CRISPR technology helps identify essential noncoding RNAs within human genome.

Genes contain instructions for making proteins, and one central dogma of biology holds that information flows from DNA to RNA and on to proteins. Unfortunately, only 2 percent of our human genome actually encodes proteins; their purposes remain largely undetermined.

Human geneticists face an ongoing challenge: to comprehend what each region of our genome contributes. Many have even called these uncharacterized regions “junk.”

Now, a recent Cell study shows that noncoding RNAs may not just be useless waste product-;they actually play important roles in our cells – including cancer development and human growth. Utilizing CRISPR technology that targets RNA instead of DNA, researchers from New York University and New York Genome Center discovered nearly 800 noncoding RNAs that play vital roles for various tissues across our genomes.

“This survey of functional noncoding RNAs furthers our understanding of human genome and illustrates how CRISPR screens that target noncoding RNA can benefit researchers,” noted Neville Sanjana, associate professor of biology at New York University’s Grossman School of Medicine as well as associate professor in neuroscience and physiology; core faculty member at New York Genome Center core Faculty; lead author.

More accurate CRISPR for RNA.

CRISPR gene editing technology has revolutionized biomedical research. From increasing crop production to treating blood disorders by editing DNA in blood cells directly, its wide array of uses span from crop improvement and enhancement to treating disorders directly.

CRISPR applications typically use Cas9 enzyme to alter genes on a DNA level; however, newer technology employs Cas13 for targeting RNA instead. Sanjana’s lab demonstrated how CRISPR-Cas13 platforms that target RNA can be optimized to screen whole transcriptomes (genetic information transformed into RNA molecules).

Many studies have used sequencing technology to decipher what RNA molecules are present within an individual cell’s transcriptome; however, understanding which specific ones actually provide critical functions has proven challenging.

“Now we have this technology, but the biological question still stands: which parts of the noncoding genome are actually functional?” stated Simon Muller, co-first author and postdoctoral associate in Sanjana’s lab.

Utilising CRISPR-Cas13 to edit RNA without off-target activity, researchers performed an in-depth investigation of almost 6,200 gene pairs of long noncoding RNAs (lncRNAs) and nearby protein-coding genes across five human cell lines containing kidney, leukemia and breast cancer cells from kidney patients, leukemia patients and breast cancer cells in a comprehensive way – kidney cells dying, proliferating less efficiently or being tolerated?-;to establish whether an LNCRNA was essential or not

“With Cas13, we can ask directly what its functions are: they’re no mere waste-product; rather they play an essential part in cell proliferation and division” according to Wen-Wei Liang of Sanjana’s lab and co-first author of Cell’s study on Cas13 transcripts.

Researchers identified 778 long noncoding RNAs essential to cell function, with 46 being universally essential and 732 having specific cell-type-related functions.

They compared essential lncRNAs with protein-coding genes for comparison purposes, finding that when one protein-coding gene was essential in one cell line it often also needed to be essential in other lines; by comparison essential lncRNAs appeared more cell type specific and may modulate nearby protein coding genes via different mechanisms than protein coding ones; yet here, an overwhelming majority of essential lncRNAs operated independently from nearby protein-coding ones.

In their research, they also discovered that essential lncRNAs modulated key pathways involved with cell proliferation – something essential in human development as well as cancer progression-;and their absence can impact cell progression or even lead to cell death. Many essential lncRNAs were highly expressed across tissues early in human development but decreased expression later on, suggesting important roles played by particular lncRNAs during growth and differentiation.

Through analysis of over 9,000 tumors, researchers identified specific lncRNAs with altered expression levels across various cancer types; further, these researchers pinpointed those lncRNAs whose expression in tumors indicated better or poorer survival of various forms.

These noncoding RNAs could provide new biomarkers and therapeutic targets for cancer therapy; their cell type-specific expression provides the possibility for personalized medicine.
Neville Sanjana, associate professor of biology and neuroscience physiology at New York University’s Grossman School of Medicine

Sydney Hart, Hans-Hermann Wessels, Alejandro Mendez-Mancilla, Akash Sookdeo, Olivia Choi Christina Caragine Alba Corman Lu Lu Olena Kolumba and Breanna Williams from NYU’s New York Genome Center contributed as study co-authors. Research funding came from National Human Genome Research Institute DP2HG010099 R01HG012790), National Cancer Institute R01CA279135 R2186668 National Institute Allergy Infectious Diseases R01AI176601/National Institute Of Allergy And Infectious Diseases R01CA218668) as well as Simons Foundation Autism Research R01AI176601/MacMillan Center For Study of Non Coding Cancer Genome Research respectively.