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Tissue specific gene network

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https://www.readbyqxmd.com/read/29785401/rheumatoid-arthritis-and-mirnas-a-critical-review-through-a-functional-view
#1
REVIEW
Maria Cristina Moran-Moguel, Stefania Petarra-Del Rio, Evangelina E Mayorquin-Galvan, Maria G Zavala-Cerna
Rheumatoid arthritis (RA) is a systemic autoimmune disease with severe joint inflammation and destruction associated with an inflammatory environment. The etiology behind RA remains to be elucidated; most updated concepts include the participation of environmental, proteomic, epigenetic, and genetic factors. Epigenetic is considered the missing link to explain genetic diversification among RA patients. Within epigenetic factors participating in RA, miRNAs are defined as small noncoding molecules with a length of approximately 22 nucleotides, capable of gene expression modulation, either negatively through inhibition of translation and degradation of the mRNA or positively through increasing the translation rate...
2018: Journal of Immunology Research
https://www.readbyqxmd.com/read/29784930/comparative-mrna-and-mirna-expression-in-european-mouflon-ovis-musimon-and-sheep-ovis-aries-provides-novel-insights-into-the-genetic-mechanisms-for-female-reproductive-success
#2
Ji Yang, Xin Li, Yin-Hong Cao, Kisun Pokharel, Xiao-Ju Hu, Ze-Hui Chen, Song-Song Xu, Jaana Peippo, Mervi Honkatukia, Juha Kantanen, Meng-Hua Li
Prolific breeds of domestic sheep (Ovis aries) are important genetic resources due to their reproductive performance, which is characterized by multiple lambs per birth and out-of-season breeding. However, the lack of a comprehensive understanding of the genetic mechanisms underlying the important reproductive traits, particularly from the evolutionary genomics perspective, has impeded the efficient advancement of sheep breeding. Here, for the first time, by performing RNA-sequencing we built a de novo transcriptome assembly of ovarian and endometrial tissues in European mouflon (Ovis musimon) and performed an mRNA-miRNA integrated expression profiling analysis of the wild species and a highly prolific domestic sheep breed, the Finnsheep...
May 21, 2018: Heredity
https://www.readbyqxmd.com/read/29783715/location-location-location-signals-in-muscle-specification
#3
REVIEW
Chih-Ning Chang, Chrissa Kioussi
Muscles control body movement and locomotion, posture and body position and soft tissue support. Mesoderm derived cells gives rise to 700 unique muscles in humans as a result of well-orchestrated signaling and transcriptional networks in specific time and space. Although the anatomical structure of skeletal muscles is similar, their functions and locations are specialized. This is the result of specific signaling as the embryo grows and cells migrate to form different structures and organs. As cells progress to their next state, they suppress current sequence specific transcription factors (SSTF) and construct new networks to establish new myogenic features...
May 18, 2018: Journal of Developmental Biology
https://www.readbyqxmd.com/read/29776629/clinical-implication-of-micrornas-in-molecular-pathology-an-update-for-2018
#4
REVIEW
Seema Sethi, Sajiv Sethi, Martin H Bluth
MicroRNAs (miRNAs) are poised to provide diagnostic, prognostic, and therapeutic targets for several diseases including malignancies for precision medicine applications. The miRNAs have immense potential in the clinical arena because they can be detected in the blood, serum, tissues (fresh and formalin-fixed paraffin-embedded), and fine-needle aspirate specimens. The most attractive feature of miRNA-based therapy is that a single miRNA could be useful for targeting multiple genes that are deregulated in cancers, which can be further investigated through systems biology and network analysis that may provide cancer-specific personalized therapy...
June 2018: Clinics in Laboratory Medicine
https://www.readbyqxmd.com/read/29775757/molecular-characterization-of-physis-tissue-by-rna-sequencing
#5
Christopher R Paradise, Catalina Galeano-Garces, Daniela Galeano-Garces, Amel Dudakovic, Todd A Milbrandt, Daniel B F Saris, Aaron J Krych, Marcel Karperien, Gabriel B Ferguson, Denis Evseenko, Scott M Riester, Andre J van Wijnen, A Noelle Larson
The physis is a well-established and anatomically distinct cartilaginous structure that is crucial for normal long-bone development and growth. Abnormalities in physis function are linked to growth plate disorders and other pediatric musculoskeletal diseases. Understanding the molecular pathways operative in the physis may permit development of regenerative therapies to complement surgically-based procedures that are the current standard of care for growth plate disorders. Here, we performed next generation RNA sequencing on mRNA isolated from human physis and other skeletal tissues (e...
