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Gene Expression Patterns: GEP

Ankita Saha, Sarika Tiwari, Subramanian Dharmarajan, Deborah C Otteson, Teri L Belecky-Adams
BACKGROUND: The acetylation state of histones has been used as an indicator of the developmental state of progenitor and differentiating cells. The goal of this study was to determine the nuclear localization patterns of Class I histone deacetylases (HDACs) in retinal progenitor cells (RPCs) and retinal ganglion cells (RGCs), as the first step in understanding their potential importance in cell fate determination within the murine retina. RESULTS: The only HDAC to label RPC nuclei at E16 and P5 was HDAC1...
September 1, 2018: Gene Expression Patterns: GEP
Lauren A Laboissonniere, Courtney L Smith, Jacquelyn Mesenbrink, Rebecca Chowdhury, Abbie Burney, Margaret Lang, Matthew Sierra, Amy Stark, Gabriel Maldonado-Casalduc, Madison Muller, Jeffrey M Trimarchi
Amyotrophic lateral sclerosis (ALS) is characterized by progressive muscle atrophy resulting from the deterioration of motor neurons in the central nervous system (CNS). Recent genome-wide association studies have revealed several genes linked to ALS, further demonstrating the complexity of the disease. The zebrafish (Danio rerio) is an attractive model organism to study the function of the rapidly expanding number of ALS-associated genes, in part, due to the development of genome editing techniques that have facilitated specific gene targeting...
August 27, 2018: Gene Expression Patterns: GEP
Atsuo Kawahara, Hitoshi Morita, Kanoko Yanagi, Tomoe Ishizaka, Kiyohito Taimatsu, Rie Ohga
Mammalian SLURP1 and SLURP2 belong to the Ly-6/uPAR superfamily and are involved in maintaining the physiological integrity of keratinocytes. However, the developmental expression and functions of other Ly-6/uPAR family genes in vertebrates are still obscure. We have isolated novel Ly-6/uPAR family genes slurp-like1 (ly2.3/ly97.3) and slurp-like2 (ly2.2/ly97.2) in zebrafish. Both the Slurp-like1 and Slurp-like2 proteins contain the typical signal sequence and carboxy-terminal CCXXXXCN (X: an arbitrary amino acid) consensus sequence of the Ly-6/uPAR family but lack a transmembrane domain and a GPI-anchoring signal sequence, suggesting that both proteins may function as secretory proteins...
August 24, 2018: Gene Expression Patterns: GEP
Tehani El Faitwri, Katrin Huber
Delta-like 1 homolog (DLK1) is a member of the epidermal growth factor (EGF)-like family and an atypical notch ligand that is widely expressed during early mammalian development with putative functions in the regulation of cell differentiation and proliferation. During later stages of development, DLK1 is downregulated and becomes increasingly restricted to specific cell types, including several types of endocrine cells. DLK1 has been linked to various tumors and associated with tumor stem cell features. Sympathoadrenal precursors are neural crest derived cells that give rise to either sympathetic neurons of the autonomic nervous system or the endocrine chromaffin cells located in the adrenal medulla or extraadrenal positions...
August 23, 2018: Gene Expression Patterns: GEP
Shruti Kumar, Tamara A Franz-Odendaal
Fibroblast Growth Factors (FGFs) play several important roles during organ morphogenesis and act as multi-functional growth factors that bind to their membrane bound receptors (FGFRs) and activate further downstream signalling pathways. Several studies have investigated the function and expression of FGF/FGFRs in endochondral bone development, however, we know little about their role in the development of neural crest derived intramembranous bones. Here, we investigate the expression of 'b' and c' isoforms of FGFRs 1-3 during the development of the scleral ossicles, a ring of neural crest derived intramembranous bones in the chicken eye...
August 22, 2018: Gene Expression Patterns: GEP
Atsuo Kawahara, Hitoshi Morita, Kanoko Yanagi, Hiroaki Suzuki, Takaaki Mori, Rie Ohga, Kiyohito Taimatsu
The cocaine- and amphetamine-regulated transcript (CART) genes are involved in the neural regulation of energy homeostasis; however, their developmental expressions and functions are not fully understood in vertebrates. We have identified a novel zebrafish cart-like gene that encodes a protein of 105 amino acids possessing sequence similarity to zebrafish and mammalian CART proteins. RT-PCR analysis revealed that the cart-like transcripts were maternally supplied and gradually decreased during the cleavage, blastula and gastrula stages; then, transcripts subsequently reaccumulated at the segmentation, pharyngula and hatching stages...
