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SBDS-dependent ribosome destabilization maintains pluripotency via regulation of translation

ABSTRACT: Unique traits of pluripotent stem cells are not fully known. Using thermal proteome profiling, we identified reduced stability of ribosomes in induced pluripotent cells (iPSCs) compared to that in somatic cells. Also, iPSCs exhibited lower protein synthesis rate and lower expression of a ribosome maturation factor, the Shwachman-Bodian-Diamond Syndrome protein (SBDS). Differentiation of iPSCs led to upregulation of SBDS and knock-down of SBDS slowed the differentiation while increasing expression of master pluripotency markers NANOG and OCT4. Mutations in the SBDS gene have been shown to impair ribosome assembly and to inhibit differentiation of hematopoietic stem cells causing the Shwachman-Diamond syndrome. Physiological SBDS-dependent destabilization of ribosomes appears to be a tool for translational control providing robustness to the state of pluripotency.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Fibroblast, Embryonic Stem Cell

SUBMITTER: Pierre Sabatier

LAB HEAD: Roman A. Zubarev

PROVIDER: PXD015874 | Pride | 2021-10-05

REPOSITORIES: Pride

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Project description:5-methylcytosine (5-mC) can be oxidized to 5-hydroxymethylcytosine (5-hmC). Genome-wide profiling of 5-hmC thus far indicated 5-hmC may not only be an intermediate form of DNA demethylation but could also constitute an epigenetic mark per se. We describe a cost-effective and selective method to detect both the hydroxymethylation and methylation status of cytosines in more than 1.8 million MspI sites in the human genome. This method involves the selective glucosylation of 5-hmC residues, short-sequence tag generation and high-throughput sequencing. We tested this method by screening H9 human embryonic stem cells and their differentiated embroid body cells, and found that differential hydroxymethylation preferentially occur in bivalent genes during cellular differentiation. Especially, our results support hydroxymethylation can regulate key transcription regulators with bivalent marks through demethylation and affect cellular decision on choosing active or inactive state of these genes upon cellular differentiation. We developed a cost-effective and selective method to detect both the hydroxymethylation and methylation status of cytosines in more than 1.8 million MspI sites in the human genome. In this method, we took advantage of the differential enzymatic sensitivities of the isoschizomers MspI and HpaII. HpaII cleaves only a completely unmodified site, any modification at either cytosine blocks the cleavage, while MspI recognizes and cleaves both 5-mC and 5-hmC, but not the newly discovered 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC). Furthermore, beta-glucosyltransferase (beta-GT) can transfer a glucose to the hydroxyl group of 5-hmC and generate beta-glucosyl-5-hydroxymethylcytosine (5-ghmC) that blocks MspI digestion. Thus, either by combining beta-GT treatment with MspI digestion or simply applying MspI/HpaII digestion, short sequence tags generated can be used for inferring hydroxymethylation or methylation status in around 1.8 million cytosine sites in the human genome. We tested this method by screening H9 human embryonic stem cells and their differentiated embroid body cells.

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SBDS-dependent ribosome destabilization maintains pluripotency via regulation of translation

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