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https://www.readbyqxmd.com/read/28436429/human-fetal-heart-specific-coexpression-network-involves-congenital-heart-disease-defect-candidate-genes
#1
Bo Wang, Guoling You, Qihua Fu
Heart development is a complex process requiring dynamic transcriptional regulation. Disturbance of this process will lead to severe developmental defects such as congenital heart disease/defect (CHD). CHD is a group of complex disorder with high genetic heterogeneity, common pathways associated with CHD remains largely unknown. In the manuscript, we focused on the tissue specific genes in human fetal heart samples to explore such pathways. We used the RNA microarray dataset of human fetal tissues from ENCODE project to identify genes with heart tissue specific expression...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28434038/emerging-potential-of-gene-silencing-approaches-targeting-anti-chondrogenic-factors-for-cell-based-cartilage-repair
#2
REVIEW
Andrea Lolli, Letizia Penolazzi, Roberto Narcisi, Gerjo J V M van Osch, Roberta Piva
The field of cartilage repair has exponentially been growing over the past decade. Here, we discuss the possibility to achieve satisfactory regeneration of articular cartilage by means of human mesenchymal stem cells (hMSCs) depleted of anti-chondrogenic factors and implanted in the site of injury. Different types of molecules including transcription factors, transcriptional co-regulators, secreted proteins, and microRNAs have recently been identified as negative modulators of chondroprogenitor differentiation and chondrocyte function...
April 22, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28431938/selective-inhibition-of-ezh2-by-a-small-molecule-inhibitor-regulates-microglial-gene-expression-essential-for-inflammation
#3
Sarder Arifuzzaman, Amitabh Das, Sun Hwa Kim, Taeho Yoon, Young Seek Lee, Kyoung Hwa Jung, Young Gyu Chai
Multiple studies have documented that Enhancer of zeste homolog 2 (EZH2) could play a role in inflammation and a wide range of malignancies; however, the underlying mechanisms remain largely unaddressed. Microglial activation is a key process in the production and release of numerous pro-inflammatory mediators that play important roles in inflammation and neurodegeneration in the central nervous system (CNS). Therefore, our aim was to investigate whether inhibition of EZH2 with the selective small molecule inhibitor EPZ-6438 protects against neonatal microglial activation...
April 18, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28426184/alterations-in-mandibular-morphology-associated-with-glypican-1-and-glypican-3-gene-mutations
#4
M Mian, S Ranjitkar, G C Townsend, P J Anderson
OBJECTIVES: Glypican 1 (GPC1) and glypican 3 (GPC3) are bone co-regulators that act downstream in many of the signalling pathways associated with craniosynostosis. Morphometric data from GPC-knockout mice were analysed to determine whether elimination of GPC1 and GPC3 genes would alter mandibular morphology. SETTING AND SAMPLE POPULATION: The murine model included five male and five female mandibles in each of GPC1-knockout, GPC1/GPC3-knockout and wild-type (control) groups...
April 20, 2017: Orthodontics & Craniofacial Research
https://www.readbyqxmd.com/read/28425446/yap-modulates-tgf-%C3%AE-1-induced-simultaneous-apoptosis-and-emt-through-upregulation-of-the-egf-receptor
#5
Yi Liu, Kai He, Ying Hu, Xiaojie Guo, Dongmei Wang, Weiwei Shi, Jingsong Li, Jianguo Song
YAP is a transcriptional co-regulator that plays important roles in various patho-physiological processes, including the survival and death of cells. However, the effect of YAP on apoptosis and EMT, simultaneously mediated by TGF-β1, is not known. In this study, we demonstrate that YAP can modulate cell fate of apoptosis versus EMT by acting as a surviving factor. Overexpression of YAP in mouse mammary epithelial (NMuMG) cells suppressed TGF-β1-induced apoptosis, which shifted the cellular response predominantly toward EMT...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28423575/activated-notch-signaling-augments-cell-growth-in-hepatocellular-carcinoma-via-up-regulating-the-nuclear-receptor-nr4a2
#6
Bo Zhu, Lichun Sun, Wei Luo, Min Li, David H Coy, Long Yu, Wenbo Yu
