A Meta-learning based Graph-Hierarchical Clustering Method for Single Cell RNA-Seq Data

Pan, Zixiang; Zeng, Yuansong; Lin, Yuefan; Yu, Weijiang; Zhang, Haokun; Yang, Yuedong

doi:10.1109/bibm55620.2022.9995640

2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2022

DOI: 10.1109/bibm55620.2022.9995640

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A Meta-learning based Graph-Hierarchical Clustering Method for Single Cell RNA-Seq Data

Zixiang Pan

Yuansong Zeng

Yuefan Lin

et al.

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2023

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Evolutionary innovations in germline biology of placental mammals revealed by transcriptomics of first wave spermatogenesis in opossum

Marshall

Stadtmauer

Maziarz

et al. 2023

Preprint

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Mammalian spermatogenesis is a deeply conserved developmental program that is essential for fitness. Paradoxically, spermatogenic development also allows rapid divergence in gene expression and is thought to be a source of evolutionary novelty and gene birth. How mammalian spermatogenic cells protect a conserved developmental program while enabling exceptionally rapid divergence in gene expression and function is unknown. Here, we comprehensively profile the spermatogenic gene expression program in grey short-tailed opossum (Monodelphis domestica, a model marsupial) and compare it to equivalent data from the mouse (Mus musculus, a model placental mammal) to discover contrasting forces underlying the unique evolutionary dynamics of gene expression during mammalian spermatogenesis. For the first time, we describe the timing of the 'first wave' of opossum spermatogenesis, and we combine bulk transcriptomic data from first-wave juvenile testes with single-cell transcriptomic data from adult testes to define conserved and divergent gene expression programs across the placental-marsupial split. We substantiate and extend our findings using genome-wide chromatin and multi-species transcriptome data and identify three classes of genes with different evolutionary trajectories: a deeply conserved central gene regulatory program governing spermatogenic progression; a separate class of spermatogenic genes exhibiting dynamic expression across placental mammals; and a third set of genes with evidence for directional selection in the placental mammal ancestor and constraint on expression levels within the placental mammalian lineage, representing placental innovations in germline gene expression and including biologically critical modules such as the DNA recombination and repair machinery.

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Evolutionary innovations in germline biology of placental mammals revealed by transcriptomics of first wave spermatogenesis in opossum

Marshall

Stadtmauer

Maziarz

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

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A Meta-learning based Graph-Hierarchical Clustering Method for Single Cell RNA-Seq Data

Cited by 1 publication

References 42 publications

Evolutionary innovations in germline biology of placental mammals revealed by transcriptomics of first wave spermatogenesis in opossum

Evolutionary innovations in germline biology of placental mammals revealed by transcriptomics of first wave spermatogenesis in opossum

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