Trends in Immunology
Volume 36, Issue 9, September 2015, Pages 507-518
Journal home page for Trends in Immunology

Feature Review
Exploiting genomics and natural genetic variation to decode macrophage enhancers

https://doi.org/10.1016/j.it.2015.07.006Get rights and content

Highlights

  • Enhancers are major determinants of cell specific gene expression.

  • Small sets of lineage-determining factors prime the majority of macrophage enhancers.

  • Tissue environment drives selective activation of macrophage enhancers.

  • Genetic variation can be exploited to discover mechanisms of enhancer activation.

The mammalian genome contains on the order of a million enhancer-like regions that are required to establish the identities and functions of specific cell types. Here, we review recent studies in immune cells that have provided insight into the mechanisms that selectively activate certain enhancers in response to cell lineage and environmental signals. We describe a working model wherein distinct classes of transcription factors define the repertoire of active enhancers in macrophages through collaborative and hierarchical interactions, and discuss important challenges to this model, specifically providing examples from T cells. We conclude by discussing the use of natural genetic variation as a powerful approach for decoding transcription factor combinations that play dominant roles in establishing the enhancer landscapes, and the potential that these insights have for advancing our understanding of the molecular causes of human disease.

Section snippets

Exploiting macrophages to understand enhancer biology and enhancer biology to understand macrophages

Macrophages (see Glossary) are phagocytic cells of the innate immune system that reside in all tissues of the body and play key roles in responding to infection and injury through signaling downstream of pattern recognition receptors 1, 2, 3. In addition to these general roles that operate throughout the body, each tissue-resident population of macrophages performs specific effector functions that contribute to the homeostasis of that tissue 2, 4. Some of the diverse roles that macrophages have

The million enhancer question

All cells in the body contain essentially the same genome. The mechanisms that govern how different cell types uniquely interpret the same set of instructions, and thereby achieve specialized functional roles, are incompletely understood. In recent years, it has become clear that on the genome scale, DNA sequences called enhancers, more so than promoters, orchestrate the majority of cell-type-specific patterns of gene expression 25, 26, 27, 28, 29. Although the distinction between enhancers and

General features of enhancers

Enhancers are discrete regions of the genome that function to increase transcription from nearby promoters [31] (reviewed in 32, 33). In the pre-genomics era, enhancers were first identified as stretches of DNA that, when inserted up- or downstream of transgenes, were able to augment gene expression irrespective of orientation [31].

In eukaryotes, DNA is wrapped around nucleosomes into chromatin, which serves as a regulatory barrier to transcription factors. Enhancer elements are bound by

Enhancer selection by LDTFs

Enhancer selection is defined here as the process by which an enhancer element in the genome is converted from an inactive to a primed, poised, or active state. Important classes of transcription factors, called pioneer transcription factors or LDTFs, are able to initiate enhancer selection by competing with nucleosomes to bind their DNA recognition motifs and establish a nucleosome-free region. This process is accompanied by concurrent or subsequent recruitment of chromatin-modifying enzymes

Chromatin dynamics

Chromatin dynamics in hematopoietic development has proven to be a powerful system to study enhancer state transitions during lineage specification 21, 61, 75. Hematopoiesis initiates with the self-renewing multipotent hematopoietic stem cell (HSC) that differentiates into either the common lymphoid progenitor (CLP) or common myeloid progenitor (CMP) [76]. CMPs further differentiate into lineage-committed progenitors called megakaryocyte–erythroid progenitors (MEPs) or granulocyte–macrophage

LDTFs direct signal responsiveness

Enhancer selection by LDTFs results in primed enhancers, but may not result in active enhancers (as measured by acetylation on histone H3 tails at lysine 27, or H3K27ac [45] and enhancer transcription 46, 47).

The transition to an active enhancer state can either be initiated from a primed state, whereby lineage factors have already established a nucleosome-free region, or from an inactive or closed state 32, 61, 86 (Figure 3). Both mechanisms of enhancer activation involve collaborative

Testing enhancer selection models using natural genetic variation

A collaborative and hierarchical model for selection and activation of cell-specific enhancers provides a framework for understanding how genetic variation perturbs enhancer function and target gene expression with cell specificity. The concept that enhancers are major determinants of cell-specific gene expression is central to the interpretation of certain types of noncoding variants associated with disease risk. Conversely, natural genetic variation can be used as a genome-wide ‘mutagenesis

Using natural genetic variation to discover regulatory networks

Macrophages are important effector cells that reside in every tissue of the body [4]. Their diverse functions in different tissue environments as well as their essential roles in health and disease make them an important experimental system to study chromatin priming, signal integration, and cooperative interactions at enhancers. To this end, transcriptomes and primed and active enhancers were compared between macrophages resident in diverse tissues in mice 19, 20, 21. Different macrophage

Implications for human disease

Recent advances in the field of gene regulation on the genome-wide scale, such as emergent properties of enhancer selection and activation by different classes of transcription factors, have valuable applications in the field of human genetics. The observation that the majority (∼88%) of risk loci for common diseases in genome-wide association studies (GWASs) are outside of the protein-coding genome [110] certainly necessitates insightful strategies for elucidating the functional sequence

