scEnhancer: a single-cell enhancer resource with annotation across hundreds of tissue/cell types in three species.

Journal: Nucleic acids research
PMID: 34761274

Abstract

Previous studies on enhancers and their target genes were largely based on bulk samples that represent 'average' regulatory activities from a large population of millions of cells, masking the heterogeneity and important effects from the sub-populations. In recent years, single-cell sequencing technology has enabled the profiling of open chromatin accessibility at the single-cell level (scATAC-seq), which can be used to annotate the enhancers and promoters in specific cell types. A comprehensive resource is highly desirable for exploring how the enhancers regulate the target genes at the single-cell level. Hence, we designed a single-cell database scEnhancer (http://enhanceratlas.net/scenhancer/), covering 14 527 776 enhancers and 63 658 600 enhancer-gene interactions from 1 196 906 single cells across 775 tissue/cell types in three species. An unsupervised learning method was employed to sort and combine tens or hundreds of single cells in each tissue/cell type to obtain the consensus enhancers. In addition, we utilized a cis-regulatory network algorithm to identify the enhancer-gene connections. Finally, we provided a user-friendly platform with seven useful modules to search, visualize, and browse the enhancers/genes. This database will facilitate the research community towards a functional analysis of enhancers at the single-cell level.

Authors

  • Tianshun Gao
    Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China.
  • Zilong Zheng
    Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China.
  • Yihang Pan
    Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China.
  • Chengming Zhu
    Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China.
  • Fuxin Wei
    Department of Orthopaedics, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China.
  • Jinqiu Yuan
    Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China.
  • Rui Sun
    The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China.
  • Shuo Fang
    Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China.
  • Nan Wang
    Department of Gastroenterology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.
  • Yang Zhou
    State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Environmental Protection, Guangzhou, China.
  • Jiang Qian
    Department of Ophthalmology, Fudan Eye & ENT Hospital, Shanghai, China.

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