Single Cell Sequencing: New Horizons in Genome Biology

Susanta Behura

Susanta K. Behura, Ph.D., Research Assistant Professor, Department of Biological Sciences and the Eck Institute for Global Health, University of Notre Dame. Indiana, USA.

The single cell sequencing technology has emerged as a powerful method to investigate the diversity of genome structure and function of cells. In a recent publication, Liang et al (2014) reviewed the science and techniques of this method to emphasize its future scope in genomic research.

The importance of single cell sequencing stems from the fact that the individual cells in a given tissue do not necessarily have the identical genomes. The individual cells also differ in their transcriptome as well as epigenetic modifications. In addition, cells differ in their origins of development, size and morphology and function. These factors make single cell sequencing a useful approach in underpinning the diversities of genome and transcriptome of individual cells.

Basic Steps of Single Cell Sequencing SEQUENCING

Basic Steps of Single Cell Sequencing

Single cell sequencing is performed in three major steps: isolation of cell, whole genome/ transcriptome amplification and sequencing.  Individual cells can be isolated by using fluorescence-activated cell sorting or Laser-capture microdissection or by simple micromanipulation (such as pipetting or performing serial dilution). Because of higher throughput, less reagent cost and better accuracy, fabricated microfluidic chips are used as a popular choice for separating single cells in recent times.


Single cell epigenome analysis. A) Single-cell reduced representation bisulfite sequencing B) Single-cell bisulfite sequencing. From J. Genet Genomics. 2014 Oct 20;41(10):513-528.

After isolation of single cells, the next step is to amplify the whole genome or transcriptome of the isolated cells so that nanogram quantities of DNA or RNA can be generated for sequencing.  Liang et al. has provided a comprehensive description of the molecular techniques that are used for amplification of whole genome and transcriptome of single cells. Also, the review meticulously guides the reader on understanding the differences in the approaches for applying the technology in studying single cell genome, transcriptome and epigenome.

The application of single cell sequencing is presently being focused on mammalian and model organisms.

Single Cell Transcriptome Profiling. From Nature Reviews Genetics 14, 618–630 (2013)

Single Cell Transcriptome Profiling. From Nature Reviews Genetics 14, 618–630 (2013)

Given the current pace of progress in genomics and transcriptomics studies of insects, it is very likely that the single cell technology will have many applications in insect biology. It can have potential applications in insect developmental biology, for example, in mapping cell fates by integrating single cell sequencing data. Also, it may be useful in performing epigenetic analysis in many insects to better understand its functional role. Additionally, single cell sequencing has potential application in unraveling the transcriptional heterogeneity of specific tissues, for example, midgut or salivary gland cells of vector mosquitoes to infection of disease causing pathogens.

The so-called ‘third generation sequencing’ methods, also mentioned in this review, are a way to think forward in these directions.

To conclude, I borrow the following line from Shapiro et al. Nature Reviews Genetics 14, 618–630 (2013):

“Single-cell analysis is not just one more step towards more-sensitive measurements, but is a decisive jump to a more-fundamental understanding of biology”.


Liang J, Cai W, Sun Z. Single-Cell Sequencing Technologies: Current and Future. J Genet Genomics. 2014 Oct 20;41(10):513-528. doi:10.1016/j.jgg.2014.09.005.

Shapiro E, Biezuner T, Linnarsson S. Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat Rev Genet. 2013 Sep;14(9):618-30. doi: 10.1038/nrg3542.


1 Comment

  1. Development of single cell sequencing technology will revolutionize the world of genomics and will change the thought process related to gene expression studies within the cell. This technology has opened up new avenues for researchers involved in expression studies. They can investigate the gene expression within a cell of interest, in group of cells without the cell of interest, in a group of cells interacting with the cell of interest in order to obtain a clear understanding of their research objective. It looks slightly complicated but will definitely be very interesting. Thanks Dr. Susanta for posting it “LIVE” in IGTRCN.

Post a Comment

Your email address will not be published. Required fields are marked *