Study sheds new light on core regulatory networks that govern cell types in vertebrates

The FANTOM Consortium has published two papers in the Genome Research journal that shed new light into the main regulatory networks that govern the types of cells found in different vertebrate species. They also provide new insights on how the RNA regulates the function and identity of cells.

Robotics system for automated large-scale perturbation of long non-coding RNAs. Image Credit: RIKEN.

Twenty years ago, the FANTOM Consortium was founded at RIKEN to go beyond genomics and study RNA—called the transcriptome.

Interpreting the transcriptome is important to achieve more advancements in the field of biology, because while the cells in the human body share the same kind of genomic DNA, their diversity is credited to their RNA composition, with over 400 types of cells defined and many more believed to exist.

Hence, interpreting the way RNA is expressed is crucial for learning how each type of cell establishes its distinctive behavior, morphology, and function by triggering particular transcriptional programs. The two studies that were published recently were built on the CAGE technology. This technology was designed at RIKEN to profile the transcriptome through next-generation sequencers.

In the initial study (Alam et al.), transcriptome data obtained from corresponding primary cell types in dog, chicken, mouse, rat, and human were compared. While the researchers observed that the transcriptome quantified by the CAGE technology for the same type of cell differed significantly between species, they noted a key regulatory network that defines each type of cell common between species.

Generally, the genes encoding products implicated in RNA biology in the cell nucleus were stimulated consistently in the same type of cell, irrespective of the species.

We identified genes acting within the nucleus whose usage was conserved for 100's of millions of years of evolution. On the other hand, genes that primarily act in communication between cells had diverged and were being used differently in different species, implying that the distinctive phenotype of each species is to a great extent due to the specific way that cells in an organism communicate with each other.”

Michiel de Hoon, Study Corresponding Author, RIKEN

The second study (Ramilowski J., Yip CW., et al.), which is part of the new edition of the project FANTOM 6—investigated human long non-coding RNAs. These RNAs outnumber the protein-coding genes in mammals but their functions still remain unclear.

With the help of an automated robotics system, the scientists selectively targeted almost 300 long non-coding RNAs to inhibit human fibroblast cells and integrated live cell imaging with the CAGE technology to watch how cells react at both the molecular and cellular levels.

It was critical to automate our efforts as much as possible to reduce biases in our experimental design, and to quickly identify and correct any that remained.”

Jay Shin, Study Corresponding Author, RIKEN

Based on the study, the researchers found that more than 25% of long non-coding RNAs affect the morphology and growth of cells and also impact the migration of cells, which is crucial in cancer.

Unexpectedly, targeting different variants or isoforms of the same long non-coding RNA resulted in profoundly different molecular and cellular phenotypes, leading to the alluring conjecture that every long non-coding RNA isoform created by a cell may have its own particular regulatory function.

Deep CAGE profiling of the molecular state of the cells after suppression of each long non-coding RNA allowed us to perform a functional analysis of long non-coding RNAs at an unprecedented level, and provides a valuable resource for a detailed investigating and understanding of the RNA biology and its potential application to enhancing human health.”

Jordan Ramilowski, Study First Author, RIKEN

Piero Carninci remarked, “Although this is still a pilot project, the results show involvement of lncRNAs in a broad variety of cellular processes and functions, which makes the case for extension of these studies to a broader number of cells and lncRNAs.”

“We are excited to see that these RNAs, often considered ‘junk’ when discovered some 15 years ago, are often proven to be functional. We also believe that that the nomenclature should shift from ‘non-coding’ to terminology that better reflects their role, such as ‘regulatory RNAs’ or ‘structural RNAs’,” concluded Carninci.