Epigenomic mapping cell-type classification

Summary

Principal Investigator: Joseph R Ecker
Salk Institute for Biological Studies
Title: "Epigenomic mapping approaches for cell-type classification in the brain"
BRAIN Category: Census of Cell Types (RFA MH-14-215)

Dr. Ecker's group will use signatures of epigenetics, the switching on-and-off of genes in response to experience, in mouse frontal cortex to help identify different classes of cells and understand their function.

Principal Investigator: Joseph R Ecker
Salk Institute for Biological Studies

Title:
“Epigenomic mapping approaches for cell-type classification in the brain”
BRAIN Category: 
Census of Cell Types (RFA MH-14-215)

Dr. Ecker’s group will use signatures of epigenetics, the switching on-and-off of genes in response to experience, in mouse frontal cortex to help identify different classes of cells and understand their function.

NIH Webpages

A Scientific Illustration of How Epigenetic Mechanisms Can Affect Health Epigenetic mechanisms are affected by several factors and processes including development in utero and in childhood, environmental chemicals, drugs and pharmaceuticals, aging, and diet. DNA methylation is what occurs when methyl groups, an epigenetic factor found in some dietary sources, can tag DNA and activate or repress genes. Histones are proteins around which DNA can wind for compaction and gene regulation. Histone modification occurs when the binding of epigenetic factors to histone "tails"; alters the extent to which DNA is wrapped around histones and the availability of genes in the DNA to be activated. All of these factors and processes can have an effect on people's health and influence their health possibly resulting in cancer, autoimmune disease, mental disorders, or diabetes among other illnesses. NIH Common Fund

A Scientific Illustration of How Epigenetic Mechanisms Can Affect Health
Epigenetic mechanisms are affected by several factors and processes including development in utero and in childhood, environmental chemicals, drugs and pharmaceuticals, aging, and diet. DNA methylation is what occurs when methyl groups, an epigenetic factor found in some dietary sources, can tag DNA and activate or repress genes. Histones are proteins around which DNA can wind for compaction and gene regulation. Histone modification occurs when the binding of epigenetic factors to histone “tails”; alters the extent to which DNA is wrapped around histones and the availability of genes in the DNA to be activated. All of these factors and processes can have an effect on people’s health and influence their health possibly resulting in cancer, autoimmune disease, mental disorders, or diabetes among other illnesses. NIH Common Fund

Project Description

Understanding the exact cell-type composition in brain regions is fundamental to integrating physiological, behavioral and neurochemical data to systematically understand the brain structure and function. At present, although the major categories of cell-types present in brain have been defined, the different subtypes within these categories, as well as their location and connectivity are far from understood. DNA methylation (mC) is a stable covalent modification that persists in post-mitotic cells throughout their lifetim, defining their cellular identity. It was recently demonstrated that mC patterns in brain are highly dynamic throughout development, and that there are clear differences between the major types of cells i.e., neurons and glia, in the rodent and human cortex. These analyses have been taken a step further and have produced data at the cell-type level that shows that each neuronal type carry specific mC signatures in their genomes that define the population they belong to. These results now open the possibility of producing a catalog of cell-types in brain defined by methylome signatures. This proposal will utilize this cell-type-specific base-resolution methylome data to produce complete maps of cell-types in the rodent brain in situ, and by this means develop a systematic inventory and census of cell types in the brain based on an integrated view of their molecular identity. Based on preliminary results showing clear-cut differences between the methylomes of specific neuronal types, we propose to use cutting edge technology to discover and test specific differentially methylated regions that define, at the molecular level, cell-populations in the frontal cortex of mice. The results obtained will be made publically available, and will serve as foundation to produce a complete genomic census of cell-types in a brain region that can be scaled to the whole brain. If successful, the approach could be ultimately tested in the primate brain. This proposal is thus responsive to RFA MH-14-215 “BRAIN Initiative: Transformative Approaches for Cell-Type Classification in the Brain (U01)”.

Public Health Relevance Statement

The ultimate goal of this research is to construct a map of the brain that identifies each unique cell type and the manner in which they are connected, through developing a technology that uniquely identifies each distinct brain cell type using “epigenomic marks”- a modification to the cytosine (C) base in DNA called methylation. We will utilize genome-wide cytosine methylation maps of brain cell populations to develop a novel in situ approach to probe the physical location of cells displaying unique methylation marks in brain slices and whole brains. This approach will result in the creation of an epigenetic map of each cell type that can be connected with existing brain gene expression atlases and connection maps, which can be further extended to the primate and human brain to serve as a reference for comparison with maps for neurological disease states such as schizophrenia or Alzheimer’s disease.

NIH Spending Category

Genetics; Human Genome; Mental Health; Neurosciences

Project Terms

Adult; Age-associated memory impairment; Alzheimer’s Disease; Atlases; base; Base of the Brain; Behavioral; bisulfite; Brain; brain cell; Brain Mapping; Brain region; Cataloging; Catalogs; Categories; cell type; Cells; Censuses; Characteristics; Classification; Cortical Cell Layer; Cytosine; Data; design; Detection; Development; DNA; DNA Methylation; Epigenetic Process; epigenomics; Equipment and supply inventories; Evaluation; Foundations; frontal lobe; Gene Expression; Genome; genome-wide; Genomics; Goals; Human; In Situ; Individual; Label; Learning; Location; Maps; Memory; Methylation; methylome; Mitotic; Modification; Molecular; Mus; nervous system disorder; neurochemistry; Neuroglia; Neuronal Plasticity; Neurons; novel; Parvalbumins; Pattern; Physiological; Population; Primary Cell Cultures; Primates; Process; public health relevance; Reading; Research; Resolution; Rodent; Schizophrenia; Slice; Specificity; Structure; Systems Biology; Technology; Testing

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