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Paul Sushmita S Biomedical Imaging and Bioinformatics Lab, and Machine Intelligence Unit, Indian Statistical Institute, Kolkata, 700 108, India. sushmita_t@isical.ac.in, - - 2014
The microRNAs or miRNAs are short, endogenous RNAs having ability to regulate mRNA expression at the post-transcriptional level. Various studies have revealed that miRNAs tend to cluster on chromosomes. The members of a cluster that are in close proximity on chromosomes are highly likely to be processed as co-transcribed units. ...
Nguyen Tung T - - 2014
The circadian clock is a critical regulator of biological functions controlling behavioral, physiological and biochemical processes. Because the liver is the primary regulator of metabolites within the mammalian body and the disruption of circadian rhythms in liver is associated with severe illness, circadian regulators would play a strong role in ...
Llobet-Navas David D Institute for Cancer Genetics, Department of Pathology, Columbia University, New York, New York 10032, - - 2014
The mammary gland is a very dynamic organ that undergoes continuous remodeling. The critical regulators of this process are not fully understood. Here we identify the microRNA cluster miR-424(322)/503 as an important regulator of epithelial involution after pregnancy. Through the generation of a knockout mouse model, we found that regression ...
Joshi Dipesh D Schizophrenia Research Institute, Liverpool St, Darlinghurst, NSW 2011, Australia; Neuroscience Research Australia, Barker St, Randwick, NSW 2031, Australia; School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, - - 2014
Neuregulin 1 and its receptor ErbB4 are confirmed risk genes for schizophrenia, but the neuropathological alterations in NRG1-ErbB4 in schizophrenia are unclear. The present investigations therefore focused on determining lamina specific (ErbB4-pan) and quantitative (pan, JMa, JMb, CYT1 and CYT2) ErbB4 mRNA changes in the dorsolateral prefrontal cortex (DLPFC) in ...
Shen Yanyue Y State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, - - 2014
Polyploidy has played an important role in promoting plant evolution through genomic merging and doubling. We used high-throughput sequencing to compare miRNA expression profiles between Brassica hexaploid and its parents. A total of 613, 784 and 742 known miRNAs were identified in Brassica rapa, Brassica carinata, and Brassica hexaploid, respectively. ...
Zhang Zhonghui Z 1 Section of Hematology/Oncology, Department of Medicine, and UIC Cancer Center, University of Illinois at Chicago. Chicago , IL, - - 2014
Abstract Small-molecule inhibitors and microRNAs (miRNAs) are two newly emerging classes of tools for optimizing induced pluripotent stem cell (iPSC) generation. We report here that sodium butyrate (NaB), a small-molecule inhibitor of histone deacetylases (HDACs), upregulates transcriptional levels of the miR-302/367 cluster by enhancing Oct4 transcriptional activity at the miR-302/367 ...
Goriaux Coline C Clermont Université Université d'Auvergne, Clermont-Ferrand, - - 2014
In Drosophila, the piRNA cluster, flamenco, produces most of the piRNAs (PIWI-interacting RNAs) that silence transposable elements in the somatic follicle cells during oogenesis. These piRNAs are thought to be processed from a long single-stranded precursor transcript. Here, we demonstrate that flamenco transcription is initiated from an RNA polymerase II ...
Kerr Kimberly S KS Department of Neurobiology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, Howard Hughes Medical Institute, Worcester, Massachusetts 01605, and National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, Massachusetts - - 2014
Glial cells are emerging as important regulators of synapse formation, maturation, and plasticity through the release of secreted signaling molecules. Here we use chromatin immunoprecipitation along with Drosophila genomic tiling arrays to define potential targets of the glial transcription factor Reversed polarity (Repo). Unexpectedly, we identified wingless (wg), a secreted ...
Laas Enora E Service de Gynécologie-Obstétrique, Hôpital Tenon, AP-HP, 4 rue de la Chine 75020 Paris, France; Institut Universitaire de Cancérologie, Université Pierre et Marie Curie, Paris 6, France. Electronic address: - - 2014
Differentiation between grade-1 endometrial cancer (EC) and atypical endometrial hyperplasia (AEH) is crucial to determine optimal surgical management. However, discrepancies exist between preoperative diagnosis of AEH and final histology. Our aim was to establish clusters of immunohistochemical markers to distinguish AEH from grade-1 EC. We studied 13 immunohistochemical markers (steroid ...
