Nucleolin loss-of-function leads to aberrant FGF signaling and craniofacial anomalies

Mapping Intimacies ◽

10.1101/2021.09.14.460382 ◽

2021 ◽

Author(s):

Soma Dash ◽

Paul Trainor

Keyword(s):

Ribosome Biogenesis ◽

Craniofacial Development ◽

Rrna Synthesis ◽

Growth Factor Signaling ◽

Craniofacial Anomalies ◽

Fgf Signaling ◽

Loss Of Function ◽

Tissue Specific ◽

Rrna Transcription ◽

Exogenous Addition

rRNA transcription and ribosome biogenesis are global processes required for growth and proliferation of all cells, yet perturbation of these processes in vertebrates leads to tissue-specific defects termed ribosomopathies. Mutations in rRNA transcription and processing proteins often lead to craniofacial anomalies, however the cellular and molecular reasons for this are poorly understood. Therefore, we examined the function of the most abundant nucleolar phosphoprotein, Nucleolin (Ncl), in vertebrate development. We discovered that Nucleolin is dynamically expressed during embryonic development with high enrichment in the craniofacial tissues. Consistent with this pattern of expression, ncl homozygous mutant (ncl-/-) zebrafish present with craniofacial anomalies such as mandibulofacial hypoplasia. We observe that ncl-/- mutants exhibit decreased rRNA synthesis and p53-dependent neuroepithelial cell death. In addition, the half-life of fgf8a mRNA is reduced in ncl-/- mutants, which perturbs Fgf signaling, resulting in misregulation of Sox9a mediated chondrogenesis and Runx2 mediated osteogenesis. Exogenous addition of human recombinant FGF8 to the mutant zebrafish significantly rescues the cranioskeletal phenotype, suggesting that Nucleolin regulates osteochondroprogenitor differentiation during craniofacial development by post-transcriptionally regulating Fgf signaling. Our work has therefore uncovered a novel tissue-specific function for Nucleolin in rRNA transcription and growth factor signaling during embryonic craniofacial development.

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Dynamic regulation and requirement for ribosomal RNA transcription during mammalian development

10.1101/2021.09.22.461379 ◽

2021 ◽

Author(s):

Karla Terrazas Falcon ◽

Kristin Watt ◽

Soma Dash ◽

Annita Achilleos ◽

Emma Moore ◽

...

Keyword(s):

Ribosomal Rna ◽

Ribosome Biogenesis ◽

Protein Translation ◽

Craniofacial Development ◽

Rrna Synthesis ◽

Craniofacial Anomalies ◽

Congenital Diseases ◽

Tissue Specific ◽

Rrna Transcription ◽

Pol I

Ribosomal RNA (rRNA) transcription by RNA Polymerase I (Pol I) is a critical rate-limiting step in ribosome biogenesis, which is essential for cell survival. Despite its global function, disruptions in ribosome biogenesis cause tissue-specific birth defects called ribosomopathies which frequently affect craniofacial development. Here, we present a cellular and molecular mechanism to explain the susceptibility of craniofacial development to disruptions in Pol I transcription. We show that Pol I subunits are highly expressed in the neuroepithelium and neural crest cells (NCC), which generate most of the craniofacial skeleton. High expression of Pol I subunits sustains elevated rRNA transcription in NCC progenitors, which supports their high tissue-specific levels of protein translation, but also makes NCC particulalry sensitive to rRNA synthesis defects. Underpinning these findings, NCC-specific deletion of Pol I subunits Polr1a, Polr1c, and associated factor Tcof1 in mice cell-autonomously diminishes rRNA synthesis, which causes an imbalance between rRNA and ribosomal proteins. This leads to increased ribosomal protein binding to Mdm2 and concomitantly diminished Mdm2 binding to p53. Consequently, p53 protein accumulates, resulting in NCC apoptosis and craniofacial anomalies. Furthermore, compound mutations in Pol I subunits and associated factors specifically exacerbates the craniofacial anomalies characteristic of the ribosomopathies Treacher Collins Syndrome and Acrofacial Dysostosis Cincinnati Type. Our novel results therefore demonstrate the dynamic spatiotemporal requirement for rRNA transcription during mammalian cranial NCC development and corresponding tissue-specific threshold sensitivities to disruptions in rRNA transcription in the pathogenesis of craniofacial congenital diseases.

