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Conservation of cis-regulatory codes over half a billion years of evolution

ABSTRACT: Conservation of cis-regulatory codes over half a billion years of evolution

PROVIDER: PRJNA1197421 | ENA |

REPOSITORIES: ENA

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Conservation of cis-regulatory codes over half a billion years of evolution

Project description:The identification of homologous cell types across species represents a crucial step in understanding cell type evolution. The retina is particularly amenable to comparative analysis because the basic morphology, connectivity, and function of its six major cell classes have remained largely invariant since the earliest stages of vertebrate evolution. We used comparative single-nucleus chromatin accessibility analysis of lamprey, fish, bird, and mammalian retinas, which began to diverge over half a billion years ago, to demonstrate cross-species conservation of cis-regulatory codes in all six retinal cell classes. In this study, we acquired retinal single-cell gene expression profiling (scRNA-seq) and single-nucleus chromatin accessibility (snATAC-seq) from sea lamprey (Petromyzon marinus), a jawless species. We also acquired long-read sequence data from lamprey retina and single-nucleus chromatin accessibility from chicken (Gallus gallus).

2025-08-18 | GSE284136 | GEO

Conservation of cis-regulatory codes over half a billion years of evolution [snATAC-Seq]

Project description:Conservation of cis-regulatory codes over half a billion years of evolution [snATAC-Seq]

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Conservation of cis-regulatory codes over half a billion years of evolution [Iso-Seq]

Project description:Conservation of cis-regulatory codes over half a billion years of evolution [Iso-Seq]

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Conservation of cis-regulatory codes over half a billion years of evolution [Iso-Seq]

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Conservation of cis-regulatory codes over half a billion years of evolution [snATAC-Seq]

2025-08-18 | GSE284128 | GEO

Conservation of cis-regulatory codes over half a billion years of evolution [multiome RNA-Seq]

2025-08-18 | GSE284131 | GEO

Conservation of cis-regulatory codes over half a billion years of evolution [multiome ATAC-Seq]

2025-08-18 | GSE284130 | GEO

Conservation of cis-regulatory codes over half a billion years of evolution [multiome RNA-Seq]

Project description:Conservation of cis-regulatory codes over half a billion years of evolution [multiome RNA-Seq]

| PRJNA1197415 | ENA

Conservation of cis-regulatory codes over half a billion years of evolution [multiome ATAC-Seq]

Project description:Conservation of cis-regulatory codes over half a billion years of evolution [multiome ATAC-Seq]

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Multi-dimensional conservation analysis reveals transcriptional codes ruling the expression of conserved long noncoding RNAs

Project description:Although long non-coding RNAs (lncRNAs) encounter weaker evolutionary constraints and exhibit lower sequences conservation than coding genes, lncRNAs can conserve their features at different aspects. Here, we employed multiple approaches to systemically evaluate the conservation between human and mouse lncRNAs from various dimensions including sequences, promoter, global synteny, and local synteny, which led to the identification of 1731 conserved lncRNAs with 427 ultraconserved ones meeting multiple criteria. The conserved lncRNAs, in comparison with non-conserved ones, in generally have longer gene bodies, higher numbers of exons and transcripts, closer connections with human diseases, and are more abundant and widespread across different tissues. The transcriptional factor profile analysis revealed a significant enrichment of TF types and numbers in the promoters of conserved lncRNAs. We further identified a set of TFs that preferentially bind to conserved lncRNAs and exert stronger impacts on their expression than non-conserved lncRNAs’ expression. Thus, our study has revealed a new set of transcriptional “codes” that rules the expression of the conserved lncRNAs.

2023-03-19 | GSE156270 | GEO

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