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Literature summary for 3.6.4.13 extracted from

  • Leone, S.; Baer, D.; Slabber, C.F.; Dalcher, D.; Santoro, R.
    The RNA helicase DHX9 establishes nucleolar heterochromatin, and this activity is required for embryonic stem cell differentiation (2017), EMBO Rep., 18, 1248-1262 .
    View publication on PubMedView publication on EuropePMC
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Activating Compound

Activating Compound Comment Organism Structure
TIP5 DHX9 associates with TIP5 independently of RNA. DHX9 requires the association of TIP5 with mature pRNA to bind to rRNA genes. DHX9 binds to rRNA genes only upon ESC differentiation and its activity guides TIP5 to rRNA genes and establishes heterochromatin Mus musculus

Protein Variants

Protein Variants Comment Organism
additional information plasmids and siRNAs are transfected in HEK-293T cells using calcium phosphate protocol. NIH 3T3 mouse fibroblasts, U2OS, and murine embryonic stem cells are transfected with the siRNA, siRNA-mediated depletions and synthetic RNA levels are monitored by quantitative RT-PCR expression analysis 3-4 days post transfection Mus musculus

Localization

Localization Comment Organism GeneOntology No. Textmining
additional information upon differentiation DHX9 drastically changes its position within the nucleus, and all cells show DHX9 with an exclusive localization within nucleoli and a weak signal in the rest of nucleoplasm Mus musculus
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nucleolus accumulation of DHX9 in nucleoli and its association with rRNA genes only upon ESC Mus musculus 5730
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ribosome
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 Mus musculus 5840
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Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ required Mus musculus

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
ATP + H2O Mus musculus
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 ADP + phosphate
-
 ?

Organism

Organism UniProt Comment Textmining
Mus musculus O70133
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-

Source Tissue

Source Tissue Comment Organism Textmining
fibroblast
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 Mus musculus
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additional information DHX9 is expressed in both ESCs and differentiated cells, the latter showing a slight increase at mRNA and protein levels Mus musculus
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NIH-3T3 cell
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 Mus musculus
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
ATP + H2O
-
 Mus musculus ADP + phosphate
-
 ?

Synonyms

Synonyms Comment Organism
DHX9
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 Mus musculus
RNA helicase DHX9
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 Mus musculus

General Information

General Information Comment Organism
evolution DHX9 belongs to the DExH/RHA family of helicase superfamily 2 Mus musculus
malfunction embryonic stem cells (ESCs) depleted of DHX9 are unable to differentiate, and this phenotype is reverted by the addition of pRNA, whereas providing IGS-rRNA and pRNA mutants deficient for TIP5 binding are not sufficient. Knockdown of TIP5 does not affect DHX9 levels. NIH 3T3 cells depleted of DHX9 show a reduction in rRNA gene silencing Mus musculus
metabolism analysis of lncRNA biogenesis during development and support of a model in which the state of rRNA gene chromatin is part of the regulatory network that controls exit from pluripotency and initiation of differentiation pathways. Critical role of pRNA biogenesis in the establishment of rRNA gene heterochromatin. DHX9 is required for the formation of heterochromatin at rRNA genes through processing of IGS-rRNA into pRNA Mus musculus
additional information DHX9 is characterized by two copies of a double-stranded RNA binding domain (DSRM) at the N-terminus, a helicase core domain (HrpA) in the central region, and an RGG-rich region at the carboxyl terminus, which confers both RNA and DNA helicase activities Mus musculus
physiological function rRNA genes undergo chromatin changes during mouse embryonic stem cell (ESC) differentiation. The establishment of heterochromatin at rRNA genes depends on the processing of IGS-rRNA into pRNA. The RNA helicase DHX9 is a regulator of pRNA processing. DHX9 binds to rRNA genes only upon ESC differentiation and its activity guides TIP5 to rRNA genes and establishes heterochromatin. The production of mature pRNA is essential since it guides the repressor TIP5 to rRNA genes. The processing of IGS-rRNA into pRNA is impaired in embryonic stem cells (ESCs) and activated only upon differentiation. IGS-rRNA abolishes the process of guiding of repressor TIP5 to rRNA genes. The RNA helicase DHX9 associates with IGS-rRNA and TIP5. DHX9 is required for the formation of heterochromatin at rRNA genes through processing of IGS-rRNA into pRNA. DHX9 requires the association of TIP5 with mature pRNA to bind to rRNA genes Mus musculus