May 15, 2018: Gene
https://www.readbyqxmd.com/read/29771984/dna-methylation-of-hepatic-iron-sensing-genes-and-the-regulation-of-hepcidin-expression
#6
Paul A Sharp, Rachel Clarkson, Ahmed Hussain, Robert J Weeks, Ian M Morison
Production of the iron regulatory peptide hepcidin is tightly controlled by a network of proteins in hepatocytes that sense levels of iron in the circulation (as diferric-transferrin) and in tissues (in ferritin). Human studies show high variability in the normal range of serum hepcidin levels. We have postulated that this may, in part, be related to inter-individual variability in the expression of genes in the iron sensing pathway, potentially governed by epigenetic factors. Here, we have investigated whether genes encoding hepatic iron sensing proteins and hepcidin are regulated by DNA methylation...
2018: PloS One
https://www.readbyqxmd.com/read/29764841/genetic-targeting-of-organ-specific-blood-vessels
#7
Wenjuan Pu, Lingjuan He, Ximeng Han, Xueying Tian, Yan Li, Hui Zhang, Qiaozhen Liu, Xiuzhen Huang, Libo Zhang, Qing-Dong Wang, Zhenyang Yu, Xiao Yang, Nicola Smart, Bin Zhou
<u>Rationale:</u> Organs of the body require vascular networks to supply oxygen and nutrients and maintain physiological function. The blood vessels of different organs are structurally and functionally heterogeneous in nature. To more precisely dissect their distinct in vivo function in individual organs, without potential interference from off-site targets, it is necessary to genetically target them in an organ-specific manner. <u>Objective:</u> To generate a genetic system that targets vascular endothelial cells in an organ- or tissue- specific manner and to exemplify the potential application of intersectional genetics for precise, target-specific gene manipulation in vivo...
May 15, 2018: Circulation Research
https://www.readbyqxmd.com/read/29763523/role-of-basic-pentacysteiene-transcription-factors-in-a-sub-set-of-cytokinin-signaling-responses
#8
Carly M Shanks, Andreas Hecker, Chia-Yi Cheng, Luise Brand, Silvio Collani, Markus Schmid, G Eric Schaller, Dierk Wanke, Klaus Harter, Joseph J Kieber
Cytokinin plays diverse roles in plant growth and development, generally acting by modulating gene transcription in target tissues. The type-B ARR transcription factors have emerged as primary targets of cytokinin signaling and are required for essentially all cytokinin-mediated changes in gene expression. The diversity of cytokinin function is likely imparted by the activity of various transcription factors working with the type-B ARRs to alter specific sets of target genes. One potential set of co-regulators modulating the cytokinin response are the BARLEY B-RECOMBINANT/BASIC PENTACYSTEINE (BBR/BPC) family of plant-specific transcription factors...
May 15, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29762780/an-intersection-network-based-on-combining-snp-co-association-and-rna-co-expression-networks-for-feed-utilization-traits-in-japanese-black-cattle
#9
D Okada, S Endo, H Matsuda, S Ogawa, Y Taniguchi, T Katsuta, T Watanabe, H Iwaisaki
Genome-wide association studies (GWAS) of quantitative traits have detected numerous genetic associations, but they encounter difficulties in pinpointing prominent candidate genes and inferring gene networks. The present study used a systems genetics approach integrating GWAS results with external RNA-expression data to detect candidate gene networks in feed utilization and growth traits of Japanese Black cattle, which are matters of concern. A SNP co-association network was derived from significant correlations between SNPs with effects estimated by GWAS across seven phenotypic traits...
May 12, 2018: Journal of Animal Science
https://www.readbyqxmd.com/read/29759817/enhancer-logic-and-mechanics-in-development-and-disease
#10
REVIEW
Ryan Rickels, Ali Shilatifard
Enhancers are distally located genomic cis-regulatory elements that integrate spatiotemporal cues to coordinate gene expression in a tissue-specific manner during metazoan development. Enhancer function depends on a combination of bound transcription factors and cofactors that regulate local chromatin structure, as well as on the topological interactions that are necessary for their activity. Numerous genome-wide studies concur that the vast majority of disease-associated variations occur within non-coding genomic sequences, in other words the 'cis-regulome', and this underscores their relevance for human health...
