Designing Cell-Type-Specific Genome-wide Experiments

Abstract

Multicellular organisms depend on cell-type-specific division of labor for survival. Specific cell types have their unique developmental program and respond differently to environmental challenges, yet are orchestrated by the same genetic blueprint. A key challenge in biology is thus to understand how genes are expressed in the right place, at the right time, and to the right level. Further, this exquisite control of gene expression is perturbed in many diseases. As a consequence, coordinated physiological responses to the environment are compromised. Recently, innovative tools have been developed that are able to capture genome-wide gene expression using cell-type-specific approaches. These novel techniques allow us to understand gene regulation in vivo with unprecedented resolution and give us mechanistic insights into how multicellular organisms adapt to changing environments. In this article, we discuss the considerations needed when designing your own cell-type-specific experiment from the isolation of your starting material through selecting the appropriate controls and validating the data.

cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation

“…In the past few years, several new tools utilizing mouse transgenic technology for molecular profiling at individual cell-type level have been described (Reviewed in (Handley et al, 2015)). We show the cTag-PABP mouse provides a robust platform for assessing the normal mouse transcriptome, as evidenced by the consistency between our cTag-PAPERCLIP data and data independently obtained through analysis of endogenous PABP using the original PAPERCLIP (Fig.…”

A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes

“…Quantitative changes to histone modifications are also likely to occur during normal tissue development and differentiation (Kurimoto et al, 2015; Zhu et al, 2013). Mint-ChIP can be applied to directly quantify cell-type-specific chromatin features with global and focal precision (Handley et al, 2015). In comparison with chromatin spike-in adjustment, we expect quantitative normalization to be advantageous for analysis of variable cell numbers or aneuploid samples, whereas the two methods could be complementary in other situations.…”

Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data

“…Marker genes, genes that are expressed in a specific subset of cells, are often used in combination with other cellular features to define different types of cells (Margolis et al, 2006; Hu et al, 2014) and facilitate their characterization by tagging the cells of interest for further studies (Tomomura et al, 2001; Lobo et al, 2006; Handley et al, 2015). Marker genes have also found use in the analysis of whole tissue “bulk” gene expression profiling data, which can be challenging to interpret due to the difficulty to determine the source of the observed expressional change.…”