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Stem Cell microRNA, Transcription Factor Interplay Uncovered

NEW YORK (GenomeWeb News) – New research is starting to piece together how regulatory circuitry involving microRNAs and key transcription factors mediate stem cell function and guide their differentiation into other cell types.
In a paper appearing in today’s issue of Cell, researchers from the Massachusetts Institute of Technology and the Whitehead Institute for Biomedical Research used ChIP-Seq — combining massively parallel sequencing with chromatin immunoprecipitation — to map the interactions between miRNAs and transcriptional regulators involved in maintaining embryonic stem cell identity. The work provides insights into stem cell biology and may also inform research on development, cellular reprogramming, and cancer.
“The first thing that we wanted to do was to look at integrating miRNAs into the circuitry of embryonic stem cells,” co-lead author Stuart Levine, research scientist at the Whitehead Institute, told GenomeWeb Daily News. “What this really allows us to do is to get a handle on how transcription factors relate to the formation of miRNAs.”
Embryonic stem cells are notorious for their ability to self-renew and to become any type of cell in the body. Transcription factors and miRNAs help to keep these stem cells in a pluripotent state and, if required, direct their differentiation into specialized cell types.
But the regulatory players that control such processes are only partly understood. In an attempt to integrate knowledge about stem cell transcription factors and miRNA function and control, Levine and his co-workers mapped the transcription start sites for miRNA genes and then determined how these genes interact with key transcription factors.
First, they used ChIP-Seq to map the genome-wide binding sites of four transcription factors — Oct4, Sox2, Nanog, and Tcf3 — that are all essential for embryonic stem cell biology. The researchers found that these transcription factors overlapped at 14,230 sites in the genome, binding very closely to one another.
Next they set out to find transcription start sites for miRNA genes, most of which were unknown. “We knew where the miRNA itself was, but we didn’t know where the promoters were,” Levine explained. To remedy that, the researchers looked for trimethylation at the lysine 4 residue of histone H3 — a telltale sign of transcription initiation sites.
Using this approach, they were able to predict the promoters for 336 mature mouse miRNAs and 441 mature human miRNAs. By superimposing the Oct4, Sox2, Nanog, and Tcf3 binding sites onto this map, the team could also predict which miRNAs are controlled by these transcription factors.
The researchers discovered that, similar to the situation for protein-coding genes, the transcription factors bind two classes of miRNA genes: active genes and repressed genes.
Most of the active miRNA genes that are apparently mediated by Oct4, Sox2, Nanog, and Tcf3 are those that are preferentially expressed in embryonic stem cells. The researchers also discovered a smaller set of miRNA genes that interact with these transcription factors but remain silent in stem cells.
Subsequent research suggested that these miRNA promoters are also occupied by a group of proteins called polycomb proteins, which keep the genes silent. And, it turns out, some of these miRNAs become active when stem cells differentiate into certain cell types.
“By understanding how master transcription factors turn microRNAs on and off, we now see how these two groups of gene regulators work together to control the state of the cell,” senior author Richard Young, a biologist affiliated with MIT and the Whitehead Institute for Biomedical Research, said in a statement.
And, the researchers noted, this high-resolution transcription factor and miRNA mapping provides a new resource for those interested in understanding everything from development to stem cell therapies to the molecular changes associated with disease states. Being able to connect transcription factors and miRNAs may also help researchers predict the changes necessary for precise cellular reprogramming, Levine noted.
“This gives us clues of which miRNAs you might want to target to direct an embryonic stem cell into another type of cell,” co-first author Alex Marson, a graduate student in Young’s lab, said in a statement. “For example, you might be able to harness a miRNA to help drive an embryonic stem cell to become a neuron, aiding with neurodegenerative disease or spinal cord injury.”