Hepatocellular carcinoma (HCC) is one of the most malignant cancers. Conventional therapies are limited due to the human liver being such a unique organ and easily showing side-effects. The unclear molecular mechanisms are tough challenges for scientists searching for new and effective anti-HCC targeting drugs. We identified that the nuclear receptor NR4A2 is a novel oncogene in HCC progression. In this study, we show that NR4A2 and the notch recceptor Notch1 were expressed highly in primary HCC tissues and immortal HCC cells by using qPCR, western blot and immuno-histochemistry assays...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422127/differential-control-of-asexual-development-and-sterigmatocystin-biosynthesis-by-a-novel-regulator-in-aspergillus-nidulans
#7
Yong Jin Kim, Yu Yeong Man, Pil Jae Maeng
The filamentous fungus Aspergillus nidulans primarily reproduces by forming asexual spores called conidia and produces the mycotoxin sterigmatocystin (ST), the penultimate precursor of aflatoxins. It has been known that asexual development and ST production are tightly co-regulated by various regulatory inputs. Here, we report that the novel regulator AslA with a C2H2 domain oppositely regulates development and ST biosynthesis. Nullifying aslA resulted in defective conidiation and reduced expression of brlA encoding a key activator of asexual development, which indicates that AslA functions as an upstream activator of brlA expression...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28419380/%C3%AE-carboxysome-bioinformatics-identification-and-evolution-of-new-bacterial-microcompartment-protein-gene-classes-and-core-locus-constraints
#8
Manuel Sommer, Fei Cai, Matthew Melnicki, Cheryl A Kerfeld
Carboxysomes are bacterial microcompartments (BMCs) that enhance CO2 fixation in all cyanobacteria. Structurally, carboxysome shell proteins are classified according to the type of oligomer formed: hexameric (BMC-H), trimeric (BMC-T) and pentameric (BMC-P) proteins. To understand the forces driving the evolution of the carboxysome shell, we conducted a bioinformatic study of genes encoding β-carboxysome shell proteins, taking advantage of the recent large increase in sequenced cyanobacterial genomes. In addition to the four well-established BMC-H (CcmK1-4) classes, our analysis reveals two new CcmK classes, which we name CcmK5 and CcmK6...
April 17, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28419278/integrative-analysis-identifies-targetable-creb1-foxa1-transcriptional-co-regulation-as-a-predictor-of-prostate-cancer-recurrence
#9
Benjamin Sunkel, Dayong Wu, Zhong Chen, Chiou-Miin Wang, Xiangtao Liu, Zhenqing Ye, Aaron M Horning, Joseph Liu, Devalingam Mahalingam, Horacio Lopez-Nicora, Chun-Lin Lin, Paul J Goodfellow, Steven K Clinton, Victor X Jin, Chun-Liang Chen, Tim H-M Huang, Qianben Wang
No abstract text is available yet for this article.
April 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28418858/the-mir-124-p63-feedback-loop-modulates-colorectal-cancer-growth
#10
Kuijie Liu, Hongliang Yao, Sanlin Lei, Li Xiong, Haizhi Qi, Ke Qian, Jiqiang Liu, Peng Wang, Hua Zhao
Among the diverse co-regulatory relationships between transcription factors (TFs) and microRNAs (miRNAs), feedback loops have received the most extensive research attention. The co-regulation of TFs and miRNAs plays an important role in colorectal cancer (CRC) growth. Here, we show that miR-124 can regulate two isoforms of p63, TAp63 and ΔNp63, via iASPP, while p63 modulates signal transducers and activators of transcription 1 (STAT1) expression by targeting miR-155. Moreover, STAT1 acts as a regulator of CRC growth by targeting miR-124...
March 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28416578/quantitative-mass-spectrometry-analysis-of-pd-l1-protein-expression-n-glycosylation-and-expression-stoichiometry-with-pd-1-and-pd-l2-in-human-melanoma
#11
Carlos A Morales-Betanzos, Hyoungjoo Lee, Paula I Gonzalez-Ericsson, Justin M Balko, Douglas B Johnson, Lisa J Zimmerman, Daniel C Liebler
Quantitative assessment of key proteins that control the tumor-immune interface is one of the most formidable analytical challenges in immunotherapeutics. We developed a targeted mass spectrometry (MS) platform to quantify programmed cell death-1 (PD-1), programmed cell death 1 ligand 1 (PD-L1), and programmed cell death 1 ligand 2 (PD-L2) at fmol/microgram protein levels in formalin fixed, paraffin-embedded sections from 22 human melanomas. PD-L1 abundance ranged 50-fold, from approximately 0.03 to 1.5 fmol/microgram protein and the PRM data were largely concordant with total PD-L1-positive cell content, as analyzed by immunohistochemistry (IHC) with the E1L3N antibody...
