Fetal γ-globin genes are regulated by the BGLT3 long noncoding RNA locus

Abstract

Long noncoding RNAs (lncRNAs) 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 <i>BGLT3</i>, an erythroid lncRNA encoded downstream of ^Aγ-globin (<i>HBG1</i>). <i>BGLT3</i> and γ-globin genes are dynamically cotranscribed in erythroid cells in vivo. Deletion of <i>BGLT3</i> using CRISPR/Cas9 editing shows that it specifically contributes to regulation of γ-globin genes. We used reduction or overexpression of the RNA and inhibition of transcription through the locus by CRISPRi to distinguish functions of the transcript vs the underlying sequence. Transcription of the <i>BGLT3</i> locus is critical for looping between the γ-globin genes and <i>BGLT3</i> sequences. In contrast, the <i>BGLT3</i> transcript is dispensable for γ-globin/<i>BGLT3</i> looping but interacts with the mediator complex on chromatin. Manipulation of the <i>BGLT3</i> locus does not compromise γ-globin gene long-range looping interactions with the β-globin locus control region (LCR). These data reveal that <i>BGLT3</i> regulates γ-globin transcription in a developmental stage-specific fashion together with the LCR by serving as a separate means to increase RNA Pol II density at the γ-globin promoters.