Concluding remarks

Rapid progress is being made with respect to how enhancers function; nonetheless, many challenges remain (Box 2). For example, the ability to predict transcription factor binding and enhancer selection based on DNA sequence and knowledge of expressed transcription factors is a distant goal. Predicting the consequences of transcription factor binding is also problematic. One challenging observation, for instance, is that the binding of NF-κB to an enhancer can result in an increase, decrease, or

Glossary

C/EBP
a family of basic-leucine zipper (bZIP) transcription factors that bind DNA and form homo-and heterodimer interactions. C/EBPα and C/EBPβ are LDTFs in macrophages.
ChIP-Seq
chromatin immunoprecipitation followed by high-throughput sequencing. This assay identifies the genomic location and frequency with which a particular protein or histone modification associates with DNA.
Chromatin
DNA that is wrapped around nucleosomes. Chromatin compaction is dynamic with spatiotemporal patterns dependent

References (127)

  • A. Barski

    High-resolution profiling of histone methylations in the human genome

    Cell

    (2007)
  • K. Schaukowitch

    Enhancer RNA facilitates NELF release from immediate early genes

    Mol. Cell

    (2014)
  • M.U. Kaikkonen

    Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription

    Mol. Cell

    (2013)
  • K.R. Kieffer-Kwon

    Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation

    Cell

    (2013)
  • S. Heinz

    Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

    Mol. Cell

    (2010)
  • J.M. Dowen

    Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes

    Cell

    (2014)
  • D. Hnisz

    Super-enhancers in the control of cell identity and disease

    Cell

    (2013)
  • W.A. Whyte

    Master transcription factors and mediator establish super-enhancers at key cell identity genes

    Cell

    (2013)
  • F. Grosveld

    Position-independent, high-level expression of the human beta-globin gene in transgenic mice

    Cell

    (1987)
  • G. May

    Dynamic analysis of gene expression and genome-wide transcription factor binding during lineage specification of multipotent progenitors

    Cell Stem Cell

    (2013)
  • S. Doulatov

    Hematopoiesis: a human perspective

    Cell Stem Cell

    (2012)
  • C.A. Gifford

    Transcriptional and epigenetic dynamics during specification of human embryonic stem cells

    Cell

    (2013)
  • R.P. Koche

    Reprogramming factor expression initiates widespread targeted chromatin remodeling

    Cell Stem Cell

    (2011)
  • J.A. Zhang

    Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity

    Cell

    (2012)
  • R. Ostuni

    Latent enhancers activated by stimulation in differentiated cells

    Cell

    (2013)
  • S. Ghisletti

    Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages

    Immunity

    (2010)
  • M. Garber

    A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals

    Mol. Cell

    (2012)
  • L.A. Cirillo

    Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4

    Mol. Cell

    (2002)
  • A.C. Mullen

    Master transcription factors determine cell-type-specific responses to TGF-beta signaling

    Cell

    (2011)
  • R.M. Samstein

    Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification

    Cell

    (2012)
  • G. Vahedi

    STATs shape the active enhancer landscape of T cell populations

    Cell

    (2012)
  • E. Trompouki

    Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration

    Cell

    (2011)
  • F. Geissmann

    Development of monocytes, macrophages, and dendritic cells

    Science

    (2010)
  • T.A. Wynn

    Macrophage biology in development, homeostasis and disease

    Nature

    (2013)
  • T. Lucas

    Differential roles of macrophages in diverse phases of skin repair

    J. Immunol.

    (2010)
  • S. Gordon

    Macrophage heterogeneity in tissues: phenotypic diversity and functions

    Immunol. Rev.

    (2014)
  • R.C. Paolicelli

    Synaptic pruning by microglia is necessary for normal brain development

    Science

    (2011)
  • S.L. Teitelbaum

    Bone resorption by osteoclasts

    Science

    (2000)
  • J.I. Odegaard

    Macrophage-specific PPARgamma controls alternative activation and improves insulin resistance

    Nature

    (2007)
  • J.R. Wright

    Clearance and recycling of pulmonary surfactant

    Am. J. Physiol.

    (1990)
  • J.W. Pollard

    Tumour-educated macrophages promote tumour progression and metastasis

    Nat. Rev. Cancer

    (2004)
  • S. Gordon

    Alternative activation of macrophages

    Nat. Rev. Immunol.

    (2003)
  • D.M. Mosser et al.

    Exploring the full spectrum of macrophage activation

    Nat. Rev. Immuno

    (2008)
  • R. Medzhitov et al.

    Transcriptional control of the inflammatory response

    Nat. Rev. Immunol.

    (2009)
  • E.L. Gautier

    Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages

    Nat. Immunol.

    (2012)
  • O. Butovsky

    Identification of a unique TGF-beta-dependent molecular and functional signature in microglia

    Nat. Neurosci.

    (2014)
  • B.F. Boyce et al.

    Biology of RANK, RANKL, and osteoprotegerin

    Arthritis Res. Ther.

    (2007)
  • N.D. Heintzman

    Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

    Nat. Genet.

    (2007)
  • N.D. Heintzman

    Histone modifications at human enhancers reflect global cell-type-specific gene expression

    Nature

    (2009)
  • E.P. Consortium

    An integrated encyclopedia of DNA elements in the human genome

    Nature

    (2012)
  • Cited by (0)

    View full text