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

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

PROVIDER: PRJNA1197416 | ENA |

REPOSITORIES: ENA

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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]

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

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).

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

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

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

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

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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]

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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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Deep learning of enhancer codes highlights similarities between mammalian and avian telencephalon cell types [multiome]

Project description:Combinations of transcription factors govern the identity of cell types, which is reflected by genomic enhancer codes. We utilized deep learning to characterize these enhancer codes and devised three novel metrics to compare cell types in the telencephalon between mammals and birds. To this end, we generated single-cell multiome and spatially-resolved transcriptomics data of the chicken telencephalon. Enhancer codes of orthologous non-neuronal and GABAergic cell types show a high degree of similarity across vertebrates, while excitatory neurons of the mammalian neocortex and avian pallium exhibit varying degrees of similarity. Enhancer codes of avian mesopallial neurons are most similar to those of mammalian deep layer neurons. With this study, we present generally applicable deep learning approaches to characterize and compare cell types solely based on genomic sequences.

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