Authors
Goldrich, M. J., Delhaye, L., Bekaert, S.-L., Decaesteker, B., Van Nieuwerburgh, F., Speleman, F., Eyckerman, S., Mestdagh, P., Ulitsky, I.
Abstract
The importance of long noncoding RNA (lncRNA) functions is recognized across biological systems, but their modes of action remain poorly understood. One mechanism proposed to be particularly common is gene expression regulation via recruitment to specific genomic regions. Several high-throughput sequencing methods were developed for studying the genome-wide chromatin occupancy of lncRNAs, including ChIRP-seq, CHART-seq, and RAP-seq. These methods utilize biotin-labeled probes targeting the RNA of interest to isolate and recover the chromatin associated with it. Surprisingly, many of the datasets obtained with these methods contain many thousands of binding sites, in apparent contradiction with the low abundance of the interrogated lncRNAs. We studied the chromatin interactome of NESPR lncRNA in cells with varying levels of endogenous expression, and then performed a meta-analysis using dozens of RNA-chromatin interaction datasets in human and mouse cells. We show that thousands of regions reported to bind lncRNAs most likely arise from spurious recovery of DNA elements with partial complementarity of the ends of the recovered DNA fragments with the probes used for the pulldown. In addition, crucial controls were rarely used in studies profiling RNA-chromatin interactions. Therefore, the vast majority of chromatin regions reported as bound by trans-acting RNAs in recent studies in mammalian cells appear to be technical artifacts. We provide suggestions for assessing RNA-chromatin dataset quality and their improvement.
Preprint server:
bioRxiv
The authors list and abstract were imported from bioRxiv on 12 Nov 2025.
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