Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE.
Jiangping He,Isaac A. Babarinde,Li Sun,Shuyang Xu,Ruhai Chen,Junjie Shi,Yuanjie Wei,Yuhao Li,Gang Ma,Qiang Zhuang,Andrew P. Hutchins,Jiekai Chen +11 more
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TLDR
In this article, a single-cell transposable element (TE) processing pipeline, scTE, was developed to report the expression of TEs in single cells in a range of biological contexts.Abstract:
Transposable elements (TEs) make up a majority of a typical eukaryote's genome, and contribute to cell heterogeneity in unclear ways. Single-cell sequencing technologies are powerful tools to explore cells, however analysis is typically gene-centric and TE expression has not been addressed. Here, we develop a single-cell TE processing pipeline, scTE, and report the expression of TEs in single cells in a range of biological contexts. Specific TE types are expressed in subpopulations of embryonic stem cells and are dynamically regulated during pluripotency reprogramming, differentiation, and embryogenesis. Unexpectedly, TEs are expressed in somatic cells, including human disease-specific TEs that are undetectable in bulk analyses. Finally, we apply scTE to single-cell ATAC-seq data, and demonstrate that scTE can discriminate cell type using chromatin accessibly of TEs alone. Overall, our results classify the dynamic patterns of TEs in single cells and their contributions to cell heterogeneity.read more
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Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq
TL;DR: In this paper , the authors perform genome-scale Perturb-seq targeting all expressed genes with CRISPR interference (CRISPRi) across >2.5 million human cells.
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Roles of transposable elements in the regulation of mammalian transcription
TL;DR: It is argued that TE-centric studies hold the key to unlocking general principles of transcription regulation and evolution, and how TEs spur regulatory evolution and facilitate the emergence of genetic novelties in mammalian physiology and development.
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Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain.
Christopher Playfoot,Julien Duc,Shaoline Sheppard,Sagane Dind,Alexandre Coudray,Evarist Planet,Didier Trono +6 more
TL;DR: In this paper, the authors reveal a distinct KZFP:TE transcriptional profile defining the late prenatal to early postnatal transition, and the spatiotemporal and cell type-specific activation of TE-derived alternative promoters driving the expression of neurogenesis-associated genes.
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Single-cell RNA-seq-based proteogenomics identifies glioblastoma-specific transposable elements encoding HLA-I-presented peptides.
Pierre-Emmanuel Bonte,YA Arribas,Antonela Merlotti,Montserrat Carrascal,J. Zhang,Elina Zueva,Zev A. Binder,Cécile Alanio,Christel Goudot,Sebastian Amigorena +9 more
TL;DR: The authors identified 370 human leukocyte antigen (HLA)-I-bound peptides encoded by transposable elements (TEs) differentially expressed in GBM patients using a proteogenomic pipeline that combines single-cell transcriptomics, bulk RNA sequencing (RNA-seq) samples from tumors and healthy-tissue cohorts, and immunopeptidomic samples.
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Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
TL;DR: The demography and genomic distribution of zebrafish TEs and their expression throughout embryogenesis are described using bulk and single-cell RNA sequencing data and reveal a highly dynamic genomic ecosystem comprising nearly 2000 distinct TE families, which vary in copy number by four orders of magnitude and span a wide range of ages.
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