August 17, 2018: Gene Expression Patterns: GEP
M Bonano, E Martín, M M Moreno Ruiz Holgado, G M Silenzi Usandivaras, G Ruiz De Bigliardo, M J Aybar
WDR68, also known as DCAF7, is a WD40 repeated domain protein highly conserved in eukaryotic organisms in both plants and animals. This protein participates in numerous cellular processes and exerts its function through interaction with other proteins. In the present work, we isolated, sequenced and characterized cDNA corresponding to the wdr68 gene in embryos of the amphibian Xenopus laevis. Syntenic analysis revealed high conservation of the genomic region containing the WDR68 locus in amniotes. Nevertheless, in fishes and amphibians, we observed that the tandem genes surrounding wdr68 undergoes certain rearrangements with respect to the organization found in amniotes...
August 17, 2018: Gene Expression Patterns: GEP
Jie Gong, Linlin Chai, Guangmin Xu, You Ni, Dong Liu
There are three isoforms of natriuretic peptide (NP) specific cell surface receptor: NP receptor-A (NPRA), receptor-B (NPRB), and receptor-C (NPRC). They are also known as NPR1, NPR2 and NPR3, respectively. NPs and their receptors were revealed to involve in diverse cellular and physiological processes including renal, cardiovascular, neuronal, and immunological aspects. However, the systematic analysis of the expression of these receptors in non-mammalian vertebrates is thus far lacking. In this study, two versions of the npr1 gene (npr1a and npr1b) in zebrafish was identified...
September 2018: Gene Expression Patterns: GEP
Ping Song, Brian D Perkins
Members of the Arf-like (Arl) family of small GTP-binding proteins regulate a number of cellular functions and play important roles in cilia structure and signaling. The small GTPase Arl13a is a close paralog to Arl13b, a small GTPase required for normal cilia formation that causes Joubert Syndrome when mutated. As mutation of arl13b causes a slow retinal degeneration in zebrafish (Song et al., 2016), we hypothesized that expression of arl13a may provide functional redundancy. We determined the expression domains of arl13a and arl13b during zebrafish development and examined subcellular localization by expression of fluorescence fusion proteins...
September 2018: Gene Expression Patterns: GEP
Ines Desanlis, Hannah L Felstead, Dylan R Edwards, Grant N Wheeler
Extracellular matrix (ECM) remodeling by metalloproteinases is crucial during development. The ADAMTS (A Disintegrin and Metalloproteinase with Thrombospondin type I motifs) enzymes are secreted, multi-domain matrix-associated zinc metalloendopeptidases that have diverse roles in tissue morphogenesis and patho-physiological remodeling. The human family includes 19 members. In this study we identified the 19 members of the ADAMTS family in Xenopus laevis and Xenopus tropicalis. Gene identification and a phylogenetic study revealed strong conservation of the ADAMTS family and contributed to a better annotation of the Xenopus genomes...
September 2018: Gene Expression Patterns: GEP
Özge Çelik, Aybüke Ekşioğlu, Enes Yağız Akdaş
The main aim of the study is to identify the genes differentially, predominantly or specifically expressed in salt tolerant tobacco mutants, improved from Akhisar 97 and İzmir Özbaş varieties via mutation breeding, with respect to unstressed control plants. Seven tobacco mutants which have different salt tolerance capacities were evaluated by Gene Fishing analysis. Under stress conditions differentially expressed 100 reproducible bands were identified (74 of up-regulated and 20 of down-regulated while 6 were unknown)...
September 2018: Gene Expression Patterns: GEP
Shuoqi Feng, Su Wang, Yashuo Wang, Qingyun Yang, Dejing Wang, Hongyan Li
Proteomic study has determined age-related changes in synthesis of carbonic anhydrase 2, myosin regulatory light chain 2 and selenium-binding protein 1 in muscle of post-menopausal women. However, little information is available regarding the expression and role of these proteins in early development and life span. In this study we showed that zebrafish ca2, myl2a, myl2b and selenbp1 were highly identical to their mammalian counterparts in primary and tertiary structures as well as genomic organization and syntenic map...
September 2018: Gene Expression Patterns: GEP
Brian S Grewe, Janet E Richmond, David E Featherstone
The Drosophila gene c12.2 was isolated in a screen examining mRNA binding proteins. Drosophila c12.2 is the mouse Vwa8 homolog. Various genome-wide associated studies have linked human Vwa8 to both neurological and oncological pathologies, which include autism, bipolar disorder, comorbid migraine, and acute myeloid leukemia, however, the function and role of the VWA8 protein remain poorly understood. To further analyze the Vwa8 gene in mouse, gene structure, protein homology modeling, and gene expression patterns were examined throughout mouse development...
