Since methods for analysing chromosome conformation in mammalian cells are either low resolution or low throughput and are technically challenging they are not widely used outside of specialised laboratories. We have re-designed the Capture-C method producing a new approach, called next generation (NG) Capture-C. This produces unprecedented levels of sensitivity and reproducibility and can be used to analyse many genetic loci and samples simultaneously. Importantly, high-resolution data can be produced on as few as 100,000 cells and SNPs can be used to generate allele specific tracks. The method is straightforward to perform and should therefore greatly facilitate the task of linking SNPs identified by genome wide association studies with the genes they influence. The complete and detailed protocol presented here, with new publicly available tools for library design and data analysis, will allow most laboratories to analyse chromatin conformation at levels of sensitivity and throughput that were previously impossible.

Many genes determining cell identity are regulated by clusters of mediator-bound enhancer elements collectively referred to as super-enhancers. These have been proposed to manifest higher-order properties important in development and disease. Here, we report a comprehensive functional dissection of one of the strongest putative super-enhancers in erythroid cells. By generating a series of mouse models, deleting each of the five regulatory elements of the α-globin super-enhancer singly and in informative combinations, we demonstrate that each constituent enhancer appears to act independently and in an additive fashion with respect to hematologic phenotype, gene expression, chromatin structure and chromosome conformation, without clear evidence of synergistic or higher-order effects. Our study highlights the importance of functional genetic analyses for the identification of new concepts in transcriptional regulation.

Long non-coding (lnc) RNAs can regulate gene expression and protein functions. However, the proportion of lncRNAs with biological activities among the thousands expressed in mammalian cells is controversial. We studied Lockd (LncRNA downstream of Cdkn1b), a 434 nt polyadenylated lncRNA originating 4 kilobases (kb) 3′ to the Cdkn1b gene. Deletion of the 25 kb Lockd locus reduced Cdkn1b transcription by approximately 70% in an erythroid cell line. In contrast, homozygous insertion of a polyadenylation cassette 80 bp downstream of the Lockd transcription start site reduced the entire lncRNA transcript level by > 90%, with no effect on Cdkn1b transcription. The Lockd promoter contains a DNase hypersensitive site, binds numerous transcription factors, and physically associates with the Cdkn1b promoter in chromosomal conformation capture studies. Thus, the Lockd gene positively regulates Cdkn1b transcription through an enhancer-like cis element, while the lncRNA itself is dispensable, which may be the case for other lncRNAs.