Neutralizing Gatad2a-Chd4-Mbd3 Axis within the NuRD Complex Facilitates Deterministic Induction of Naïve Pluripotency

AbstractThe Nucleosome Remodeling and Deacytelase (NuRD) complex is a co-repressive complex involved in many pathological and physiological processes in the cell. Previous studies have identified one of its components, Mbd3, as a potent inhibitor for reprogramming of somatic cells to pluripotency. Following OSKM induction, early and partial depletion of Mbd3 protein followed by applying naïve ground-state pluripotency conditions, results in a highly efficient and near-deterministic generation of mouse iPS cells. Increasing evidence indicates that the NuRD complex assumes multiple mutually exclusive protein complexes, and it remains unclear whether the deterministic iPSC phenotype is the result of a specific NuRD sub complex. Since complete ablation of Mbd3 blocks somatic cell proliferation, here we aimed to identify alternative ways to block Mbd3-dependent NuRD activity by identifying additional functionally relevant components of the Mbd3/NuRD complex during early stages of reprogramming. We identified Gatad2a (also known as P66α), a relatively uncharacterized NuRD-specific subunit, whose complete deletion does not impact somatic cell proliferation, yet specifically disrupts Mbd3/NuRD repressive activity on the pluripotency circuit during both stem cell differentiation and reprogramming to pluripotency. Complete ablation of Gatad2a in somatic cells, but not Gatad2b, results in a deterministic naïve iPSC reprogramming where up to 100% of donor somatic cells successfully complete the process within 8 days. Genetic and biochemical analysis established a distinct sub-complex within the NuRD complex (Gatad2a-Chd4-Mbd3) as the functional and biochemical axis blocking reestablishment of murine naïve pluripotency. Disassembly of this axis by depletion of Gatad2a, results in resistance to conditions promoting exit of naïve pluripotency and delays differentiation. We further highlight context- and posttranslational dependent modifications of the NuRD complex affecting its interactions and assembly in different cell states. Collectively, our work unveils the distinct functionality, composition and interactions of Gatad2a-Chd4-Mbd3/NuRD subcomplex during the resolution and establishment of mouse naïve pluripotency.

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The Tale of CHD4 in DNA Damage Response and Chemotherapeutic Response

Cancer Research and Cellular Therapeutics ◽

10.31579/2640-1053/052 ◽

2019 ◽

Vol 3 (1) ◽

pp. 01-03

Author(s):

Shiaw-Yih Lin ◽

Jing Zhang ◽

David J.H. Shih

Keyword(s):

Dna Damage ◽

Cancer Progression ◽

Tumor Biology ◽

Stem Cell Differentiation ◽

Chemotherapeutic Agents ◽

Nurd Complex ◽

Independent Manner ◽

Nucleosome Remodeling ◽

Damage Repair ◽

Chemotherapeutic Response

The chromatin remodeling factor chromodomain helicase DNA-binding protein 4 (CHD4) is a core component of the nucleosome remodeling and deacetylase (NuRD) complex. Due to its important role in DNA damage repair, CHD4 has been identified as a key determinant in cancer progression, stem cell differentiation, and T cell and B cell development. Accumulating evidence has revealed that CHD4 can function in NuRD dependent and independent manner in response to DNA damage. Mutations of CHD4 have been shown to diminish its functions, which indicates that interpretation of its mutations may provide tangible benefit for patients. The expression of CHD4 play a dual role in sensitizing cancer cells to chemotherapeutic agents, which provides new insights into the contribution of CHD4 to tumor biology and new therapeutic avenues.

