Holo-Seq: single-cell sequencing of holo-transcriptome

Current single-cell RNA-seq approaches are hindered by preamplification bias, loss of strand of origin information, and the inability to observe small-RNA and mRNA dual transcriptomes. Here, we introduce a single-cell holo-transcriptome sequencing (Holo-Seq) that overcomes all three hurdles. Holo-Seq has the same quantitative accuracy and uniform coverage with a complete strand of origin information as bulk RNA-seq. Most importantly, Holo-Seq can simultaneously observe small RNAs and mRNAs in a single cell. Furthermore, we acquire small RNA and mRNA dual transcriptomes of 32 human hepatocellular carcinoma single cells, which display the genome-wide super-enhancer activity and hepatic neoplasm kinetics of these cells.

[1]  Lee E. Edsall,et al.  A map of the cis-regulatory sequences in the mouse genome , 2012, Nature.

[2]  R. Young,et al.  Super-Enhancers in the Control of Cell Identity and Disease , 2013, Cell.

[3]  Oliver J. Rando,et al.  Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals , 2016, Science.

[4]  Gioele La Manno,et al.  Quantitative single-cell RNA-seq with unique molecular identifiers , 2013, Nature Methods.

[5]  N. Hacohen,et al.  Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors , 2017, Science.

[6]  T. Golub,et al.  Impaired microRNA processing enhances cellular transformation and tumorigenesis , 2007, Nature Genetics.

[7]  D. Wei,et al.  HLA class I expression in primary hepatocellular carcinoma. , 2002, World journal of gastroenterology.

[8]  Alvaro Plaza Reyes,et al.  Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos , 2016, Cell.

[9]  O. Warburg.  [Origin of cancer cells]. , 1956, Oncologia.

[10]  P. Massion,et al.  Investigation of complement activation product c4d as a diagnostic and prognostic biomarker for lung cancer. , 2013, Journal of the National Cancer Institute.

[11]  N. Harrison,et al.  Rediscovering pluripotency: from teratocarcinomas to embryonic stem cells. Cardiff, 10-12 October 2011. , 2012, The International journal of developmental biology.

[12]  K. Nakai,et al.  Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis , 2013, Genes & development.

[13]  I. Ng,et al.  The microRNA miR-139 suppresses metastasis and progression of hepatocellular carcinoma by down-regulating Rho-kinase 2. , 2011, Gastroenterology.

[14]  Yiliang Zhang,et al.  Hepatitis C virus‐induced up‐regulation of microRNA‐155 promotes hepatocarcinogenesis by activating Wnt signaling , 2012, Hepatology.

[15]  S. Lowe,et al.  miR-221 overexpression contributes to liver tumorigenesis , 2009, Proceedings of the National Academy of Sciences.

[16]  Hongshan Guo,et al.  Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos , 2015, Genome Biology.

[17]  Rickard Sandberg,et al.  Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos , 2016, Cell.

[18]  Margaret S. Ebert,et al.  Roles for MicroRNAs in Conferring Robustness to Biological Processes , 2012, Cell.

[19]  Charles H. Yoon,et al.  Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq , 2016, Science.

[20]  Shuqiang Li,et al.  CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq , 2016, Genome Biology.

[21]  D. Hanahan,et al.  Hallmarks of Cancer: The Next Generation , 2011, Cell.

[22]  Jeong Eon Lee,et al.  Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer , 2017, Nature Communications.

[23]  Tetsutaro Hayashi,et al.  Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads , 2017, Genome Biology.

[24]  R. Young,et al.  A Phase Separation Model for Transcriptional Control , 2017, Cell.

[25]  T. Hashimshony,et al.  CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. , 2012, Cell reports.

[26]  S. Linnarsson,et al.  Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. , 2011, Genome research.

[27]  Michael Levine,et al.  Enhancer Control of Transcriptional Bursting , 2016, Cell.

[28]  Shawn M. Gillespie,et al.  Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma , 2014, Science.

[29]  Stephanie Roessler,et al.  MicroRNA expression, survival, and response to interferon in liver cancer. , 2009, The New England journal of medicine.

[30]  Jie Quan,et al.  Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap , 2015, BMC Genomics.

[31]  Miki Ohira,et al.  Recent trends in microRNA research into breast cancer with particular focus on the associations between microRNAs and intrinsic subtypes , 2016, Journal of Human Genetics.

[32]  A. Coulon,et al.  Eukaryotic transcriptional dynamics: from single molecules to cell populations , 2013, Nature Reviews Genetics.

[33]  L. Cantley,et al.  Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation , 2009, Science.

[34]  V. Afshar-Kharghan.  The role of the complement system in cancer , 2017, The Journal of clinical investigation.

[35]  I. Nikaido,et al.  Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs , 2018, Nature Communications.

[36]  C. Bracken,et al.  Experimental strategies for microRNA target identification , 2011, Nucleic acids research.

[37]  V. Villegas,et al.  Neighboring Gene Regulation by Antisense Long Non-Coding RNAs , 2015, International journal of molecular sciences.

[38]  R. Sandberg,et al.  Full-Length mRNA-Seq from single cell levels of RNA and individual circulating tumor cells , 2012, Nature Biotechnology.

[39]  I. Kurochkin,et al.  Long noncoding RNAs: a potential novel class of cancer biomarkers , 2015, Front. Genet..

[40]  Allan Balmain,et al.  TGF-β signaling in tumor suppression and cancer progression , 2001, Nature Genetics.

[41]  Hsien-Da Huang,et al.  miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions , 2017, Nucleic Acids Res..

[42]  Chenghang Zong,et al.  Effective detection of variation in single-cell transcriptomes using MATQ-seq , 2017, Nature Methods.

[43]  David A. Orlando,et al.  Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes , 2013, Cell.

[44]  Phillip A. Sharp,et al.  Super-Enhancer-Mediated RNA Processing Revealed by Integrative MicroRNA Network Analysis , 2017, Cell.

[45]  Keji Zhao,et al.  Expression and regulation of lincRNAs during T cell development and differentiation , 2013, Nature Immunology.

[46]  Richard A Young,et al.  Models of human core transcriptional regulatory circuitries , 2016, Genome research.

[47]  Catalin C. Barbacioru,et al.  mRNA-Seq whole-transcriptome analysis of a single cell , 2009, Nature Methods.

[48]  Z. Lu,et al.  Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells. , 2016, Cell stem cell.

[49]  L. Steinmetz,et al.  Gene regulation by antisense transcription , 2013, Nature Reviews Genetics.

[50]  Megan F. Cole,et al.  Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells , 2008, Cell.

[51]  Åsa K. Björklund,et al.  Smart-seq2 for sensitive full-length transcriptome profiling in single cells , 2013, Nature Methods.

[52]  I. Ng,et al.  MicroRNA‐125b suppressesed human liver cancer cell proliferation and metastasis by directly targeting oncogene LIN28B 2 , 2010, Hepatology.

[53]  Rickard Sandberg,et al.  Single-cell sequencing of the small-RNA transcriptome , 2016, Nature Biotechnology.

[54]  H. Ueda,et al.  Erratum to: Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity , 2017, Genome Biology.

[55]  N. Neff,et al.  Quantitative assessment of single-cell RNA-sequencing methods , 2013, Nature Methods.