Tissue-selective alternate promoters guide NLRP6 expression

Abstract

The pryin domain (PYD) domain is involved in protein interactions that lead to assembly of immune-sensing complexes such as inflammasomes. The repertoire of PYD-containing genes expressed by a cell type arms tissues with responses against a range of stimuli. The transcriptional regulation of the PYD gene family however is incompletely understood. Alternative promoter utilization was identified as a mechanism regulating the tissue distribution of human PYD gene family members, including NLRP6 that is translationally silenced outside of intestinal tissue. Results show that alternative transcriptional promoters mediate NLRP6 silencing in mice and humans, despite no upstream genomic synteny. Human NLRP6 contains an internal alternative promoter within exon 2 of the PYD, resulting in a truncated mRNA in nonintestinal tissue. In mice, a proximal promoter was used that expanded the 5′ leader sequence restricting nuclear export and abolishing translational efficiency. Nlrp6 was dispensable in disease models targeting the kidney, which expresses noncanonical isoforms. Thus, alternative promoter use is a critical mechanism not just for isoform modulation but for determining expression profile and function of PYD family members.

Physiological and pathophysiological functions of NLRP6: pro- and anti-inflammatory roles

“…NLRP6 is highly expressed in the digestive system 20 , 24 and most of the functional studies of NLRP6 focus on this system and its related diseases. However, NLRP6 is also expressed in other tissues such as the kidney, liver and lung and in cells such as neurons, lymphocytes, or bone marrow-derived cells 7 , 20 , 25 .…”

“…However, NLRP6 is also expressed in other tissues such as the kidney, liver and lung and in cells such as neurons, lymphocytes, or bone marrow-derived cells 7 , 20 , 25 . NLRP6 is a gene with multiple alternative transcriptional promoters that determine its distribution and expression across selective tissue and cell types 24 . In humans, NLRP6 has three alternative transcription starting sites (TSS), the first is located exon 1 (in the 5′ untranslated region), which is selective for intestine expression, the second is located in exon 2 (in the middle of the PYD domain), which is selective for expression in kidney, lung, liver, spleen, and brain, and the third is located in exon 3 (in the region between PYD and NACHT domains) 24 .…”

“…NLRP6 is a gene with multiple alternative transcriptional promoters that determine its distribution and expression across selective tissue and cell types 24 . In humans, NLRP6 has three alternative transcription starting sites (TSS), the first is located exon 1 (in the 5′ untranslated region), which is selective for intestine expression, the second is located in exon 2 (in the middle of the PYD domain), which is selective for expression in kidney, lung, liver, spleen, and brain, and the third is located in exon 3 (in the region between PYD and NACHT domains) 24 . All three TSS are present in the kidney, although its predominant transcription starting site is the second (exon 2), meaning that the NLRP6 detected there is truncated.…”

“…In contrast, in the small intestine, the predominant transcription starting site is the first (exon 1), meaning that in this case, the NLRP6 protein is endogenous, full-length, and highly detectable. Therefore, the translational repression of human NLRP6 occurs in a tissue-specific context (outside the intestinal epithelium) and is the result of alternative promoters 24 . In mouse, the Nlrp6 gene is expressed in kidney, liver, and intestinal tissue; however, only endogenous NLRP6 protein was detected in the intestine 24 .…”

“…Therefore, the translational repression of human NLRP6 occurs in a tissue-specific context (outside the intestinal epithelium) and is the result of alternative promoters 24 . In mouse, the Nlrp6 gene is expressed in kidney, liver, and intestinal tissue; however, only endogenous NLRP6 protein was detected in the intestine 24 . This is due to two distinct alternative promoter isoforms of Nlrp6 , one expressed in the intestine (in the exon 1 containing the canonical 5′ untranslated region of 185 bp) and the other expressed in the kidney and liver with an expanded 5′ untranslated region sequence of 1749 bp that results from complex alternative splicing comprising the exon 1 of Nlrp6 , two upstream intergenic exons and the exon 1 of the adjacent upstream gene BC024386 (expressed in kidney and liver but not in the colon), thus generating an alternative promoter 24 .…”