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Direct Regulation of rRNA Transcription by Fibroblast Growth Factor 2

Molecular and Cellular Biology ◽

10.1128/mcb.25.21.9419-9426.2005 ◽

2005 ◽

Vol 25 (21) ◽

pp. 9419-9426 ◽

Cited By ~ 26

Author(s):

Zhi Sheng ◽

Yanping Liang ◽

Chih-Yin Lin ◽

Lucio Comai ◽

William J. Chirico

Keyword(s):

Growth Factor ◽

Cell Growth ◽

Fibroblast Growth Factor ◽

Ribosome Biogenesis ◽

Secretory Pathway ◽

Rrna Genes ◽

Fibroblast Growth Factor 2 ◽

Rrna Synthesis ◽

Fibroblast Growth ◽

Rrna Transcription

ABSTRACT Fibroblast growth factor 2 (FGF-2), which is highly expressed in developing tissues and malignant cells, regulates cell growth, differentiation, and migration. Five isoforms (18 to ∼34 kDa) of FGF-2 are derived from alternative initiation codons of a single mRNA. The 18-kDa FGF-2 isoform is released from cells by a nonclassical secretory pathway and regulates gene expression by binding to cell surface receptors. This isoform also localizes to the nucleolus, raising the possibility that it may directly regulate ribosome biogenesis, a rate-limiting process in cell growth. Although several growth factors have been shown to accumulate in the nucleolus, their function and mechanism of action remain unclear. Here we show that 18-kDa FGF-2 interacts with upstream binding factor (UBF), an architectural transcription factor essential for rRNA transcription. The maximal activation of rRNA transcription in vitro by 18-kDa FGF-2 requires UBF. The 18-kDa FGF-2 localizes to rRNA genes and is necessary for the full activation of pre-rRNA synthesis in vivo. Our results demonstrate that 18-kDa FGF-2 directly regulates rRNA transcription.

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Phosphorylation of Eukaryotic Translation Initiation Factor 2α Coordinates rRNA Transcription and Translation Inhibition during Endoplasmic Reticulum Stress

Molecular and Cellular Biology ◽

10.1128/mcb.00260-09 ◽

2009 ◽

Vol 29 (15) ◽

pp. 4295-4307 ◽

Cited By ~ 65

Author(s):

Jenny B. DuRose ◽

Donalyn Scheuner ◽

Randal J. Kaufman ◽

Lawrence I. Rothblum ◽

Maho Niwa

Keyword(s):

Endoplasmic Reticulum ◽

Ribosome Biogenesis ◽

Critical Role ◽

Mammalian Target Of Rapamycin ◽

Protein Translation ◽

Translation Initiation Factor ◽

Initiation Factor ◽

Rrna Synthesis ◽

Cell Physiology ◽

Rrna Transcription

ABSTRACT The endoplasmic reticulum (ER) is the major cellular compartment where folding and maturation of secretory and membrane proteins take place. When protein folding needs exceed the capacity of the ER, the unfolded protein response (UPR) pathway modulates gene expression and downregulates protein translation to restore homeostasis. Here, we report that the UPR downregulates the synthesis of rRNA by inactivation of the RNA polymerase I basal transcription factor RRN3/TIF-IA. Inhibition of rRNA synthesis does not appear to involve the well-characterized mTOR (mammalian target of rapamycin) pathway; instead, PERK-dependent phosphorylation of eIF2α plays a critical role in the inactivation of RRN3/TIF-IA. Downregulation of rRNA transcription occurs simultaneously or slightly prior to eIF2α phosphorylation-induced translation repression. Since rRNA is the most abundant RNA species, constituting ∼90% of total cellular RNA, its downregulation exerts a significant impact on cell physiology. Our study demonstrates the first link between regulation of translation and rRNA synthesis with phosphorylation of eIF2α, suggesting that this pathway may be broadly utilized by stresses that activate eIF2α kinases in order to coordinately regulate translation and ribosome biogenesis during cellular stress.

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ZNF545 loss promotes ribosome biogenesis and protein translation to initiate colorectal tumorigenesis in mice

Oncogene ◽

10.1038/s41388-021-01938-8 ◽

2021 ◽

Author(s):

Shiyan Wang ◽

Chi Chun Wong ◽

Yanquan Zhang ◽

Junzhe Huang ◽

Chuangen Li ◽

...

Keyword(s):

