scholarly journals Functions of Heterogeneous Nuclear Ribonucleoproteins in Stem Cell Potency and Differentiation

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Qishan Chen ◽  
Min Jin ◽  
Jianhua Zhu ◽  
Qingzhong Xiao ◽  
Li Zhang
Keyword(s):  
Gene Expression ◽  
Stem Cell ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Cell Cycle Control ◽  
Nucleic Acid Metabolism ◽  
Specific Gene ◽  
Self Renewal ◽  
Regulatory Pathways ◽  
Heterogeneous Nuclear Ribonucleoproteins

Stem cells possess huge importance in developmental biology, disease modelling, cell replacement therapy, and tissue engineering in regenerative medicine because they have the remarkable potential for self-renewal and to differentiate into almost all the cell types in the human body. Elucidation of molecular mechanisms regulating stem cell potency and differentiation is essential and critical for extensive application. Heterogeneous nuclear ribonucleoproteins (hnRNPs) are modular proteins consisting of RNA-binding motifs and auxiliary domains characterized by extensive and divergent functions in nucleic acid metabolism. Multiple roles of hnRNPs in transcriptional and posttranscriptional regulation enable them to be effective gene expression regulators. More recent findings show that hnRNP proteins are crucial factors implicated in maintenance of stem cell self-renewal and pluripotency and cell differentiation. The hnRNPs interact with certain sequences in target gene promoter regions to initiate transcription. In addition, they recognize 3′UTR or 5′UTR of specific gene mRNA forming mRNP complex to regulate mRNA stability and translation. Both of these regulatory pathways lead to modulation of gene expression that is associated with stem cell proliferation, cell cycle control, pluripotency, and committed differentiation.

scholarly journals Enforcing Post-Transcriptional Circuitries to Achieve Human Hematopoietic Stem Cell Expansion

Blood ◽  
2017 ◽  
Vol 130 (Suppl_1) ◽  
pp. SCI-46-SCI-46
Author(s):  
Kristin Hope
Keyword(s):  
Stem Cell ◽  
Hematopoietic Stem Cell ◽  
Transcriptional Control ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Conflicts Of Interest ◽  
Ex Vivo ◽  
Self Renewal ◽  
Control Of Gene Expression ◽  
Hematopoietic Stem

Abstract The balance between hematopoietic stem cell (HSC) differentiation and self-renewal is central to clinical regenerative paradigms. Unravelling the precise molecular mechanisms that govern HSC fate choices will thus have far reaching consequences for the development of effective therapies for hematopoietic and immunological disorders. There is an emerging recognition that beyond transcription, HSC homeostasis is subject to post-transcriptional control by RNA-binding proteins (RBPs) that ensure precise control of gene expression by modulating mRNA splicing, polyadenylation, localization, degradation or translation. RBPs can synchronously regulate the fates of operationally similar RNAs, in what have been termed RNA regulons. We have used a variety of functional approaches, in combination with unbiased genome- and proteome-scale, methods to define the tenets that govern this regulation and to determine key downstream circuitries of stem cell-regulating RBPs whose targeting could provide the basis for novel regenerative treatments. Through loss-of-function efforts, we have identified the RBP, MSI2, as a required factor for human HSC maintenance. By contrast, at supraphysiological levels, MSI2 has a profound positive effect on human HSC self-renewal decisions. Using a combination of global profiling, including mapping MSI2's targets through cross-linking immunoprecipitation (CLIP)-seq, we show that MSI2 achieves its ex vivo self-renewal-promoting effects by directing a co-ordinated post-transcriptional repression of key targets within the aryl hydrocarbon receptor (AHR) pathway. We are currently exploring the "rules" by which MSI2 influences its downstream effects on target RNAs and how it functions, in combination with other protein interactors, to instill a putative RBP regulatory code in HSCs. HSCs exhibit highly unique epigenomes, transcriptomes and proteomes and it is this distinctive molecular landscape that provides the canvas upon which MSI2, and indeed any other HSC-specific RBP exert their post-transcriptional influence over stem cell function. As such, to decipher the bona fide RNA networks that RBPs function upon in HSCs and to understand how they influence this network to enforce self-renewal, we are working towards performing systematic studies of RBP regulons in these cells specifically. In turn these approaches are elucidating a host of RBPs and post-transcriptional control mechanisms previously unappreciated for their role in HSC control. When modulated appropriately, we can successfully tailor these post-transcriptional regulons to enforce desired HSC outputs ex vivo. In summary, approaches to elucidate key HSC-regulatory RBPs and their protein and RNA interactomes provide valuable insights into a layer of HSC control previously not well understood, and one that can be capitalized on to achieve successful HSC expansion. Disclosures No relevant conflicts of interest to declare.