May 11, 2018: Trends in Cell Biology
https://www.readbyqxmd.com/read/29754405/ghl1l1-affects-cell-fate-specification-by-regulating-ghpin1-mediated-auxin-distribution
#11
Jiao Xu, Xiyan Yang, Baoqi Li, Lin Chen, Ling Min, Xianlong Zhang
Auxin is as an efficient initiator and regulator of cell fate during somatic embryogenesis (SE), but the molecular mechanisms and regulating networks of this process are not well understood. In this report, we analysed SE process induced by Leafy cotyledon1-like 1 (GhL1L1), a NF-YB subfamily gene specifically expressed in embryonic tissues in cotton. We also identified the target gene of GhL1L1, and its role in auxin distribution and cell fate specification during embryonic development was analysed. Overexpression of GhL1L1 accelerated embryonic cell formation, associated with an increased concentration of IAA in embryogenic calluses (ECs) and in the shoot apical meristem (SAM), corresponding to altered expression of the auxin transport gene GhPIN1...
May 13, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29751546/genome-wide-identification-and-analysis-of-arabidopsis-sodium-proton-antiporter-nhx-and-human-sodium-proton-exchanger-nhe-homologs-in-sorghum-bicolor
#12
P Hima Kumari, S Anil Kumar, Katam Ramesh, Palakolanu Sudhakar Reddy, M Nagaraju, A Bhanu Prakash, Trushar Shah, Ashley Henderson, Rakesh K Srivastava, G Rajasheker, A Chitikineni, Rajeev K Varshney, P Rathnagiri, M Lakshmi Narasu, P B Kavi Kishor
Na⁺ transporters play an important role during salt stress and development. The present study is aimed at genome-wide identification, in silico analysis of sodium-proton antiporter (NHX) and sodium-proton exchanger (NHE)-type transporters in Sorghum bicolor and their expression patterns under varied abiotic stress conditions. In Sorghum , seven NHX and nine NHE homologs were identified. Amiloride (a known inhibitor of Na⁺/H⁺ exchanger activity) binding motif was noticed in both types of the transporters...
May 3, 2018: Genes
https://www.readbyqxmd.com/read/29746605/daily-variation-of-gene-expression-in-diverse-rat-tissues
#13
Panteleimon D Mavroudis, Debra C DuBois, Richard R Almon, William J Jusko
Circadian information is maintained in mammalian tissues by a cell-autonomous network of transcriptional feedback loops that have evolved to optimally regulate tissue-specific functions. An analysis of daily gene expression in different tissues, as well as an evaluation of inter-tissue circadian variability, is crucial for a systems-level understanding of this transcriptional circuitry. Affymetrix gene chip measurements of liver, muscle, adipose, and lung tissues were obtained from a rich time series light/dark experiment, involving 54 normal rats sacrificed at 18 time points within the 24-hr cycle...
2018: PloS One
https://www.readbyqxmd.com/read/29743718/expressional-analysis-of-disease-relevant-signalling-pathways-in-primary-tumours-and-metastasis-of-head-and-neck-cancers
#14
Dorothee Goesswein, Negusse Habtemichael, Aslihan Gerhold-Ay, Johanna Mazur, Désirée Wünsch, Shirley K Knauer, Julian Künzel, Christoph Matthias, Sebastian Strieth, Roland H Stauber
Head and neck squamous cell carcinoma (HNSCC) often metastasize to lymph nodes resulting in poor prognosis for patients. Unfortunately, the underlying molecular mechanisms contributing to tumour aggressiveness, recurrences, and metastasis are still not fully understood. However, such knowledge is key to identify biomarkers and drug targets to improve prognosis and treatments. Consequently, we performed genome-wide expression profiling of 15 primary HNSSCs compared to corresponding lymph node metastases and non-malignant tissue of the same patient...
May 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29741608/jak-inhibitor-improves-type-i-interferon-induced-damage-proof-of-concept-in-dermatomyositis
#15
Leandro Ladislau, Xavier Suárez-Calvet, Ségolène Toquet, Océane Landon-Cardinal, Damien Amelin, Marine Depp, Mathieu P Rodero, Denisa Hathazi, Darragh Duffy, Vincent Bondet, Corinna Preusse, Boris Bienvenu, Flore Rozenberg, Andreas Roos, Claudia F Benjamim, Eduard Gallardo, Isabel Illa, Vincent Mouly, Werner Stenzel, Gillian Butler-Browne, Olivier Benveniste, Yves Allenbach
Dermatomyositis is an acquired auto-immune disease characterized by skin lesions and muscle-specific pathological features such as perifascicular muscle fibre atrophy and vasculopathy. Dermatomyositis patients display an upregulation of type I interferon-inducible genes in muscle fibres, endothelial cells, skin and peripheral blood. However, the effect of type I interferon on muscle tissue has not yet been determined. Our aim was to study the pathogenicity of type I interferon in vitro and to evaluate the efficacy of the type I interferon pathway blockade for therapeutic purposes...
