@article{TEXTUAL,
      recid = {6248},
      author = {Sun, Xiangying and Wang, Zhezhen and Hall, Johnathon M.  and Perez-Cervantes, Carlos and Ruthenburg, Alexander J.  and Moskowitz, Ivan P. and Gribskov, Michael and Yang,  Xinan H.},
      title = {Chromatin-enriched RNAs mark active and repressive  cis-regulation: An analysis of nuclear RNA-seq},
      journal = {PLOS Computational Biology},
      address = {2020-02-10},
      number = {TEXTUAL},
      abstract = {Long noncoding RNAs (lncRNAs) localize in the cell nucleus  and influence gene expression through a variety of  molecular mechanisms. Chromatin-enriched RNAs (cheRNAs) are  a unique class of lncRNAs that are tightly bound to  chromatin and putatively function to locally cis-activate  gene transcription. CheRNAs can be identified by  biochemical fractionation of nuclear RNA followed by RNA  sequencing, but until now, a rigorous analytic pipeline for  nuclear RNA-seq has been lacking. In this study, we survey  four computational strategies for nuclear RNA-seq data  analysis and develop a new pipeline, Tuxedo-ch, which  outperforms other approaches. Tuxedo-ch assembles a more  complete transcriptome and identifies cheRNA with higher  accuracy than other approaches. We used Tuxedo-ch to  analyze benchmark datasets of K562 cells and further  characterize the genomic features of intergenic cheRNA  (icheRNA) and their similarity to enhancer RNAs (eRNAs). We  quantify the transcriptional correlation of icheRNA and  adjacent genes and show that icheRNA is more positively  associated with neighboring gene expression than eRNA or  cap analysis of gene expression (CAGE) signals. We also  explore two novel genomic associations of cheRNA, which  indicate that cheRNAs may function to promote or repress  gene expression in a context-dependent manner. IcheRNA loci  with significant levels of H3K9me3 modifications are  associated with active enhancers, consistent with the  hypothesis that enhancers are derived from ancient mobile  elements. In contrast, antisense cheRNA (as-cheRNA) may  play a role in local gene repression, possibly through  local RNA:DNA:DNA triple-helix formation.},
      url = {http://knowledge.uchicago.edu/record/6248},
}