scholarly journals Ecdysone signaling promotes expression of multifunctional RNA binding proteins essential for ovarian germline stem cell self-renewal in Drosophila

2018 ◽  
Author(s):  
Danielle S. Finger ◽  
Vivian V. Holt ◽  
Elizabeth T. Ables
Keyword(s):  
Stem Cell ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Bmp Signaling ◽  
Germline Stem Cell ◽  
Self Renewal ◽  
Bmp Receptors ◽  
Morphogenetic Protein ◽  
Ecdysone Signaling

ABSTRACTSteroid hormones promote stem cell self-renewal in many tissues; however, the molecular mechanisms by which hormone signaling is integrated with niche-derived signals are largely uncharacterized. In the Drosophila ovary, the steroid hormone ecdysone promotes germline stem cell (GSC) self-renewal. Despite strong evidence that ecdysone modulates the reception of bone morphogenetic protein (BMP) signals in GSCs, transcriptional targets of ecdysone signaling that facilitate BMP reception are unknown. Here, we report that ecdysone signaling promotes the expression of the heterogeneous nuclear ribonucleoproteins (hnRNPs) squid, hephaestus, Hrb27C, and Hrb87F in GSCs. These hnRNPs functionally interact with ecdysone signaling to control GSC number and are cell autonomously required in GSCs for their maintenance. We demonstrate that hnRNPs promote GSC self-renewal by binding to transcripts essential for proper BMP signaling, including the BMP receptors thickveins and punt. Our findings support the model that stem cells coordinate local and long-range signals at the transcriptional and post-transcriptional levels to maintain self-renewal in response to physiological demand.GRAPHICAL ABSTRACTEcdysone signaling regulates distinct hnRNPs that bind to BMP signaling targets to control GSC self-renewal.SUMMARY STATEMENTEcdysone signaling promotes expression of heterogeneous ribonucleoproteins that modulate BMP-dependent germline stem cell self-renewal in the Drosophila ovary.

scholarly journals The Splicing Factor RBM17 Supports Leukemia Stem Cell Self-Renewal

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1238-1238
Author(s):  
Lina Liu ◽  
Ana Vujovic ◽  
Joshua Xu ◽  
Kristin Hope ◽  
Yu Lu
Keyword(s):  
Stem Cell ◽  
Alternative Splicing ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Conflicts Of Interest ◽  
Splicing Factor ◽  
Binding Motif ◽  
Aberrant Splicing ◽  
Self Renewal ◽  
Hematopoietic Stem