April 17, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28412749/diagnostic-and-prognostic-relevance-of-cp2c-and-yy1-expression-in-hepatocellular-carcinoma
#12
Ji Sook Kim, Seung Han Son, Min Young Kim, DongHo Choi, Ik-Soon Jang, Seung Sam Paik, Ji Hyung Chae, Vladimir N Uversky, Chul Geun Kim
Recent studies have demonstrated an oncogenic role of the transcription factor (TF) CP2c in hepatocellular carcinoma (HCC) based on a strong correlation between CP2c expression, tumor grade, and aggressiveness. We recently found that CP2c directly interacts with another TF, YY1, which is also overexpressed in multiple cancers, including HCC. To evaluate if these proteins are co-regulated in carcinogenesis, we analyzed the expression of CP2c and YY1 in HCC (n = 136) tissues and examined the correlation between their expression and clinicopathological characteristics of HCC...
February 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/28408660/a-global-co-expression-network-approach-for-connecting-genes-to-specialized-metabolic-pathways-in-plants
#13
Jennifer H Wisecaver, Alexander T Borowsky, Vered Tzin, Georg Jander, Daniel J Kliebenstein, Antonis Rokas
Plants produce diverse specialized metabolites (SMs), but the genes responsible for their production and regulation remain largely unknown, hindering efforts to tap plant pharmacopeia. Given that genes comprising SM pathways exhibit environmentally dependent co-regulation, we hypothesized that genes within a SM pathway would form tight associations (modules) with each other in co-expression networks, facilitating their identification. To evaluate this hypothesis, we used 10 global co-expression datasets, each a meta-analysis of hundreds to thousands of experiments, across eight plant species to identify hundreds of co-expressed gene modules per dataset...
April 13, 2017: Plant Cell
https://www.readbyqxmd.com/read/28404662/slc25-family-member-genetic-interactions-identify-a-role-for-hem25-in-yeast-electron-transport-chain-stability
#14
J Noelia Dufay, J Pedro Fernández-Murray, Christopher R McMaster
The SLC25 family member SLC25A38 (Hem25 in yeast) was recently identified as a mitochondrial glycine transporter that provides substrate to initiate heme/hemoglobin synthesis. Mutations in the human SLC25A38 gene cause congenital sideroblastic anemia. The full extent to which SLC25 family members co-regulate heme synthesis with other mitochondrial functions is not clear. In this study, we surveyed 29 non-essential SLC25 family members in Saccharomyces cerevisiae for their ability to support growth in the presence and absence of HEM25...
April 12, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28401021/integrated-mrna-and-lncrna-expression-profiling-for-exploring-metastatic-biomarkers-of-human-intrahepatic-cholangiocarcinoma
#15
Lisheng Lv, Miaoyan Wei, Peiyi Lin, Zhisheng Chen, Peng Gong, Zhiwei Quan, Zhaohui Tang
Long noncoding RNAs (lncRNAs) is crucial for various human cancers, but the function and mechanism of lncRNAs is largely unknown in human intrahepatic cholangiocarcinoma (ICC), the second most common liver cancer. In this study, we performed transcriptomic profiling of ICC and normal tissues, and found 2148 lncRNAs and 474 mRNAs were significantly upregulated, whereas 568 lncRNAs and 409 mRNAs were downregulated in ICC tissues. Enrichment analysis suggests these differentially expressed genes mainly focus on response to stimulus, development, and cell proliferation...