May 8, 2018: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/29737552/competing-endogenous-rna-network-crosstalk-reveals-novel-molecular-markers-in-colorectal-cancer
#16
Nehal Samir, Marwa Matboli, Hanaa El-Tayeb, Ahmed El-Tawdi, Mohmed K Hassan, Sherif El-Khamisy, Hesham A E El-Akkad, Mohamed G Ramadan, Tarek N Al-Belkini, Farid El-Asmar
The competing endogenous RNA networks play a pivotal role in cancer diagnosis and progression. Novel properstrategies for early detection of colorectal cancer (CRC) are strongly needed. We investigated a novel CRC-specific RNA-based integrated competing endogenous network composed of lethal3 malignant brain tumor like1 (L3MBTL1) gene, long non-coding intergenic RNA- (lncRNA RP11-909B2.1) and homo sapiens microRNA-595 (hsa-miRNA-595) using in silico data analysis. RT-qPCR-based validation of the network was achieved in serum of 70 patients with CRC, 40 patients with benign colorectal neoplasm, and 20 healthy controls...
May 8, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29737531/specific-expression-network-analysis-of-diabetic-nephropathy-kidney-tissue-revealed-key-methylated-sites
#17
Yan-Zhe Wang, Wen-Wei Xu, Ding-Yu Zhu, Nan Zhang, Yong-Lan Wang, Miao Ding, Xin-Miao Xie, Lin-Lin Sun, Xiao-Xia Wang
Diabetic nephropathy (DN) is one of the most common and serious complication in diabetes patients. However, the evidences of gene regulation mechanism and epigenetic modification with DN remain unclear. Therefore, it is necessary to search regulating genes for early diagnosis on DN. We identified tissue specific genes through mining the gene expression omnibus (GEO) public database, enriched function by gene ontology (GO), and kyoto encyclopedia of genes and genomes (KEGG) analysis, and further compared tissue-specific network...
May 8, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29736807/quantitative-detection-of-low-abundance-transcripts-at-single-cell-level-in-human-epidermal-keratinocytes-by-digital-droplet-reverse-transcription-polymerase-chain-reaction
#18
Frédéric Auvré, Julien Coutier, Michèle T Martin, Nicolas O Fortunel
Genetic and epigenetic characterization of the large cellular diversity observed within tissues is essential to understanding the molecular networks that ensure the regulation of homeostasis, repair, and regeneration, but also pathophysiological processes. Skin is composed of multiple cell lineages and is therefore fully concerned by this complexity. Even within one particular lineage, such as epidermal keratinocytes, different immaturity statuses or differentiation stages are represented, which are still incompletely characterized...
May 8, 2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29736721/a-quantitative-systems-pharmacology-approach-to-infer-pathways-involved-in-complex-disease-phenotypes
#19
Mark E Schurdak, Fen Pei, Timothy R Lezon, Diane Carlisle, Robert Friedlander, D Lansing Taylor, Andrew M Stern
Designing effective therapeutic strategies for complex diseases such as cancer and neurodegeneration that involve tissue context-specific interactions among multiple gene products presents a major challenge for precision medicine. Safe and selective pharmacological modulation of individual molecular entities associated with a disease often fails to provide efficacy in the clinic. Thus, development of optimized therapeutic strategies for individual patients with complex diseases requires a more comprehensive, systems-level understanding of disease progression...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29736258/mtf2-prc2-control-of-canonical-wnt-signaling-is-required-for-definitive-erythropoiesis
#20
Janet L Manias Rothberg, Harinad B Maganti, Hani Jrade, Christopher J Porter, Gareth A Palidwor, Christopher Cafariello, Hannah L Battaion, Safwat T Khan, Theodore J Perkins, Robert F Paulson, Caryn Y Ito, William L Stanford
Polycomb repressive complex 2 (PRC2) accessory proteins play substoichiometric, tissue-specific roles to recruit PRC2 to specific genomic loci or increase enzymatic activity, while PRC2 core proteins are required for complex stability and global levels of trimethylation of histone 3 at lysine 27 (H3K27me3). Here, we demonstrate a role for the classical PRC2 accessory protein Mtf2/Pcl2 in the hematopoietic system that is more akin to that of a core PRC2 protein. Mtf2 -/- erythroid progenitors demonstrate markedly decreased core PRC2 protein levels and a global loss of H3K27me3 at promoter-proximal regions...
2018: Cell Discovery
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