Zinc Finger ◽

Ribosome Biogenesis ◽

Zinc Finger Protein ◽

Transcriptional Repressor ◽

Protein Translation ◽

Rrna Synthesis ◽

Synthesis Inhibitor ◽

Colorectal Tumorigenesis ◽

Normal Tissues ◽

Rrna Transcription

AbstractRibosome biogenesis plays a pivotal role in tumorigenesis by supporting robust protein translation. We investigate the functional and molecular mechanism of Zinc finger protein 545 (ZNF545), a transcriptional repressor for ribosomal RNA (rRNA), in colorectal cancer (CRC). ZNF545 was silenced in CRC compared to adjacent normal tissues (P < 0.0001), implying a tumor-suppressive role. Colon-specific Znf545 knockout in mice accelerated CRC in ApcMin/+ and azoxymethane/dextran sulfate sodium-induced CRC. Mechanistically, we demonstrated that ZNF545 uses its two zinc finger clusters to bind to minimal rDNA promoter, where it assembled transcriptional repressor complex by interacting with KAP1. Znf545 deletion in mouse embryonic fibroblasts not only increased rRNA transcription rate and the nucleolar size and number but also altered the nucleolar composition and architecture with an increased number of fibrillar centers surrounded by net-like dense fibrillar components. Consequently, Znf545 deletion promoted the gene expression of translation machinery, protein translation, and cell growth. Consistent with its tumor-suppressive role, ZNF545 overexpression in CRC cells induced growth arrest and apoptosis. Finally, administration of rRNA synthesis inhibitor, CX-5461, inhibited CRC development in Znf545Δ/ΔApcMin/+ mice. In conclusion, ZNF545 suppresses CRC through repressing rRNA transcription and protein translation. Targeting rRNA biosynthesis in ZNF545-silenced tumors is a potential therapeutic strategy for CRC.

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Inhibitor of Growth 4 (ING4) is a positive regulator of rRNA synthesis

Scientific Reports ◽

10.1038/s41598-019-53767-1 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Duc-Anh Trinh ◽

Ryutaro Shirakawa ◽

Tomohiro Kimura ◽

Natsumi Sakata ◽

Kota Goto ◽

...

Keyword(s):

Ribosome Biogenesis ◽

Rrna Synthesis ◽

Wild Type ◽

Cellular Functions ◽

Nucleolar Structure ◽

Nucleolar Proteins ◽

Rrna Transcription ◽

Plant Homeodomain ◽

Exogenous Expression ◽

Active Genes

AbstractRibosome biogenesis is essential for maintaining basic cellular activities although its mechanism is not fully understood. Inhibitor of growth 4 (ING4) is a member of ING family while its cellular functions remain controversial. Here, we identified several nucleolar proteins as novel ING4 interacting proteins. ING4 localized in the nucleus with strong accumulation in the nucleolus through its plant homeodomain, which is known to interact with histone trimethylated H3K4, commonly present in the promoter of active genes. ING4 deficient cells exhibited slower proliferation and the alteration in nucleolar structure with reduced rRNA transcription, which was rescued by exogenous expression of GFP-ING4 to the similar levels of wild type cells. In the ING4 deficient cells, histone H3K9 acetylation and the key rRNA transcription factor UBF at the promoter of rDNA were reduced, both of which were also recovered by exogenous GFP-ING4 expression. Thus, ING4 could positively regulate rRNA transcription through modulation of histone modifications at the rDNA promoter.

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The in vivo functions of ARPF2 and ARRS1 in ribosomal RNA processing and ribosome biogenesis in Arabidopsis

Journal of Experimental Botany ◽

10.1093/jxb/eraa019 ◽

2020 ◽

Vol 71 (9) ◽

pp. 2596-2611

Author(s):

Ilyeong Choi ◽

Young Jeon ◽

Youngki Yoo ◽

Hyun-Soo Cho ◽

Hyun-Sook Pai

Keyword(s):

Ribosomal Proteins ◽

Ribosome Biogenesis ◽

Critical Role ◽

Ribosomal Subunit ◽

Ribosome Profiling ◽

Production Factor ◽

Rrna Synthesis ◽

Binary Complex ◽

Rrna Processing ◽

Loss Of Function

Abstract Yeast Rpf2 plays a critical role in the incorporation of 5S rRNA into pre-ribosomes by forming a binary complex with Rrs1. The protein characteristics and overexpression phenotypes of Arabidopsis Ribosome Production Factor 2 (ARPF2) and Arabidopsis Regulator of Ribosome Synthesis 1 (ARRS1) have been previously studied. Here, we analyze loss-of-function phenotypes of ARPF2 and ARRS1 using virus-induced gene silencing to determine their functions in pre-rRNA processing and ribosome biogenesis. ARPF2 silencing in Arabidopsis led to pleiotropic developmental defects. RNA gel blot analysis and circular reverse transcription–PCR revealed that ARPF2 depletion delayed pre-rRNA processing, resulting in the accumulation of multiple processing intermediates. ARPF2 fractionated primarily with the 60S ribosomal subunit. Metabolic rRNA labeling and ribosome profiling suggested that ARPF2 deficiency mainly affected 25S rRNA synthesis and 60S ribosome biogenesis. ARPF2 and ARRS1 formed the complex that interacted with the 60S ribosomal proteins RPL5 and RPL11. ARRS1 silencing resulted in growth defects, accumulation of processing intermediates, and ribosome profiling similar to those of ARPF2-silenced plants. Moreover, depletion of ARPF2 and ARRS1 caused nucleolar stress. ARPF2-deficient plants excessively accumulated anthocyanin and reactive oxygen species. Collectively, these results suggest that the ARPF2–ARRS1 complex plays a crucial role in plant growth and development by modulating ribosome biogenesis.

