed compensatory TCR cascade components utilized by different species. Inter-species comparison of core gene programs demonstrated mouse species has the highest similarity in immune transcriptomes to human.ConclusionsTherefore, our comparative study reveals gene transcription characteristics across multiple vertebrate species during the evolution of immune system, providing insights for species-specific immunity as well as the translation of animal studies to human physiology and disease.

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The evolutionary landscape of alternative splicing in vertebrate species

Project description:How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the transcriptomes of multiple organs from vertebrate species spanning ~350 million years of evolution, we observe significant differences in alternative splicing complexity between the main vertebrate lineages, with the highest complexity in the primate lineage. Moreover, within as little as six million years, the splicing profiles of physiologically-equivalent organs have diverged to the extent that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are governed by the highly variable use of a largely conserved cis-regulatory code. However, a smaller number of pronounced species-dependent splicing changes are predicted to remodel interactions involving factors acting at multiple steps in gene regulation. These events are expected to further contribute to the dramatic diversification of alternative splicing as well as to other gene regulatory changes that contribute to phenotypic differences among vertebrate species.

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Project description:Adaptive immunity and the five vertebrate NF-kB/Rel family members first appeared in cartilaginous fish, suggesting that NF-kB family expansion allowed the acquisition of new functions to regulate adaptive immune responses. Transcriptome profiling revealed that, even in macrophages, the NF-kB family member, c-Rel, most potently regulates a cytokine gene linked to adaptive immunity, Il12b, with limiting roles at key regulators of innate immunity. Neofunctionalization of c-Rel to regulate Il12b depends on its unique DNA-binding properties, which we examined using structural, biochemical, functional, and genomic approaches. Among our findings was functional c-Rel homodimer binding to motifs with little resemblance to canonical NF-kB motifs. To determine whether c-Rel’s unique binding properties drove c-Rel-RelA divergence, we compared binding properties in various vertebrate species. c-Rel-RelA binding properties diverged in mammals and amphibians but were comparable in earlier vertebrates, suggesting that divergent DNA binding emerged relatively late during vertebrate evolution to support increasing complexity of adaptive immune regulation.

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Stepwise Neofunctionalization of c-Rel during Vertebrate Evolution (RNA-Seq)

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