• Researchers at the Centre for Genomic Regulation (CRG), a BIST centre, are part of a collaboration that has shown that cells in the human body can be classified into five major groups.
• The proportion of each cell group differs between human tissue, providing new insight into how human tissues are composed and are an important first step in characterising disease
• The findings, published on the cover of the journal Genome Research, are complementary to the results of the third phase of the international ENCODE project, published in Nature.
Scientists from around the world have published the results of the third phase of the Encyclopedia of DNA Elements (ENCODE) in Nature. The international consortium of approximately 500 scientists conducted around 6000 experiments to identify more than 900,000 candidate regulatory elements from the human genome and more than 300,000 from the mouse, which can be explored through a new online browser.
“When the first draft of the human genome was completed…it became immediately clear that while we had the primary sequence of the genome, or we had a draft of it…we needed to have an annotation for the genome,” says Cold Spring Harbor Laboratory Professor Thomas Gingeras, whose team has been contributing to the ENCODE project since its inception. “We knew where the genes were located. Where the regulatory mechanisms and loci were located was significantly underdeveloped.”
Funded by the National Human Genome Research Institute, ENCODE launched in 2003, soon after the human genome was first sequenced. Its researchers are developing a comprehensive catalogue of the human and mouse genomes’ functional elements—dense arrays of protein-coding genes, noncoding genes, and regulatory elements. Thousands of researchers worldwide have taken advantage of ENCODE data, using it to shed light on cancer biology, cardiovascular disease, human genetics, and other topics.
In a second publication in Genome Research, complementary to the ENCODE report, a team led by Thomas Gingeras from Cold Spring Harbour Laboratory (CHSL) and Roderic Guigó at the Centre for Genomic Regulation (CRG), a BIST centre, detail that cells in the human body can be classified into five major groups. The researchers created this new classification by monitoring the transcriptome (variety of gene transcripts) of primary cells from multiple organs.
The five cell groups act as elemental building blocks, from which tissues and organs are “assembled”. Based on the expression of these genes, the authors estimated the cellular composition of tissues, and they found this composition to reflect phenotypic traits of tissues, and to change with age, sex, and disease states.
“Our work redefines, based on gene expression, the basic histological types in which tissues have been traditionally classified,” says Roderic Guigó, last author of the study and Coordinator of the CRG Bioinformatics and Genomics Programme.
“Understanding how these five groups of cells compose human tissue is a good first step towards aiding in characterising disease,” says Manuel Muñoz Aguirre, one of the co-authors and CRG researcher. “For example, if we study a healthy group of individuals, we have an idea of how cells in these groups behave. Then, when we study a group of individuals affected by disease, we can look at the differences in the levels of these cells. Thus, this is a starting point for understanding what things could go wrong during disease at the cellular level.”
More information can be found on the CRG website.