2017: American Journal of Cancer Research
https://www.readbyqxmd.com/read/28400425/the-logic-of-transcriptional-regulator-recruitment-architecture-at-cis-regulatory-modules-controlling-liver-functions
#16
Julie Dubois-Chevalier, Vanessa Dubois, Hélène Dehondt, Parisa Mazrooei, Claire Mazuy, Aurélien A Sérandour, Céline Gheeraert, Guillaume Penderia, Eric Baugé, Bruno Derudas, Nathalie Hennuyer, Réjane Paumelle, Guillemette Marot, Jason S Carroll, Mathieu Lupien, Bart Staels, Philippe Lefebvre, Jérôme Eeckhoute
Control of gene transcription relies on concomitant regulation by multiple transcriptional regulators (TR). However, how recruitment of a myriad of TR is orchestrated at cis-regulatory modules (CRM) to account for co-regulation of specific biological pathways is only partially understood. Here, we have used mouse liver CRM involved in regulatory activities of the hepatic TR, NR1H4 (FXR; farnesoid X receptor), as our model system to tackle this question. Using integrative cistromic, epigenomic, transcriptomic and interactomic analyses, we reveal a logical organization where trans-regulatory modules (TRM), which consist of subsets of preferentially and co-ordinately co-recruited TR, assemble into hierarchical combinations at hepatic CRM...
April 11, 2017: Genome Research
https://www.readbyqxmd.com/read/28396297/the-co-regulators-src-1-and-smrt-are-involved-in-interleukin-6-induced-androgen-receptor-activation
#17
Qi Wang, Hui Wang, Qiang Ju, Zhen Ding, Xing Ge, Qiao-Mei Shi, Ji-Long Zhou, Xiao-Long Zhou, Jin-Peng Zhang, Mei-Rong Zhang, Hong-Min Yu, Li-Chun Xu
BACKGROUND: The androgen receptor (AR) can be stimulated by interleukin-6 (IL-6) in the absence of androgens to induce prostate cancer progression. The purpose of this study was to investigate whether the co-activator steroid receptor coactivator-1 (SRC-1) and co-repressor silencing mediator for retinoid and thyroid hormone receptors (SMRT) are involved in IL-6-induced AR activation. METHODS: The effects of IL-6 on LNCaP cell proliferation were monitored using real-time cell analysis (RTCA) iCELLigence system...
November 1, 2016: European Cytokine Network
https://www.readbyqxmd.com/read/28394946/the-integrative-omics-of-white-rot-fungus-pycnoporus-coccineus-reveals-co-regulated-cazymes-for-orchestrated-lignocellulose-breakdown
#18
Shingo Miyauchi, David Navarro, Sacha Grisel, Didier Chevret, Jean-Guy Berrin, Marie-Noelle Rosso
Innovative green technologies are of importance for converting plant wastes into renewable sources for materials, chemicals and energy. However, recycling agricultural and forestry wastes is a challenge. A solution may be found in the forest. Saprotrophic white-rot fungi are able to convert dead plants into consumable carbon sources. Specialized fungal enzymes can be utilized for breaking down hard plant biopolymers. Thus, understanding the enzymatic machineries of such fungi gives us hints for the efficient decomposition of plant materials...
2017: PloS One
https://www.readbyqxmd.com/read/28391641/promiscuity-in-post-transcriptional-control-of-gene-expression-drosophila-sex-lethal-and-its-regulatory-partnerships
#19
REVIEW
Rebecca Moschall, Monika Gaik, Jan Medenbach
The Drosophila RNA-binding protein Sex-lethal (Sxl) is a potent post-transcriptional regulator of gene expression that controls female development. It regulates the expression of key factors involved in sex-specific differences in morphology, behaviour, and dosage compensation. Functional Sxl protein is only expressed in female flies, where it binds to U-rich RNA motifs present in its target mRNAs to regulate their fate. Sxl is a very versatile regulator that, by shuttling between the nucleus and the cytoplasm, can regulate almost all aspects of post-transcriptional gene expression including RNA processing, nuclear export, and translation...
April 9, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28387997/genome-wide-functional-characterization-of-putative-peroxidases-in-the-head-blight-fungus-fusarium-graminearum
#20
Yoonji Lee, Hokyoung Son, Ji Young Shin, Gyung Ja Choi, Yin-Won Lee
Reactive oxygen species (ROS) are associated with various developmental processes and host-pathogen interactions in pathogenic fungi. Peroxidases are a group of ROS-detoxifying enzymes that are involved in the oxidative stress response and in a variety of physiological processes. In this study, we performed a genome-wide functional characterization of putative peroxidase genes in Fusarium graminearum, a head blight pathogen of cereal crops. We identified 31 putative peroxidase genes and generated deletion mutants for these genes...
April 7, 2017: Molecular Plant Pathology
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