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Faculty Opinions recommendation of AKT promotes rRNA synthesis and cooperates with c-MYC to stimulate ribosome biogenesis in cancer.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.13200027.14542192 ◽

2011 ◽

Author(s):

Larry Kane ◽

Jing Cheng

Keyword(s):

Ribosome Biogenesis ◽

Rrna Synthesis

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Commuting to Work: Nucleolar Long Non-Coding RNA Control Ribosome Biogenesis from Near and Far

Non-Coding RNA ◽

10.3390/ncrna7030042 ◽

2021 ◽

Vol 7 (3) ◽

pp. 42

Author(s):

Victoria Mamontova ◽

Barbara Trifault ◽

Lea Boten ◽

Kaspar Burger

Keyword(s):

Gene Expression ◽

Rna Polymerase Ii ◽

Ribosome Biogenesis ◽

Intergenic Spacer ◽

Cellular Growth ◽

Rrna Synthesis ◽

Protein Coding ◽

Non Coding Rna ◽

And Function ◽

In Cis

Gene expression is an essential process for cellular growth, proliferation, and differentiation. The transcription of protein-coding genes and non-coding loci depends on RNA polymerases. Interestingly, numerous loci encode long non-coding (lnc)RNA transcripts that are transcribed by RNA polymerase II (RNAPII) and fine-tune the RNA metabolism. The nucleolus is a prime example of how different lncRNA species concomitantly regulate gene expression by facilitating the production and processing of ribosomal (r)RNA for ribosome biogenesis. Here, we summarise the current findings on how RNAPII influences nucleolar structure and function. We describe how RNAPII-dependent lncRNA can both promote nucleolar integrity and inhibit ribosomal (r)RNA synthesis by modulating the availability of rRNA synthesis factors in trans. Surprisingly, some lncRNA transcripts can directly originate from nucleolar loci and function in cis. The nucleolar intergenic spacer (IGS), for example, encodes nucleolar transcripts that counteract spurious rRNA synthesis in unperturbed cells. In response to DNA damage, RNAPII-dependent lncRNA originates directly at broken ribosomal (r)DNA loci and is processed into small ncRNA, possibly to modulate DNA repair. Thus, lncRNA-mediated regulation of nucleolar biology occurs by several modes of action and is more direct than anticipated, pointing to an intimate crosstalk of RNA metabolic events.

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miR-16-5p Promotes Erythroid Maturation of Erythroleukemia Cells by Regulating Ribosome Biogenesis

Pharmaceuticals ◽

10.3390/ph14020137 ◽

2021 ◽

Vol 14 (2) ◽

pp. 137

Author(s):

Christos I. Papagiannopoulos ◽

Nikoleta F. Theodoroula ◽

Ioannis S. Vizirianakis

Keyword(s):

Ribosomal Proteins ◽

Ribosome Biogenesis ◽

Cultured Cells ◽

Erythroid Differentiation ◽

Underlying Mechanism ◽

Loss Of Function ◽

Functional Studies ◽

Differentiated Cells ◽

Erythroleukemia Cells ◽

Murine Erythroleukemia

miRNAs constitute a class of non-coding RNA that act as powerful epigenetic regulators in animal and plant cells. In order to identify putative tumor-suppressor miRNAs we profiled the expression of various miRNAs during differentiation of erythroleukemia cells. RNA was purified before and after differentiation induction and subjected to quantitative RT-PCR. The majority of the miRNAs tested were found upregulated in differentiated cells with miR-16-5p showing the most significant increase. Functional studies using gain- and loss-of-function constructs proposed that miR-16-5p has a role in promoting the erythroid differentiation program of murine erythroleukemia (MEL) cells. In order to identify the underlying mechanism of action, we utilized bioinformatic in-silico platforms that incorporate predictions for the genes targeted by miR-16-5p. Interestingly, ribosome constituents, as well as ribosome biogenesis factors, were overrepresented among the miR-16-5p predicted gene targets. Accordingly, biochemical experiments showed that, indeed, miR-16-5p could modulate the levels of independent ribosomal proteins, and the overall ribosomal levels in cultured cells. In conclusion, miR-16-5p is identified as a differentiation-promoting agent in erythroleukemia cells, demonstrating antiproliferative activity, likely as a result of its ability to target the ribosomal machinery and restore any imbalanced activity imposed by the malignancy and the blockade of differentiation.

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