Background: Acute myeloid leukemia (AML) is thought to be sustained by sub-populations of leukemia stem cells (LSCs), which possess the capacity for self-renewal and differentiation and are believed to be responsible for disease initiation, relapse and chemoresistance. There is therefore an urgent need to develop therapies that target the LSC population to achieve effective AML treatment. To date there has been limited success in this endeavor, highlighting the importance of gaining a more comprehensive understanding of the mechanistic elements that underpin LSC function. Aberrant alternative splicing is recognized as a key driver of cancer. In the context of AML, genome-wide sequencing studies have shown that approximately one third of genes are differentially spliced in primitive CD34+ cells in AML patients compared to those obtained from normal controls. In particular, LSCs also have a unique splicing profile when compared to normal aging HSCs, underscoring the importance of understanding the mechanistic controls of aberrant splicing in LSC function. Results: Previous studies examining the link between aberrant splicing and AML focused on spliceosome genes with somatic mutations in AML patients. To examine mechanisms that mediate aberrant alternative splicing in LSC beyond splicing factor mutations, we performed a data-mining survey of 203 known mRNA splicing factors. Strikingly, RNA-binding motif protein 17 (RBM17) is the only splicing factor that is both strongly linked to poor AML prognosis and significantly elevated in LSC-enriched subsets of primary AML samples based on a recent study of 78 AML samples with normal karyotype. RBM17 has been implicated in regulating alternative splicing and cancer chemotherapy resistance. However, its function in AML or LSCs is not known. From our studies, we found that the level of RBM17 protein is elevated in the phenotypically primitive subsets of primary AML samples (n=8, RBM17+%: 67.42% in CD34+ versus 34.66% in CD34-fractions). Depletion of RBM17 with shRNAs in 3 human primary AML samples resulted in reduced colony formation compared to shScramble controls. More importantly, knockdown of RBM17 in a primary AML sample greatly impeded AML engraftment in immune-deficient mice (mean of 0.89 control versus mean of 0.1671 and 0.3171 shRNAs), suggesting that RBM17 is required for the stem and progenitor potential of AML and maintenance of LSC populations. Intriguingly, in contrast to the situation for the malignant hierarchy, the level of RBM17 in normal HSCs is lower than that in more committed cell populations in the normal hematopoietic system. To determine if RBM17 plays different roles in malignant LSC and normal hematopoietic stem and progenitor cells (HSPCs), we depleted RBM17 with shRNAs in human cord blood (CB) derived CD34+ HSPCs, and found RBM17 knockdown had negligible adverse impact on both CB total colony and primitive GEMM colony outputs and yielded no increase in apoptosis, indicating no defects were apparent to primitive cells of CB as read out in vitro. To uncover the molecular mechanisms underlying the role of RBM17 in LSC functions, we preformed RBM17 eCLIP-seq in the K562 and HL60 human leukemic cell lines. We then cross-analyzed the CLIP-seq datasets with a published ENCODE RNA-seq dataset (RBM17 knockdown in K562 cells), where we found RBM17 directly binds to transcripts of stem cell program-related genes and regulates the splicing of these genes, including MADD (MAP kinase activating death domain) and MRPS18C (mitochondrial ribosomal protein S18C). We further demonstrated that the splicing patterns of MADD and MRPS18C are mediated by RBM17 in primary AML samples. In our ongoing functional validation experiments, isoform-specific knockdown of MADD or MRPS18C splice variants downstream of RBM17 impeded colony forming capacity and induced myeloid differentiation in the MOLM13 AML cell line. These results suggest that RBM17-mediated splicing events impact primitive cell function in AML. Conclusion: We have identified RBM17 as a novel LSC-regulating factor, plays an important role in maintaining AML LSC function through regulating the alternative splicing of stem cell program-related genes. The potential LSC-selective role for RBM17, along with its downstream splicing events, represent promising putative therapeutic targets whose modulation could offer attractive therapeutic windows in AML treatment. Disclosures No relevant conflicts of interest to declare.

scholarly journals Compendium of Methods to Uncover RNA-Protein Interactions In Vivo

2021 ◽  
Vol 4 (1) ◽  
pp. 22
Author(s):  
Mrinmoyee Majumder ◽  
Viswanathan Palanisamy
Keyword(s):  
Gene Expression ◽  
Protein Interactions ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Expression Patterns ◽  
Control Of Gene Expression ◽  
Regulatory Pathways ◽  
Advantages And Disadvantages ◽  
Protein Nucleic Acid