September 2018: Gene Expression Patterns: GEP
Zimei Dong, Yibo Yang, Guangwen Chen, Dezeng Liu
The runt family genes play important roles in physiological processes in eukaryotic organisms by regulation of protein transcription, such as hematopoietic system, proliferation of gastric epithelial cells and neural development. However, it remains unclear about the specific functions of these genes. In this study, the full-length cDNA sequences of two runt genes are first cloned from Dugesia japonica, and their roles are investigated by WISH and RNAi. The results show that: (1) the Djrunts are conserved during evolution; (2) the Djrunts mRNA are widely expressed in intact and regenerative worms, and their expression levels are up-regulated significantly on day 1 after amputation; (3) loss of Djrunts function lead to lysis or regeneration failure in the intact and regenerating worms...
September 2018: Gene Expression Patterns: GEP
Ryotaro Tsutsumi, Taro Chaya, Takahisa Furukawa
Cilia are essential for sensory and motile functions across species. In humans, ciliary dysfunction causes "ciliopathies", which show severe developmental abnormalities in various tissues. Several missense mutations in intestinal cell kinase (ICK) gene lead to endocrine-cerebro-osteodysplasia syndrome or short rib-polydactyly syndrome, lethal recessive developmental ciliopathies. We and others previously reported that Ick-deficient mice exhibit neonatal lethality with developmental defects. Mechanistically, Ick regulates intraflagellar transport and cilia length at ciliary tips...
September 2018: Gene Expression Patterns: GEP
Joanna K Ledwon, Sergey Y Turin, Arun K Gosain, Jolanta M Topczewska
Fibroblast growth factor (FGF) signaling is essential for many developmental processes and plays a pivotal role in skeletal homeostasis, regeneration and wound healing. FGF signals through one of five tyrosine kinase receptors: Fgfr1a, -1b, -2, -3, -4. To characterize the expression of zebrafish fgfr3 from the larval stage to adulthood, we used RNAscope in situ hybridization on paraffin sections of the zebrafish head. Our study revealed spatial and temporal distribution of fgfr3 transcript in chondrocytes of the head cartilages, osteoblasts involved in bone formation, ventricular zone of the brain, undifferentiated mesenchymal cells of the skin, and lens epithelium of the eye...
September 2018: Gene Expression Patterns: GEP
Wei Wei, Jeremy Lotto, Pamela A Hoodless
The Hippo signaling pathway regulates many cellular processes, but has been specifically associated with control organ size and tumor growth. Yes-associated protein 1 (YAP1) is a transcriptional cofactor, in the Hippo pathway, that regulates gene expression when localized in the nucleus. Elevated expression of YAP1 in adult mouse liver leads to hepatomegaly and can cause hepatocellular carcinoma; while the loss of function studies reveal its importance in regulating cholangiocyte development. Here, we report the expression of YAP1 in mouse embryonic and postnatal hepatic cells, using AFP-GFP transgenic mice to identify the hepatocyte lineage...
September 2018: Gene Expression Patterns: GEP
Rasoul Godini, Haider Yabr Lafta, Hossein Fallahi
Epigenetic modifications are involved in global reprogramming of the cell transcriptome. Therefore, synchronized major shifts in the expression of many genes could be achieved through epigenetic changes. The regulation of gene expression could be implemented by different epigenetic events including histone modifications, DNA methylation and chromatin remodelling. Interestingly, it has been documented that reprogramming of somatic cells to induced pluripotent stem (iPS) cells is also a typical example of epigenetic modifications...
September 2018: Gene Expression Patterns: GEP
Sabrina Kragness, Mark A A Harrison, Joby J Westmoreland, Adam Burstain, Laurie R Earls
22q11.2 deletion syndrome (22q11.2DS) carries increased risk for both physical and psychiatric symptoms, including a high risk for schizophrenia. Understanding the genetic elements within the deletion region therefore has the potential to unlock the mysteries of both diseases. While most of the protein-coding genes in this region have been characterized, novel elements, such as non-coding RNAs and small Open Reading Frames (sORFs) remain unstudied. We have identified a novel, highly-conserved mouse sORF in a region of the mouse genome that is orthologous to a portion of the 22q11...
June 2018: Gene Expression Patterns: GEP
Maria Emilia Isolani, Renata Batistoni, Chiara Ippolito, Anna Maria Bianucci, Silvia Marracci, Leonardo Rossi
Planarian flatworms possess extraordinary regenerative capability and body plasticity, which rely on a composite population of stem cells, the neoblasts. Despite impressive advances have been recently achieved in the knowledge of neoblast biology, few is still known about factors that are released by differentiated tissues and influence the neoblast fate. Extracellular matrix (ECM) is a fundamental component of the stem cell niche and its remodeling affects stem cell fate. Here we provide the characterization of the astacin gene family of metalloproteinases in planarians, good candidate enzymes for generating dynamicity in the ECM...
June 2018: Gene Expression Patterns: GEP
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