Geisberg Joseph V JV Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, - - 2014
We measured half-lives of 21,248 mRNA 3' isoforms in yeast by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process. Interestingly, half-lives of mRNA isoforms from the same gene, including nearly identical isoforms, often vary widely. Based on clusters of isoforms with ...
Chaulk Steven G SG Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada and Department of Oncology, University of Alberta, Edmonton, Alberta T6G 2H7, - - 2014
While functional mature microRNAs (miRNAs) are small ∼22 base oligonucleotides that target specific mRNAs, miRNAs are initially expressed as long transcripts (pri-miRNAs) that undergo sequential processing to yield the mature miRNAs. We have previously reported that the pri-miR-17∼92 cluster adopts a compact globular folded structure that internalizes a 3' core ...
Zatakia Hardik M HM Department of Biological Sciences, Virginia Tech, Life Sciences I, Blacksburg, VA - - 2014
Type IVb pili in enteropathogenic bacteria function as a host-colonization factor by mediating tight adherence to host cells, but their role in bacteria-plant symbiosis is currently unknown. The genome of the symbiotic soil bacterium Sinorhizobium meliloti contains two clusters encoding proteins for Type IVb pili of the Flp (fimbrial low-molecular-weight ...
Hoss Andrew G AG Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America ; Graduate Program in Genetics and Genomics, Boston University School of Medicine, Boston, Massachusetts, United States of - - 2014
Transcriptional dysregulation has long been recognized as central to the pathogenesis of Huntington's disease (HD). MicroRNAs (miRNAs) represent a major system of post-transcriptional regulation, by either preventing translational initiation or by targeting transcripts for storage or for degradation. Using next-generation miRNA sequencing in prefrontal cortex (Brodmann Area 9) of twelve ...
Agranat-Tamir Lily L Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel, Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel and Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, - - 2014
MicroRNAs (miRNAs) are central regulators of gene expression, and a large fraction of them are encoded in introns of RNA polymerase II transcripts. Thus, the biogenesis of intronic miRNAs by the microprocessor and the splicing of their host introns by the spliceosome require coordination between these processing events. This cross-talk ...
Velazquez-Fernandez David D D Velazquez-fernandez, DEPARTMENT OF MOLECULAR MEDICINE AND SURGERY, KAROLINSKA INSTITUTET, SWEDEN, - - 2014
The adrenocortical adenoma (ACA) entity includes aldosterone-producing (APA), cortisol-producing (CPA) and non-hyperfunctioning (NHFA) phenotypes. While gene mutations and mRNA expression profiles have been partly characterized, less is known about alterations involving microRNA (miRNA) expression. To characterize miRNA expression profile in relation to the subtypes of ACAs. miRNA expression profiles were ...
Boguslawska J J Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, Warsaw, - - 2014
microRNAs, short non-coding RNAs, influence key physiological processes, including hormonal regulation, by affecting the expression of genes. In this study we hypothesized that the expression of microRNAs targeting thyroid hormone pathway genes may be in turn regulated by thyroid hormone signalling. It is known that the expression of DIO1, a ...
Wang Minghua M Department of Biochemical and Molecular Biology, Medical College, Soochow University, Suzhou, Jiangsu, - - 2014
MicroRNAs (miRNAs) are a class of small non-coding RNAs generated from endogenous transcripts that form hairpin structures. The hairpin precursor is processed into two mature miRNAs that form major/minor duplexes. Mature miRNAs regulate gene expression by cleaving mRNA or repressing protein translation. Numerous miRNAs have been discovered via deep sequencing. ...
Guo Li L Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, - - 2014
MicroRNAs (miRNAs) are small, noncoding regulatory molecules. They are involved in many essential biological processes and act by suppressing gene expression. The present work reports an integrative analysis of miRNA-mRNA and miRNA-miRNA interactions and their regulatory patterns using high-throughput miRNA and mRNA datasets. Aberrantly expressed miRNA and mRNA profiles were ...
Li Xiao Ling - - 2013
The tumor suppressor p21 acts as a cell cycle inhibitor and has also been shown to regulate gene expression by functioning as a transcription co-repressor. Here, we identified p21-regulated microRNAs (miRNAs) by sequencing small RNAs from isogenic p21+/+ and p21-/- cells. Three abundant miRNA clusters, miR-200b-200a-429, miR-200c-141 and miR-183-96-182 were ...