Control of gene expression is critical in shaping the pro-and eukaryotic organisms’ genotype and phenotype. The gene expression regulatory pathways solely rely on protein–protein and protein–nucleic acid interactions, which determine the fate of the nucleic acids. RNA–protein interactions play a significant role in co- and post-transcriptional regulation to control gene expression. RNA-binding proteins (RBPs) are a diverse group of macromolecules that bind to RNA and play an essential role in RNA biology by regulating pre-mRNA processing, maturation, nuclear transport, stability, and translation. Hence, the studies aimed at investigating RNA–protein interactions are essential to advance our knowledge in gene expression patterns associated with health and disease. Here we discuss the long-established and current technologies that are widely used to study RNA–protein interactions in vivo. We also present the advantages and disadvantages of each method discussed in the review.

scholarly journals Inter-species functional compatibility of the Theobroma cacao and Arabidopsis FT orthologs: 90 million years of functional conservation of meristem identity genes

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
S. F. Prewitt ◽  
A. Shalit-Kaneh ◽  
S. N. Maximova ◽  
M. J. Guiltinan
Keyword(s):  
Gene Expression ◽  
Tissue Culture ◽  
Gene Family ◽  
Flowering Time ◽  
Molecular Mechanisms ◽  
Regulatory Pathways ◽  
Late Flowering ◽  
Precocious Flowering ◽  
Transition To Flowering

Abstract Background In angiosperms the transition to flowering is controlled by a complex set of interacting networks integrating a range of developmental, physiological, and environmental factors optimizing transition time for maximal reproductive efficiency. The molecular mechanisms comprising these networks have been partially characterized and include both transcriptional and post-transcriptional regulatory pathways. Florigen, encoded by FLOWERING LOCUS T (FT) orthologs, is a conserved central integrator of several flowering time regulatory pathways. To characterize the molecular mechanisms involved in controlling cacao flowering time, we have characterized a cacao candidate florigen gene, TcFLOWERING LOCUS T (TcFT). Understanding how this conserved flowering time regulator affects cacao plant’s transition to flowering could lead to strategies to accelerate cacao breeding. Results BLAST searches of cacao genome reference assemblies identified seven candidate members of the CENTRORADIALIS/TERMINAL FLOWER1/SELF PRUNING gene family including a single florigen candidate. cDNA encoding the predicted cacao florigen was cloned and functionally tested by transgenic genetic complementation in the Arabidopsis ft-10 mutant. Transgenic expression of the candidate TcFT cDNA in late flowering Arabidopsis ft-10 partially rescues the mutant to wild-type flowering time. Gene expression studies reveal that TcFT is spatially and temporally expressed in a manner similar to that found in Arabidopsis, specifically, TcFT mRNA is shown to be both developmentally and diurnally regulated in leaves and is most abundant in floral tissues. Finally, to test interspecies compatibility of florigens, we transformed cacao tissues with AtFT resulting in the remarkable formation of flowers in tissue culture. The morphology of these in vitro flowers is normal, and they produce pollen that germinates in vitro with high rates. Conclusion We have identified the cacao CETS gene family, central to developmental regulation in angiosperms. The role of the cacao’s single FT-like gene (TcFT) as a general regulator of determinate growth in cacao was demonstrated by functional complementation of Arabidopsis ft-10 late-flowering mutant and through gene expression analysis. In addition, overexpression of AtFT in cacao resulted in precocious flowering in cacao tissue culture demonstrating the highly conserved function of FT and the mechanisms controlling flowering in cacao.

scholarly journals RNA–Binding Protein HuD as a Versatile Factor in Neuronal and Non–Neuronal Systems

Biology ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 361
Author(s):  
Myeongwoo Jung ◽  
Eun-Kyung Lee
Keyword(s):  
Gene Expression ◽  
Neural Plasticity ◽  
Molecular Mechanisms ◽  
Neuronal Development ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Novel Treatments ◽  
Target Mrnas ◽  
Neuronal Systems

