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RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA
Published on: April 10, 2018
Reference-guided Genome Assembly of Long Non-coding RNA Transcripts Reveals Target Genes Associated With Crohn's
Meaghan M Kennedy Ng1,2, Sophie Silverstein3, Nina C Nishiyama1,2
1Curriculum in Bioinformatics and Computational Biology, Department of Genetics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Abstract:
Crohn's disease (CD) is highly heterogeneous in presentation and progression with no cure. Molecular phenotyping has been used to elucidate cellular and tissue-based alterations to characterize drivers and effects of disease. One currently understudied class of functional molecules is long non-coding RNAs (lncRNAs). Studying the full lncRNA landscape in IBD is challenging due in part to an incomplete lncRNA annotation and a lack of their functional characterization in tissues of interest. We used a genome-guided alignment strategy to assemble predicted lncRNA transcripts using short RNA-sequencing data from colon tissue of adult patient samples. When combining our predicted lncRNAs with previous lncRNA annotations, we determined 98 that were differentially expressed, recapitulating many from previous IBD studies while also uncovering new ones. We built gene co-expression networks to cluster lncRNAs with functionally characterized protein-coding genes. Clusters containing differential lncRNAs were correlated to disease status and associated with pathways related to the humoral immune response, metabolism, and tissue regeneration. We uncovered multiple differential lncRNAs whose expression significantly correlated with nearby differential protein-coding genes that have also been differentially expressed in other IBD datasets, such as PITX2. We focused on a predicted lncRNA that is antisense to the PITX2-adjacent lncRNA PANCR, which we called PANCR-AS1, and provide multiple lines of evidence that support PANCR-AS1 functioning as an enhancer of PITX2 expression. Overall, we determined lncRNAs that are potential contributors to CD pathogenesis. We developed a robust pipeline for identifying lncRNAs in diseased and non-diseased tissue that are absent from reference annotations. We also outlined a framework to pinpoint significant disease-associated lncRNAs with potential functional activity related to their nearby protein-coding genes.
Insights
Researchers identified novel long non-coding RNAs (lncRNAs) in Crohn's disease (CD) colon tissue, revealing their potential roles in immune response and metabolism. A new pipeline aids in discovering these crucial molecules for understanding CD pathogenesis.
Area of Science:
- Genomics
- Molecular Biology
- Gastroenterology
Background:
- Crohn's disease (CD) is a heterogeneous inflammatory bowel disease (IBD) with no cure.
- Long non-coding RNAs (lncRNAs) are understudied in IBD pathogenesis.
- Challenges exist in lncRNA annotation and functional characterization in relevant tissues.
Purpose of the Study:
- To identify and characterize novel lncRNAs in colon tissue from CD patients.
- To explore the functional roles of lncRNAs in CD pathogenesis.
- To develop a pipeline for lncRNA discovery in IBD.
Main Methods:
- Genome-guided alignment of short RNA-sequencing data to assemble predicted lncRNA transcripts.
- Integration of predicted lncRNAs with existing annotations to identify differentially expressed lncRNAs.
- Gene co-expression network construction to cluster lncRNAs with protein-coding genes.
- Correlation analysis of lncRNA expression with disease status and pathways.
Main Results:
- Identified 98 differentially expressed lncRNAs, including novel candidates, in CD colon tissue.
- Discovered lncRNA clusters associated with immune response, metabolism, and tissue regeneration pathways.
- Found correlations between differential lncRNAs and nearby protein-coding genes, such as PITX2.
- Provided evidence for a novel lncRNA, PANCR-AS1, enhancing PITX2 expression.
Conclusions:
- lncRNAs are potential contributors to Crohn's disease pathogenesis.
- A robust pipeline was developed for identifying novel lncRNAs in diseased tissues.
- A framework was established to pinpoint disease-associated lncRNAs with functional relevance to nearby genes.
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