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daughterlesscoordinates somatic cell proliferation, differentiation and germline cyst survival during follicle formation inDrosophila

Development ◽

10.1242/dev.129.13.3255 ◽

2002 ◽

Vol 129 (13) ◽

pp. 3255-3267 ◽

Cited By ~ 4

Author(s):

John E. Smith ◽

Craig A. Cummings ◽

Claire Cronmiller

Keyword(s):

Cell Proliferation ◽

Somatic Cell ◽

Genetic Interaction ◽

Somatic Cells ◽

Loss Of Function ◽

Convergence And Extension ◽

Germline Cyst ◽

Abundance And Diversity ◽

Stem Cell Populations ◽

Genetic Regulator

During Drosophila oogenesis two distinct stem cell populations produce either germline cysts or the somatic cells that surround each cyst and separate each formed follicle. From analyzing daughterless (da) loss-of-function, overexpression and genetic interaction phenotypes, we have identified several specific requirements for da+ in somatic cells during follicle formation. First, da is a critical regulator of somatic cell proliferation. Also, da is required for the complete differentiation of polar and stalk cells, and elevated da levels can even drive the convergence and extension that is characteristic of interfollicular stalks. Finally, da is a genetic regulator of an early checkpoint for germline cyst progression: Loss of da function inhibits normally occurring apoptosis of germline cysts at the region 2a/2b boundary of the germarium, while da overexpression leads to postmitotic cyst degradation. Collectively, these da functions govern the abundance and diversity of somatic cells as they coordinate with germline cysts to form functional follicles.

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Mapping of Protein-Protein Interactions: Web-Based Resources for Revealing Interactomes

Current Medicinal Chemistry ◽

10.2174/0929867325666180214113704 ◽

2019 ◽

Vol 26 (21) ◽

pp. 3890-3910 ◽

Cited By ~ 6

Author(s):

Branislava Gemovic ◽

Neven Sumonja ◽

Radoslav Davidovic ◽

Vladimir Perovic ◽

Nevena Veljkovic

Keyword(s):

Drug Discovery ◽

Protein Interactions ◽

Protein Complexes ◽

Experimental Studies ◽

Protein Protein Interactions ◽

Web Based ◽

Prediction Tools ◽

Physiological Processes ◽

Modern Drug ◽

Ppi Prediction

Background: The significant number of protein-protein interactions (PPIs) discovered by harnessing concomitant advances in the fields of sequencing, crystallography, spectrometry and two-hybrid screening suggests astonishing prospects for remodelling drug discovery. The PPI space which includes up to 650 000 entities is a remarkable reservoir of potential therapeutic targets for every human disease. In order to allow modern drug discovery programs to leverage this, we should be able to discern complete PPI maps associated with a specific disorder and corresponding normal physiology. Objective: Here, we will review community available computational programs for predicting PPIs and web-based resources for storing experimentally annotated interactions. Methods: We compared the capacities of prediction tools: iLoops, Struck2Net, HOMCOS, COTH, PrePPI, InterPreTS and PRISM to predict recently discovered protein interactions. Results: We described sequence-based and structure-based PPI prediction tools and addressed their peculiarities. Additionally, since the usefulness of prediction algorithms critically depends on the quality and quantity of the experimental data they are built on; we extensively discussed community resources for protein interactions. We focused on the active and recently updated primary and secondary PPI databases, repositories specialized to the subject or species, as well as databases that include both experimental and predicted PPIs. Conclusion: PPI complexes are the basis of important physiological processes and therefore, possible targets for cell-penetrating ligands. Reliable computational PPI predictions can speed up new target discoveries through prioritization of therapeutically relevant protein–protein complexes for experimental studies.

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DPP3/CDK1 contributes to the progression of colorectal cancer through regulating cell proliferation, cell apoptosis, and cell migration

Cell Death and Disease ◽

10.1038/s41419-021-03796-4 ◽

2021 ◽

Vol 12 (6) ◽

Author(s):

Yixin Tong ◽

Yuan Huang ◽

Yuchao Zhang ◽

Xiangtai Zeng ◽

Mei Yan ◽

...