HuD (also known as ELAVL4) is an RNA–binding protein belonging to the human antigen (Hu) family that regulates stability, translation, splicing, and adenylation of target mRNAs. Unlike ubiquitously distributed HuR, HuD is only expressed in certain types of tissues, mainly in neuronal systems. Numerous studies have shown that HuD plays essential roles in neuronal development, differentiation, neurogenesis, dendritic maturation, neural plasticity, and synaptic transmission by regulating the metabolism of target mRNAs. However, growing evidence suggests that HuD also functions as a pivotal regulator of gene expression in non–neuronal systems and its malfunction is implicated in disease pathogenesis. Comprehensive knowledge of HuD expression, abundance, molecular targets, and regulatory mechanisms will broaden our understanding of its role as a versatile regulator of gene expression, thus enabling novel treatments for diseases with aberrant HuD expression. This review focuses on recent advances investigating the emerging role of HuD, its molecular mechanisms of target gene regulation, and its disease relevance in both neuronal and non–neuronal systems.

Serial analysis of gene expression (SAGE) during porcine embryo development

2004 ◽  
Vol 16 (2) ◽  
pp. 87 ◽  
Author(s):  
Le Ann Blomberg ◽  
Kurt A. Zuelke
Keyword(s):  
Gene Expression ◽  
Functional Genomics ◽  
Embryo Development ◽  
Molecular Mechanisms ◽  
Physiological Role ◽  
Transgenic Animals ◽  
Specific Gene ◽  
Research Strategies

Functional genomics provides a powerful means for delving into the molecular mechanisms involved in pre-implantation development of porcine embryos. High rates of embryonic mortality (30%), following either natural mating or artificial insemination, emphasise the need to improve the efficiency of reproduction in the pig. The poor success rate of live offspring from in vitro-manipulated pig embryos also hampers efforts to generate transgenic animals for biotechnology applications. Previous analysis of differential gene expression has demonstrated stage-specific gene expression for in vivo-derived embryos and altered gene expression for in vitro-derived embryos. However, the methods used to date examine relatively few genes simultaneously and, thus, provide an incomplete glimpse of the physiological role of these genes during embryogenesis. The present review will focus on two aspects of applying functional genomics research strategies for analysing the expression of genes during elongation of pig embryos between gestational day (D) 11 and D12. First, we compare and contrast current methodologies that are being used for gene discovery and expression analysis during pig embryo development. Second, we establish a paradigm for applying serial analysis of gene expression as a functional genomics tool to obtain preliminary information essential for discovering the physiological mechanisms by which distinct embryonic phenotypes are derived.

scholarly journals The Role of Translation Initiation Regulation in Haematopoiesis

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Godfrey Grech ◽  
Marieke von Lindern
Keyword(s):  
Gene Expression ◽  
Translation Initiation ◽  
Translational Control ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Regulation Of Gene Expression ◽  
Mrna Translation ◽  
Translation Control ◽  
Haematological Disorders

Organisation of RNAs into functional subgroups that are translated in response to extrinsic and intrinsic factors underlines a relatively unexplored gene expression modulation that drives cell fate in the same manner as regulation of the transcriptome by transcription factors. Recent studies on the molecular mechanisms of inflammatory responses and haematological disorders indicate clearly that the regulation of mRNA translation at the level of translation initiation, mRNA stability, and protein isoform synthesis is implicated in the tight regulation of gene expression. This paper outlines how these posttranscriptional control mechanisms, including control at the level of translation initiation factors and the role of RNA binding proteins, affect hematopoiesis. The clinical relevance of these mechanisms in haematological disorders indicates clearly the potential therapeutic implications and the need of molecular tools that allow measurement at the level of translational control. Although the importance of miRNAs in translation control is well recognised and studied extensively, this paper will exclude detailed account of this level of control.

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