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MYSM1 maintains ribosomal protein gene expression in hematopoietic stem cells to prevent hematopoietic dysfunction
Jad I. Belle, HanChen Wang, Amanda Fiore, Jessica C. Petrov, Yun Hsiao Lin, Chu-Han Feng, Thi Tuyet Mai Nguyen, Jacky Tung, Philippe M. Campeau, Uta Behrends, Theresa Brunet, Gloria Sarah Leszinski, Philippe Gros, David Langlais, Anastasia Nijnik
Jad I. Belle, HanChen Wang, Amanda Fiore, Jessica C. Petrov, Yun Hsiao Lin, Chu-Han Feng, Thi Tuyet Mai Nguyen, Jacky Tung, Philippe M. Campeau, Uta Behrends, Theresa Brunet, Gloria Sarah Leszinski, Philippe Gros, David Langlais, Anastasia Nijnik
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Research Article Hematology Stem cells

MYSM1 maintains ribosomal protein gene expression in hematopoietic stem cells to prevent hematopoietic dysfunction

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Abstract

Ribosomopathies are congenital disorders caused by mutations in the genes encoding ribosomal and other functionally related proteins. They are characterized by anemia, other hematopoietic and developmental abnormalities, and p53 activation. Ribosome assembly requires coordinated expression of many ribosomal protein (RP) genes; however, the regulation of RP gene expression, especially in hematopoietic stem cells (HSCs), remains poorly understood. MYSM1 is a transcriptional regulator essential for HSC function and hematopoiesis. We established that HSC dysfunction in Mysm1 deficiency is driven by p53; however, the mechanisms of p53 activation remained unclear. Here, we describe the transcriptome of Mysm1-deficient mouse HSCs and identify MYSM1 genome-wide DNA binding sites. We establish a direct role for MYSM1 in RP gene expression and show a reduction in protein synthesis in Mysm1–/– HSCs. Loss of p53 in mice fully rescues Mysm1–/– anemia phenotype but not RP gene expression, indicating that RP gene dysregulation is a direct outcome of Mysm1 deficiency and an upstream mediator of Mysm1–/– phenotypes through p53 activation. We characterize a patient with a homozygous nonsense MYSM1 gene variant, and we demonstrate reduced protein synthesis and increased p53 levels in patient hematopoietic cells. Our work provides insights into the specialized mechanisms regulating RP gene expression in HSCs and establishes a common etiology of MYSM1 deficiency and ribosomopathy syndromes.

Authors

Jad I. Belle, HanChen Wang, Amanda Fiore, Jessica C. Petrov, Yun Hsiao Lin, Chu-Han Feng, Thi Tuyet Mai Nguyen, Jacky Tung, Philippe M. Campeau, Uta Behrends, Theresa Brunet, Gloria Sarah Leszinski, Philippe Gros, David Langlais, Anastasia Nijnik

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Figure 4

Validation of the direct role of MYSM1 in the regulation of ribosomal protein gene expression.

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Validation of the direct role of MYSM1 in the regulation of ribosomal pr...
(A) Consolidation of ChIP-Seq and RNA-Seq data sets showing that gene-proximal MYSM1 binding sites preferentially locate near Cluster I genes dysregulated in Mysm1-deficient HSC/MPP cells. The percentages of MYSM1 binding sites that have at least 1 significantly dysregulated gene TSS within the indicated search window are plotted. The random genes cluster consists of 10 groups of 300 genes randomly selected from 10,169 expressed genes. The random binding sites consist of 10 groups of 2000 genomic locations randomly selected from the mm9 genome. A binding site with more than 1 gene TSS from the same gene cluster is counted only once. Fisher Exact Test is used to calculate the P value. (B) Genomic snapshots of select dysregulated genes. ChIP-Seq tracks of input DNA, MYSM1, H3K27ac, and H2AK119ub are shown on the top 4 lanes. The gene feature track is shown in the middle. Averaged RNA-Seq tracks are in the bottom 6 lanes, with fold changes comparing expression levels in WT and KO samples indicated for each cell type. The maximum data range of each track is indicated at the top right corner of the track. (C) Enrichment of MYSM1 at RP gene promoter sites, validated with ChIP-qPCRs in MYSM1-FLAG Ba/F3 hematopoietic progenitor cells. Data presented is from 1 experiment and were reproduced in 3 independent experiments. (D) Downregulation of RP gene expression in knockdown shMysm1 Ba/F3 cells relative to control shFF Ba/F3 cells, validated with qPCRs. Each dot represents relative fold change from 1 of 3 independent experiments. Two to 3 technical replicates were performed per experiment. (E) Representative H3K27ac ChIP-qPCRs showing reduced relative enrichments in knockdown shMysm1 Ba/F3 cells relative to control shFF Ba/F3 cells. Data presented are from 1 experiment and were reproduced in 2 independent experiments.

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