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Researchers at the University of California, San Diego have produced a single-cell chromatin atlas of the human genome. Chromatin is a complex of DNA and proteins found in eukaryotic cells. Chromatin regions of key gene regulatory elements appear in open configurations in the nucleus of certain cells. Accurate identification of accessible chromatin regions in cells of various human tissue types will be a key step towards understanding the role of gene regulatory elements (non-coding DNA) in human health or disease.
The results are published online in the issue of November 12, 2021 prison cell.
To scientists, the human genome, known as the “book of life”, is largely unwritten. Or at least unread. While science has put the well-known (estimated) number of all the protein-coding genes needed to build humans, close to 20,000+, these estimates don’t really begin to explain exactly how the building process works or, in the case of disease, it may be wrong.
says Ping Ren, PhD, director of the Center for Genetics, professor of cellular and molecular medicine at the University of California San Diego School of Medicine and a member of the Ludwig Cancer Research Institute at UCSD.
“One of the main reasons is that the vast majority of human DNA sequences, more than 98 percent, are non-protein coding, and we don’t yet have the genetic code book to unlock the information embedded in these sequences.”
In other words, it’s like figuring out the chapter title but with the rest of the page left blank.
Attempts to fill in the blanks are widely reported in an ongoing international effort called the Encyclopedia of DNA Elements (ENCODE), and include the work of Ren and colleagues. In particular, they investigated the role and function of chromatin, which is the complex of DNA and proteins that make up the chromosomes in the nucleus eukaryotic cell.
DNA carries the genetic instructions for cells. Key proteins in chromatin, called histones, help assemble DNA tightly into a compact shape that fits into the cell nucleus. (There are about six feet of DNA stored in the nucleus of every cell and about 10 billion miles away in every human body.) Changes in the way chromatin assembles DNA are linked to DNA replication and gene expression.
after, after Working with miceRen and collaborators turned their attention to a single-cell atlas of chromatin in the human genome.
They applied the test to more than 600,000 people cell Thirty adult human tissues were sampled from multiple donors, and this information was then combined with similar data from 15 fetal tissue types to reveal chromatin status on approximately 1.2 million cis-filters.organizational elements in 222 different cell types.
Study co-author Sebastian Presel, PhD, and co-director of Single Cell Genomics at the UC San Diego Center for Epigenomics, a collaborative research center that conducted the test, said.
The cis regulatory elements are non-coding regions of DNA that regulate the transcription (copying of a portion of DNA into RNA) of neighboring genes. Transcription is the basic process that converts genetic information into action.
“Studies in the last decade have shown that noncoding DNA sequence variation is a key driver of polygenic traits and diseases in humans, such as diabetes, Alzheimer’s disease and autoimmune disease,” said study co-author Kyle J. Gulton, Ph.D., assistant professor in the department. pediatrics at the University of California, San Diego School of Medicine.
“A new model that helps explain how these non-coding variants contribute to disease suggests that these sequence changes disrupt the function of transcriptional regulatory elements and lead to defective gene expression in disease-associated cell types, such as neurons, immune cells, or epithelial cells. cells,” said the authors. The first participant Kai Zhang, PhD, is a postdoctoral fellow in the Department of Cellular and Molecular Medicine. “The main barrier to unlocking the functionality of non-coding risk variants, however, is the lack of cell-type-specific mapping of transcriptional regulatory elements in human genes. ”
The new findings identify cell types relevant to the pathological features of 240 polygenic traits and diseases, and illustrate the risk of non-coding variants, Ren said.
“We believe these resources will greatly facilitate the study of mechanisms in various human diseases for many years to come.”
The chromatin atlas will also allow the scientific community to uncover differences in the tissue environment for cell types found in some tissues, such as fibroblasts, immune cells or endothelial cells, Presel said.
Cell-type-specific insights into the function of risk factors in coronary artery disease
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Kai Zhang et al., Single-celled atlas of chromatin accessibility in the human genome, prison cell (2021). DOI: 10.1016 / j.cell.2021.10.024
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Introduction
University of California – San Diego
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quote: Explaining dark matter in human DNA (2021, 12 November) Accessed 13 November 2021 from https://phys.org/news/2021-11-illuminating-dark-human-dna.html
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