Employing core regulatory circuits to define cell identity

Abstract

The interplay between extrinsic signaling and downstream gene networks controls the establishment of cell identity during development and its maintenance in adult life. Advances in next-generation sequencing and single-cell technologies have revealed additional layers of complexity in cell identity. Here, we review our current understanding of transcription factor (TF) networks as key determinants of cell identity. We discuss the concept of the core regulatory circuit as a set of TFs and interacting factors that together define the gene expression profile of the cell. We propose the core regulatory circuit as a comprehensive conceptual framework for defining cellular identity and discuss its connections to cell function in different contexts.

Keywords: GRN; cell identity; core regulatory circuit; regenerative medicine; transcription factor.

Box 1 Figure. The role of Pbx1 in the CRC of olfactory bulb DA neurons.

Figure 1. Cell identity is regulated by CRCs

(A) Conceptualizing different types of information (e.g., transcriptomics, epigenomics) in the flow of biological information from DNA to function in order to shape our knowledge of CRCs. Downstream processes (purple), such as gene and protein expression, are routinely measured using transcriptomics and proteomics. Further downstream of this is cellular phenotype, a more complex readout which is measured using various assays and microscopy techniques. Factors that influence the CRC of a cell (green) include intrinsic factors and extrinsic factors, such as epigenetic memory and the external environment, respectively. While an overall flow of information is unidirectional (from top to bottom), many factors influence each other in more complex ways. (B) Model of cell identity being regulated by GRNs through development and CRCs in differentiated cells. We propose that CRCs define differentiated cell types and GRNs are temporally transient networks which drive cellular differentiation during development. GRNs adapt in response to external signals and other influences during development, resulting in a series of different developing cell states. Once cells become terminally differentiated, the TF network becomes more stable and can be defined as a CRC, which is autoregulating and activates the expression of the terminal effector gene battery. While GRNs and CRCs can be identified using similar methods, studies of GRNs additionally benefit from lineage tracing and pseudotime analysis to account for their temporal aspect.

Figure 2. Methods employed to identify CRCs

(A) Single‐cell transcriptomics allows the identification of cell populations or states (top). Putative CRC components for these cell identities can be identified by defining the TFs and downstream genes enriched in these cells (bottom). (B) Epigenetic methods allow the identification of cis‐regulatory elements that make up the CRC. Chromosome conformation capture (3C/HiC) identifies regions of DNA, which are in close contact with each other, potentially including enhancer–promoter interactions (left). ATAC‐/DNase‐ and ChIP‐seq for histone modifications identify regions of open chromatin, which can be used to identify enhancers as well as promoters and actively transcribed genes (right). (C) Computational methods are used in multiple aspects of CRC identification. Clustering of single‐cell transcriptomics data allows discovery of previously unknown cell types, while pseudotime analysis help identify transcriptional states when cell fate decisions along developmental trajectories are made (top). Several algorithms can make data‐driven predictions of CRCs by analyzing TF co‐expression and performing GRN inference (middle). Other relevant data supplied by users or deposited in databases can inform on CRC mechanisms (e.g., chromatin accessibility, promoter and enhancer states, TF‐binding and protein–protein interactions) and be integrated to refine CRC predictions (bottom).

Box 2 Figure. CRCs maintain distinct endocrine and exocrine cell type in the pancreas.