Genes provide the blueprint for protein production, and a key principle in biology is that information moves from DNA to RNA, and finally to proteins. However, only two percent of our genome is responsible for coding proteins, leaving the function of the remaining 98 percent largely a mystery. A major challenge in human genetics is to uncover the roles, if any, of these genomic regions. Historically, many have deemed these areas as ‘junk.’ New research published in the journal Cell uncovers that some noncoding RNAs are indeed functional and have significant roles within our cells, particularly concerning cancer and human development.
Genes provide the blueprint for protein production, and a key principle in biology is that information moves from DNA to RNA, and finally to proteins. However, only two percent of our genome is responsible for coding proteins, leaving the function of the remaining 98 percent largely a mystery.
A key challenge in human genetics is understanding the purpose of these noncoding regions – if they serve any function at all. In the past, some have referred to these portions of our DNA as “junk.”
Recent findings in Cell indicate that certain noncoding RNAs are not just filler — they serve vital functions and are crucial for various cellular processes, including those related to cancer and human growth. By employing CRISPR technology that targets RNA, researchers at New York University and the New York Genome Center explored the genome and identified nearly 800 noncoding RNAs critical for the functionality of various human tissue cells.
“This examination of functional noncoding RNAs enhances our grasp of the human genome and showcases the possibilities of CRISPR screens aimed specifically at RNA — even those that do not produce proteins,” explained Neville Sanjana, an associate professor at NYU and senior author of the study.
A more precise CRISPR for RNA
The introduction of CRISPR gene-editing technology has transformed medical research, offering applications that range from improving agricultural yields to treating blood conditions by modifying the DNA in blood cells.
Many CRISPR techniques utilize the enzyme Cas9 to make DNA-level edits. A newer approach employs Cas13, which allows for more precise targeting of RNA without interrupting adjacent protein-coding genes and other regulatory functions. Sanjana’s team had previously shown how a CRISPR-Cas13 method could be refined to evaluate the entire transcriptome – the RNA-derived genetic information.
While numerous studies have employed sequencing tools to analyze RNA expression, it has been challenging to determine if particular RNA molecules are necessary for cell function.
“We now possess this technology, but a key biological question persists: which aspects of the noncoding genome are functional?” questioned Simon Müller, co-first author of the Cell study and postdoctoral researcher in Sanjana’s lab.
Not junk after all
By utilizing CRISPR-Cas13 to edit RNA while minimizing off-target effects, the researchers meticulously analyzed around 6,200 pairs of long noncoding RNAs (lncRNAs) alongside nearby protein-coding genes in five different human cell lines, including those from kidney, leukemia, and breast cancer. They employed CRISPR to disrupt each lncRNA to observe the impact – whether the cell dies, stops multiplying, or endures – to assess the lncRNA’s necessity.
“With Cas13, we can directly inquire, ‘What are the roles of these transcripts?’ They are not junk; we have discovered they are essential for cell growth and division,” remarked Wen-Wei Liang, co-first author of the Cell study and postdoctoral associate within Sanjana’s lab.
The research identified 778 lncRNAs that are crucial for cellular function, which includes a core group of 46 lncRNAs that are universally essential, as well as 732 that have specific functions tied to certain cell types.
When comparing essential lncRNAs to protein-coding genes, researchers noted that if a gene was essential in one of the five cell lines, it likely was essential in the others as well. Conversely, the functional significance of essential lncRNAs was more reliant on cell type. They aimed to investigate whether essential lncRNAs influenced nearby protein-coding genes, a question previously unexamined for noncoding RNAs. They found that the majority of essential lncRNAs function independently of the nearest protein-coding genes.
Furthermore, the team found that essential lncRNAs play a role in major pathways governing cell proliferation — a crucial process for both human development and cancer — and that their absence could hinder cell progress and promote cell death. Notably, several essential lncRNAs showed high expression in various tissues during early human development but decreased in later stages, indicating their critical roles during development.
In analyzing approximately 9,000 tumors, the team identified lncRNAs with altered expression in specific tumors, associating their expression levels with patient survival rates across various cancers.
“These noncoding RNAs could lead to new biomarkers and therapeutic targets for cancer treatments, presenting opportunities for personalized medicine based on their cell-type specific expression,” Sanjana added.
The co-authors of the study include Sydney Hart, Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Akash Sookdeo, Olivia Choi, Christina Caragine, Alba Corman, Lu Lu, Olena Kolumba, and Breanna Williams from NYU and the New York Genome Center. The research received support from the National Human Genome Research Institute (DP2HG010099, R01HG012790), the National Cancer Institute (R01CA279135 and R01CA218668), the National Institute of Allergy and Infectious Diseases (R01AI176601), the Simons Foundation for Autism Research, and the MacMillan Center for the Study of the Noncoding Cancer Genome.