Keyword(s):

Colorectal Cancer ◽

Cell Proliferation ◽

Cell Migration ◽

Cell Apoptosis ◽

Downstream Target ◽

Normal Tissues ◽

Physiological Processes ◽

Mutual Regulation

AbstractAt present, colorectal cancer (CRC) has become a serious threat to human health in the world. Dipeptidyl peptidase 3 (DPP3) is a zinc-dependent hydrolase that may be involved in several physiological processes. However, whether DPP3 affects the development and progression of CRC remains a mystery. This study is the first to demonstrate the role of DPP3 in CRC. Firstly, the results of immunohistochemistry analysis showed the upregulation of DPP3 in CRC tissues compared with normal tissues, which is statistically analyzed to be positively correlated with lymphatic metastasis, pathological stage, positive number of lymph nodes. Moreover, the high expression of DPP3 predicts poor prognosis in CRC patients. In addition, the results of cell dysfunction experiments clarified that the downregulation of DPP3 significantly inhibited cell proliferation, colony formation, cell migration, and promoted apoptosis in vitro. DPP3 depletion could induce cell apoptosis by upregulating the expression of BID, BIM, Caspase3, Caspase8, HSP60, p21, p27, p53, and SMAC. In addition, downregulation of DPP3 can reduce tumorigenicity of CRC cells in vivo. Furthermore, CDK1 is determined to be a downstream target of DPP3-mediated regulation of CRC by RNA-seq, qPCR, and WB. The interaction between DPP3 and CDK1 shows mutual regulation. Specifically, downregulation of DPP3 can accentuate the effects of CDK1 knockdown on the function of CRC cells. Overexpression of CDK1 alleviates the inhibitory effects of DPP3 knockdown in CRC cells. In summary, DPP3 has oncogene-like functions in the development and progression of CRC by targeting CDK1, which may be an effective molecular target for the prognosis and treatment of CRC.

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Müllerian Inhibiting Substance Is Required for Germ Cell Proliferation during Early Gonadal Differentiation in Medaka (Oryzias latipes)

Endocrinology ◽

10.1210/en.2007-1535 ◽

2007 ◽

Vol 149 (4) ◽

pp. 1813-1819 ◽

Cited By ~ 47

Author(s):

Eri Shiraishi ◽

Norifumi Yoshinaga ◽

Takeshi Miura ◽

Hayato Yokoi ◽

Yuko Wakamatsu ◽

...

Keyword(s):

Cell Proliferation ◽

Germ Cell ◽

Germ Cells ◽

Sex Differentiation ◽

Somatic Cells ◽

Oryzias Latipes ◽

Cell Number ◽

Gonadal Differentiation ◽

Loss Of Function ◽

Germ Cell Proliferation

Müllerian inhibiting substance (MIS) is a glycoprotein belonging to the TGF-β superfamily. In mammals, MIS is responsible for the regression of Müllerian ducts in the male fetus. However, the role of MIS in gonadal sex differentiation of teleost fish, which have no Müllerian ducts, has yet to be clarified. In the present study, we examined the expression pattern of mis and mis type 2 receptor (misr2) mRNAs and the function of MIS signaling in early gonadal differentiation in medaka (teleost, Oryzias latipes). In situ hybridization showed that both mis and misr2 mRNAs were expressed in the somatic cells surrounding the germ cells of both sexes during early sex differentiation. Loss-of-function of either MIS or MIS type II receptor (MISRII) in medaka resulted in suppression of germ cell proliferation during sex differentiation. These results were supported by cell proliferation assay using 5-bromo-2′-deoxyuridine labeling analysis. Treatment of tissue fragments containing germ cells with recombinant eel MIS significantly induced germ cell proliferation in both sexes compared with the untreated control. On the other hand, culture of tissue fragments from the MIS- or MISRII-defective embryos inhibited proliferation of germ cells in both sexes. Moreover, treatment with recombinant eel MIS in the MIS-defective embryos dose-dependently increased germ cell number in both sexes, whereas in the MISRII-defective embryos, it did not permit proliferation of germ cells. These results suggest that in medaka, MIS indirectly stimulates germ cell proliferation through MISRII, expressed in the somatic cells immediately after they reach the gonadal primordium.

