Developmentally regulated promoter-switch transcriptionally controls Runx1 function during embryonic hematopoiesis

<p>Abstract</p> <p>Background</p> <p>Alternative promoters usage is an important paradigm in transcriptional control of mammalian gene expression. However, despite the growing interest in alternative promoters and their role in genome diversification, very little is known about how and on what occasions those promoters are differentially regulated. Runx1 transcription factor is a key regulator of early hematopoiesis and a frequent target of chromosomal translocations in acute leukemias. Mice deficient in <it>Runx1 </it>lack definitive hematopoiesis and die in mid-gestation. Expression of <it>Runx1 </it>is regulated by two functionally distinct promoters designated P1 and P2. Differential usage of these two promoters creates diversity in distribution and protein-coding potential of the mRNA transcripts. While the alternative usage of P1 and P2 likely plays an important role in <it>Runx1 </it>biology, very little is known about the function of the P1/P2 switch in mediating tissue and stage specific expression of <it>Runx1 </it>during development.</p> <p>Results</p> <p>We employed mice bearing a hypomorphic <it>Runx1 </it>allele, with a largely diminished P2 activity, to investigate the biological role of alternative P1/P2 usage. Mice homozygous for the hypomorphic allele developed to term, but died within a few days after birth. During embryogenesis the P1/P2 activity is spatially and temporally modulated. P2 activity is required in early hematopoiesis and when attenuated, development of liver hematopoietic progenitor cells (HPC) was impaired. Early thymus development and thymopoiesis were also abrogated as reflected by thymic hypocellularity and loss of corticomedullary demarcation. Differentiation of CD4/CD8 thymocytes was impaired and their apoptosis was enhanced due to altered expression of T-cell receptors.</p> <p>Conclusion</p> <p>The data delineate the activity of P1 and P2 in embryogenesis and describe previously unknown functions of Runx1. The findings show unequivocally that the role of P1/P2 during development is non redundant and underscore the significance of alternative promoter usage in Runx1 biology.</p

Absence of Runx3 expression in normal gastrointestinal epithelium calls into question its tumour suppressor function

The Runx3 transcription factor regulates cell fate decisions during embryonic development and in adults. It was previously reported that Runx3 is strongly expressed in embryonic and adult gastrointestinal tract (GIT) epithelium (Ep) and that its loss causes gastric cancer. More than 280 publications have based their research on these findings and concluded that Runx3 is indeed a tumour suppressor (TS). In stark contrast, using various measures, we found that Runx3 expression is undetectable in GIT Ep. Employing a variety of biochemical and genetic techniques, including analysis of Runx3-GFP and R26LacZ/Runx3Cre or R26tdTomato/Runx3Cre reporter strains, we readily detected Runx3 in GIT-embedded leukocytes, dorsal root ganglia, skeletal elements and hair follicles. However, none of these approaches revealed detectable Runx3 levels in GIT Ep. Moreover, our analysis of the original Runx3LacZ/LacZ mice used in the previously reported study failed to reproduce the GIT expression of Runx3. The lack of evidence for Runx3 expression in normal GIT Ep creates a serious challenge to the published data and undermines the notion that Runx3 is a TS involved in cancer pathogenesis

The False Paradigm of RUNX3 Function as Tumor Suppressor in Gastric Cancer

EgyptColo

Runx3 prevents spontaneous colitis by directing the differentiation of anti-inflammatory mononuclear phagocytes.

Mice deficient in the transcription factor Runx3 develop a multitude of immune system defects, including early onset colitis. This paper demonstrates that Runx3 is expressed in colonic mononuclear phagocytes (MNP), including resident macrophages (RM) and dendritic cell subsets (cDC2). Runx3 deletion in MNP causes early onset colitis due to their impaired maturation. Mechanistically, the resulting MNP subset imbalance leads to up-regulation of pro-inflammatory genes as occurs in IL10R-deficient RM. In addition, RM and cDC2 display a marked decrease in expression of anti-inflammatory/TGF β-regulated genes and β-catenin signaling associated genes, respectively. MNP transcriptome and ChIP-seq data analysis suggest that a significant fraction of genes affected by Runx3 loss are direct Runx3 targets. Collectively, Runx3 imposes intestinal immune tolerance by regulating maturation of colonic anti-inflammatory MNP, befitting the identification of RUNX3 as a genome-wide associated risk gene for various immune-related diseases in humans, including gastrointestinal tract diseases such as Crohn's disease and celiac

Enriched motifs within Runx3-bound regions in resting cells.

<p>(A) Overrepresentation of RUNX motif variants among Runx3-bound regions in CD8-TC. (B and C) Results of de novo motif finding analysis spanning Runx3-bound regions in CD8-TC and NKC. The 3 most enriched motifs in Runx3-bound promoter (B) and enhancer (C) regions are shown. </p

Runx3-bound regions and their corresponding annotated genes in IL-2-activated compared to resting CD8-TC and NKC.

<p>(A) Overlap of Runx3-bound (upper panels) regions or their corresponding genes (lower panels) in resting and IL-2-activated CD8-TC (left) or NKC (right). The genes corresponding to Runx3-bound regions were derived using GREAT [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080467#B19" target="_blank">19</a>]. (B) Recruitment of Runx3 to de novo IL-2-activated regions in Gzme-Gzmc (top) and Serpinb1c-Serpinb1b (bottom) loci, in NKC and CD8-TC, respectively. Brown tracing and rectangles represent Runx3 ChIP-seq wiggle files and the positions of Runx3 peaks, respectively, as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080467#pone-0080467-g001" target="_blank">Figure 1</a>. Note that some de novo Runx3-bound regions in Serpin genes in IL-2-activated CD8-TC appear to bind Runx3 in resting CD8-TC, but these regions are not scored by MACS as peaks in resting CD8-TC due to the higher background. (C) Overlap of Runx3-bound regions (upper panel) and their corresponding genes (lower panel) in IL-2-activated CD8-TC and NKC. </p

Common Runx3-regulated genes in IL-2-activated CD8-TC/NKC and T-bet/p300 bound genes in Th1.

<p>(A) The majority of the 118 common Runx3-regulated genes in IL-2-activated CD8-TC and NKC (R3_CD8_NK_T) harbor overlapping T-bet (R3CD8_Tbet) and p300 (R3_CD8_p300) bound regions in Th1 cells. (B) Transcription factors/regulators that are common Runx3-regulated genes in IL-2-activated CD8-TC and NKC. </p