Related Experiment Video

Updated: May 27, 2026

RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA
09:36

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, 111 Mason Farm Road, Chapel Hill, NC, USA, 27599.

Scientific Reports
|May 25, 2026
PubMed

Insights

Researchers identified novel long non-coding RNAs (lncRNAs) in Crohn's disease (CD) colon tissue. These lncRNAs are linked to immune response and metabolism, offering new insights into CD pathogenesis.

Area of Science:

  • Genomics
  • Molecular Biology
  • Gastroenterology

Background:

  • Crohn's disease (CD) is a complex inflammatory bowel disease (IBD) with heterogeneous presentation and no known cure.
  • Long non-coding RNAs (lncRNAs) are an understudied class of functional molecules with potential roles in disease.
  • Characterizing the lncRNA landscape in CD is hindered by incomplete annotations and lack of functional data.

Purpose of the Study:

  • To identify and characterize novel lncRNAs in colon tissue from Crohn's disease patients.
  • To investigate the association of lncRNAs with disease status and relevant biological pathways.
  • To explore the functional relationship between lncRNAs and protein-coding genes in CD pathogenesis.

Main Methods:

  • Genome-guided alignment of short RNA-sequencing data from colon tissues to assemble novel lncRNA transcripts.
  • Integration of predicted lncRNAs with existing annotations to identify differentially expressed lncRNAs.
  • Construction of gene co-expression networks to cluster lncRNAs with protein-coding genes and pathway analysis.

Main Results:

  • Identified 98 differentially expressed lncRNAs, including novel ones not present in current annotations.
  • Discovered lncRNA clusters associated with disease status, humoral immune response, metabolism, and tissue regeneration pathways.
  • Found differential lncRNAs, like PANCR-AS1, whose expression correlates with nearby protein-coding genes (e.g., PITX2) implicated in IBD.

Conclusions:

  • lncRNAs are potential contributors to Crohn's disease pathogenesis.
  • Developed a robust pipeline for identifying novel lncRNAs in diseased tissues.
  • Established a framework for pinpointing disease-associated lncRNAs with functional relevance to nearby genes.
Keywords:
Crohn’s diseaselong non-coding RNAstranscriptomics

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