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ZBTB2 protein is a new partner of the Nucleosome Remodeling and Deacetylase (NuRD) complex

International Journal of Biological Macromolecules ◽

10.1016/j.ijbiomac.2020.12.029 ◽

2021 ◽

Vol 168 ◽

pp. 67-76

Author(s):

Rosita Russo ◽

Veronica Russo ◽

Francesco Cecere ◽

Mariangela Valletta ◽

Maria Teresa Gentile ◽

...

Keyword(s):

Nurd Complex ◽

Nucleosome Remodeling

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Effect of somatic cell count on dairy products: a review

Asian Journal of Medical and Biological Research ◽

10.3329/ajmbr.v3i1.32030 ◽

2017 ◽

Vol 3 (1) ◽

pp. 1-9 ◽

Cited By ~ 2

Author(s):

Mukta Talukder ◽

HM Manir Ahmed

Keyword(s):

Somatic Cell ◽

Cell Count ◽

Somatic Cell Count ◽

Proteolytic Enzymes ◽

Somatic Cells ◽

Raw Milk ◽

Microbial Count ◽

Endogenous Enzymes ◽

Fluid Milk

Somatic cells are the most essential factors naturally present in milk, and somatic cell count (SCC) is used as an indicator of monitoring mastitis incidence in the herd and also to assess the quality of milk. In addition, SCC is frequently used to determine quality payments to dairy producers. The SCC is directly related to get maximum milk production from individual cow and a lower SCC indicates better animal health, as somatic cells originate only from inside the animal's udder. SCC monitoring is important because as the number of somatic cells increases, milk yield is likely to fall, primarily due to the damage to milk-producing tissue in the udder caused by mastitis pathogens and the toxins they produce, particularly when epithelial cells are lost. Keeping low SSC will allow good quality more raw milk and provide a better product to milk processors whether used as fluid milk or converted to milk based products. Somatic cells containing lipolytic and proteolytic enzymes lead to degrade major nutrients fats and proteins, respectively. Elevated SCC is related to udder inflammation, which leads to alter the normal microbial count and physicochemical parameters of milk, as well as the quality of heat treated fluid milk and milk based product. The objective of this review is to discuss on the SSC and endogenous enzymes released from somatic cells in raw milk as well as effect of somatic cells count and their endogenous enzymes in processed milk and milk based products.Asian J. Med. Biol. Res. March 2017, 3(1): 1-9

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A RUNX3 enhancer polymorphism associated with ankylosing spondylitis influences recruitment of Interferon Regulatory Factor 5 and factors of the Nucleosome Remodelling Deacetylase Complex in CD8+ T-cells

10.1101/832840 ◽

2019 ◽

Author(s):

Matteo Vecellio ◽

Adrian Cortes ◽

Sarah Bonham ◽

Carlo Selmi ◽

Julian C Knight ◽

...

Keyword(s):

T Cells ◽

Ankylosing Spondylitis ◽

Cd8 T Cells ◽

Binding Protein ◽

Interferon Regulatory Factor ◽

Regulatory Factor ◽

Nurd Complex ◽

Nucleosome Remodeling ◽

Nuclear Extracts ◽

Functional Consequences

ABSTRACTObjectivesTo investigate the functional consequences of the single nucleotide polymorphism rs4648889 in a putative enhancer upstream of the RUNX3 promoter strongly associated with ankylosing spondylitis (AS).MethodsThe effects of rs4648889 on transcription factor (TF) binding were tested by DNA pull-down and quantitative mass spectrometry. The results were validated by electrophoretic mobility gel shift assays (EMSA), Western blot (WB) analysis of the pulled-down eluates, and chromatin immuno-precipitation (ChIP)-qPCR.ResultsSeveral TFs showed differential allelic binding to a 50bp DNA probe spanning rs4648889. Binding was increased to the AS-risk A allele for IKZF3 (aiolos) in nuclear extracts from CD8+ T-cells (3.7-fold, p<0.03) and several components of the NUcleosome Remodeling Deacetylase (NuRD) complex, including Chromodomain-Helicase-DNA-binding protein 4 (3.6-fold, p<0.05) and Retinoblastoma-Binding Protein 4 (4.1-fold, p<0.02). In contrast, binding of interferon regulatory factor (IRF) 5 was increased to the AS-protective G allele. These results were confirmed by EMSA, WB and ChIP-qPCR.ConclusionsThe association of AS with rs4648889 most likely results from its influence on the binding of this enhancer-like region to TFs, including IRF5, IKZF3 and members of the NuRD complex. Further investigation of these factors and RUNX3-related pathways may reveal important new therapeutic possibilities in AS.

