Opposing roles for the lncRNA Haunt and its genomic locus in regulating HOXA gene activation during embryonic stem cell differentiation

Long noncoding RNAs (lncRNAs) have been implicated in controlling various aspects of embryonic stem cell (ESC) biology, although the functions of specific lncRNAs, and the molecular mechanisms through which they act, remain unclear. Here, we demonstrate discrete and opposing roles for the lncRNA transcript Haunt and its genomic locus in regulating the HOXA gene cluster during ESC differentiation. Reducing or enhancing Haunt expression, with minimal disruption of the Haunt locus, led to up- or down-regulation of HOXA genes, respectively. In contrast, increasingly large genomic deletions within the Haunt locus attenuated HOXA activation. The Haunt DNA locus contains potential enhancers of HOXA activation, whereas Haunt RNA acts to prevent aberrant HOXA expression. This work reveals a multi-faceted model of lncRNA-mediated transcriptional regulation of the HOXA cluster, with distinct roles for a lncRNA transcript and its genomic locus, while illustrating the power of rapid CRISPR/Cas9-based genome editing for assigning lncRNA functions.

长链非编码RNA（long noncoding RNAs, lncRNAs）已被证实参与调控胚胎干细胞（embryonic stem cell, ESC）生命活动的诸多方面，尽管特定lncRNA的功能及其发挥作用的分子机制仍未明确。本研究中，我们揭示了长链非编码RNA转录本Haunt及其基因组位点在胚胎干细胞分化过程中调控HOXA基因簇时所发挥的截然不同且相互对立的作用。在仅轻微干扰Haunt基因组位点的前提下，降低或增强Haunt的表达，分别会导致HOXA基因的上调或下调。与之相反，在Haunt基因组位点中进行逐步增大的基因组片段缺失，则会削弱HOXA基因的激活。Haunt的DNA位点包含HOXA激活的潜在增强子，而Haunt RNA则起到抑制HOXA基因异常表达的作用。本研究揭示了一种由lncRNA介导的HOXA基因簇转录调控的多维度模型，明确区分了lncRNA转录本与其基因组位点的不同功能，同时也展现了基于CRISPR/Cas9的快速基因组编辑技术在解析lncRNA功能方面的强大能力。