Mouse knockout models reveal largely dispensable but context-dependent functions of IncRNAs during development

Dear Editor, In mammalian genomes, pervasive transcription produces thousands of long non-coding RNA （IncRNA） transcripts （Olebali et al., 2012; Hon et al., 2017）. Compared to protein-coding mRNAs, IncRNAs are less conserved, and often exhibit low-level, developmental stage-and tissue-specific expression （Pauli et al., 2011; Hu et al., 2012; Lee, 2012; Ulitsky and Bartel, 2013; Cech and Steitz, 2014; Hon et al., 2017）. Many IncRNAs are strongly correlated with their neighboring mRNA genes in terms of expression and function, and tend to regulate nearby transcription （Orom et al., 2010; Engreitz et al., 2016; Luo etal., 2016）. It has been implicated that IncRNAs play versatile roles in regulating diverse aspects of cell biology through mechanisms at multiple levels （Pauli et al., 2011; Lee.

LncRNA Platr22 promotes super-enhancer activity and stem cell pluripotency

Super-enhancers(SEs)comprise large clusters of enhancers,which are co-occupied by multiple lineage-specific and master tran-scription factors,and play pivotal roles in regulating gene expression and cell fate determination.However,it is still largely un-known whether and how SEs are regulated by the noncoding portion of the genome.Here,through genome-wide analysis,wefound that tpng noncoding RNA(IncRNA)genes preferentially lie next to SEs.In mouse embryonic stem cells(mESCs),depletionof$E-associated IlncRNA transcripts dysregulated the activity of their nearby SEs.Specifically,we revealed a critical regulatoryrole of the IncRNA gene Platr22 in modulating the activity of a nearby SE and the expression of the nearby pluripotency regulatorZFP281.Through these regulatory events,Platr22 contributes to pluripotency maintenance and proper differentiation of mESCs.Mechanistically,Platr22 transcripts coat chromatin near the SE region and interact with DDX5 and hnRNP-L.DDX5 further recruitsp300 and other factors related to active transcription.We propose that these factors assemble into a transcription hub,thus pro-moting an open and active epigenetic chromatin state.0ur study highlights an unanticipated role for a class of lncRNAs in epige-netically controlling the activity and vulnerability to perturbation of nearby SEs for cell fate determination.

Tn5-FISH,a novel cytogenetic method to image chromatin interactions with sub-kilobase resolution

There is an increasing interest in understanding how three-dimensional(3D)organization of the genome is regulated.Different strategies have been employed to identify genome-wide chromatin interactions.However,due to current limitations in resolving genomic contacts,visualization and validation of these genomic loci with sub-kilobase resolution remain unsolved to date.Here,we describe Tn5 transposase-based Fluorescencein situhybridization(Tn5-FISH),a PCR-based,cost-effective imaging method,which can co-localize the genomic loci with sub-kilobase resolution,dissect genome architecture,and verify chromatin interactions detected by chromatin configuration capture(3C)-derived methods.To validate this method,short-range interactions in keratin-encoding gene(KRT)locus in topologically associated domain(TAD)were imaged by triple-color Tn5-FISH,indicating that Tn5-FISH is very useful to verify short-range chromatin interactions inside the contact domain and TAD.Therefore,Tn5-FISH can be a powerful molecular tool for the clinical detection of cytogenetic changes in numerous genetic diseases such as cancers.