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Intrinsically disordered proteins identified in the aggregate proteome serve as biomarkers of neurodegeneration

Metabolic Brain Disease ◽

10.1007/s11011-021-00791-8 ◽

2021 ◽

Author(s):

Srinivas Ayyadevara ◽

Akshatha Ganne ◽

Meenakshisundaram Balasubramaniam ◽

Robert J. Shmookler Reis

Keyword(s):

Intrinsically Disordered Proteins ◽

Protein Complexes ◽

Disordered Proteins ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Physiological Processes ◽

Protein Partners ◽

And Function ◽

Computational Analyses ◽

Disordered Regions

AbstractA protein’s structure is determined by its amino acid sequence and post-translational modifications, and provides the basis for its physiological functions. Across all organisms, roughly a third of the proteome comprises proteins that contain highly unstructured or intrinsically disordered regions. Proteins comprising or containing extensive unstructured regions are referred to as intrinsically disordered proteins (IDPs). IDPs are believed to participate in complex physiological processes through refolding of IDP regions, dependent on their binding to a diverse array of potential protein partners. They thus play critical roles in the assembly and function of protein complexes. Recent advances in experimental and computational analyses predicted multiple interacting partners for the disordered regions of proteins, implying critical roles in signal transduction and regulation of biological processes. Numerous disordered proteins are sequestered into aggregates in neurodegenerative diseases such as Alzheimer’s disease (AD) where they are enriched even in serum, making them good candidates for serum biomarkers to enable early detection of AD.

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CHD4 and the NuRD complex directly control cardiac sarcomere formation

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1722219115 ◽

2018 ◽

Vol 115 (26) ◽

pp. 6727-6732 ◽

Cited By ~ 11

Author(s):

Caralynn M. Wilczewski ◽

Austin J. Hepperla ◽

Takashi Shimbo ◽

Lauren Wasson ◽

Zachary L. Robbe ◽

...

Keyword(s):

Smooth Muscle ◽

Transcriptional Control ◽

Cardiac Development ◽

Nurd Complex ◽

Catalytic Core ◽

Nucleosome Remodeling ◽

Cardiac Sarcomere ◽

Developing Heart ◽

Genome Wide ◽

Formation Function

Cardiac development relies on proper cardiomyocyte differentiation, including expression and assembly of cell-type-specific actomyosin subunits into a functional cardiac sarcomere. Control of this process involves not only promoting expression of cardiac sarcomere subunits but also repressing expression of noncardiac myofibril paralogs. This level of transcriptional control requires broadly expressed multiprotein machines that modify and remodel the chromatin landscape to restrict transcription machinery access. Prominent among these is the nucleosome remodeling and deacetylase (NuRD) complex, which includes the catalytic core subunit CHD4. Here, we demonstrate that direct CHD4-mediated repression of skeletal and smooth muscle myofibril isoforms is required for normal cardiac sarcomere formation, function, and embryonic survival early in gestation. Through transcriptomic and genome-wide analyses of CHD4 localization, we identified unique CHD4 binding sites in smooth muscle myosin heavy chain, fast skeletal α-actin, and the fast skeletal troponin complex genes. We further demonstrate that in the absence of CHD4, cardiomyocytes in the developing heart form a hybrid muscle cell that contains cardiac, skeletal, and smooth muscle myofibril components. These misexpressed paralogs intercalate into the nascent cardiac sarcomere to disrupt sarcomere formation and cause impaired cardiac function in utero. These results demonstrate the genomic and physiological requirements for CHD4 in mammalian cardiac development.

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