Chromatin Structure, Epigenetic and Developmental Regulation of Mammalian Gene

National Institute Of Diabetes And Digestive And Kidney Diseases

Investigators

Linked publications & trials

Abstract

The eukaryotic genome is organized at varying levels into chromosome territories, transcriptional compartments and topologically associating domains (TADs), which are architectural features largely shared between different cell types and across species. In contrast, within TADs, chromatin loops connect enhancers and their target genes to establish unique transcriptomes that distinguish cells and tissues from each other and underlie development and differentiation. We have been studying the widely expressed Lim domain binding 1 protein, LDB1, which plays a critical role in connecting enhancers and genes by forming complexes with cell-type specificity across diverse developmental pathways including neurogenesis, cardiogenesis, retinogenesis and hematopoiesis. Long non-coding RNAs (lncRNA) are increasingly being appreciated as participants in regulation of important cellular processes, including transcription. Because lncRNAs are highly cell-type specific, they have the potential to contribute to the unique transcriptional repertoire of diverse cells, but underlying mechanisms are unclear. We studied BGLT3, an erythroid lncRNA encoded downstream of Agamma-globin (HBG1). BGLT3 is occupied by the LDB1 complex, similar to the locus control region (LCR) enhancer, which depends on this complex for chromatin looping to active globin genes. BGLT3 and gamma-globin genes are dynamically co-transcribed in erythroid cells in vivo. Deletion of BGLT3 using CRISPR/Cas9 editing shows that it is a positive regulator of gamma globin transcription. Transcription of the BGLT3 locus is critical for looping between the gamma-globin genes and BGLT3 sequences. In contrast, the BGLT3 transcript itself is dispensable for gamma-globin/BGLT3 looping but interacts with and recruits the Mediator complex to the globin locus. These data reveal that BGLT3 regulates gamma-globin transcription in a developmental stage-specific fashion, together with the LCR, by serving as a separate means to increase RNA Pol II and Mediator density at the gamma-globin promoters.