Ramalingam Pradeep - - 2013
miRNAs are generally classified as "intergenic" or "intronic" based upon their genomic location. Intergenic miRNAs are known to be transcribed as independent transcription units, while intronic miRNAs are believed to be processed from the introns of their hosting transcription units and hence share common regulatory mechanisms and expression patterns with ...
Liu Chang-Zheng - - 2013
Methods The expression of myoD and miR-29 family was detected by using real-time PCR and Western blot analysis. The potential promoter and transcription factors binding sites of miR-29 clusters were predicted by Promoter scan and transcriptional factor search. The promoter sequence of miR-29b1-a and miR-29b2-c cluster was cloned into a ...
Garg Neha - - 2013
The transcription factor Nanog plays a critical role in the self-renewal of embryonic stem cells as well as in neural stem cells (NSCs). microRNAs (miRNAs) are also involved in stemness regulation. However, the miRNA network downstream of Nanog is still poorly understood. High-throughput screening of miRNA expression profiles in response ...
Kishikawa Takahiro - - 2013
Hepatocellular carcinoma (HCC) is a threat to public health worldwide. We previously identified the association of a single nucleotide polymorphism (SNP) at the promoter region of the MHC class I polypeptide-related sequence A (MICA) gene with the risk of hepatitis-virus-related HCC. Because this SNP affects MICA expression levels, regulating MICA ...
Xiao Jun - - 2013
The circadian clock enables organisms to adjust to daily environmental changes and synchronize multiple molecular, biochemical, physiological, and behavioral processes accordingly. In mammalian clock work, Bmal1 is the most important core clock gene, which works with another core clock gene Clock to drive the expression of other clock genes and ...
Yu Ai-Qing - - 2013
Dorsal as a crucial component of Toll signaling pathway, played important roles in induction and regulation of innate immune responses. In this study, we cloned a NF-κB-like transcription factor Dorsal from Eriocheir sinensis and designated it as EsDorsal. The full-length cDNA of EsDorsal was 2,493 bp with a 2,022-bp open ...
Wu Yan - - 2013
microRNAs (miRNAs) have been reported to play an essential role in the regulation of brown adipocyte adipogenesis. In the present study, we investigated the role of the miR-106b-93 cluster in the differentiation of brown adipocytes. We found that knockdown of miR-106b and miR-93 significantly induced the expression of brown fat-specific ...
Schreiner Alexandra E - - 2013
Astrocytes express two sodium-coupled transporters, GLAST and GLT-1, which are essential for the maintenance of low extracellular glutamate levels. Here, we performed a comparative analysis of the laminar and subcellular expression profile of GLAST and GLT-1 in the developing postnatal mouse hippocampus using immunohistochemistry and western blotting and employing high-resolution ...
Dubash Adi D AD Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, - - 2013
Although much is known about signaling factors downstream of Rho GTPases that contribute to epidermal differentiation, little is known about which upstream regulatory proteins (guanine nucleotide exchange factors [GEFs] or GTPase-activating proteins [GAPs]) are involved in coordinating Rho signaling in keratinocytes. Here we identify the GEF breakpoint cluster region (Bcr) ...
Thomas-Jinu Swapna - - 2013
Neurexophilin 1 (Nxph1) is a specific endoligand of α-neurexins that is essential for trans-synaptic activation. Here, we report its dynamic expression during development in zebrafish. Our study revealed an early onset of expression of nxph1. RT-PCR on a series of embryonic stages showed that it is maternally deposited, although only ...
Engelsvold David H DH Department of Ophthalmology, Stavanger University Hospital, Stavanger, Norway; Department of Clinical Medicine, Section of Ophthalmology, University of Bergen, Bergen, - - 2013
The current study investigates whether microRNA (miRNA) regulators of epithelial-mesenchymal transition (EMT), tissue fibrosis, and angiogenesis are differentially expressed in human primary pterygium. Genome-wide miRNA and mRNA expression profiling of paired pterygium and normal conjunctiva was performed in the context of conventional excision of pterygium with autotransplantation of conjunctiva (n = 8). ...
Schillig Rebecca - - 2013
The zinc cluster proteins are a family of transcription factors that are unique to the fungal kingdom. In the pathogenic yeast Candida albicans, zinc cluster transcription factors control the expression of virulence-associated traits and play key roles in the development of antifungal drug resistance. Gain-of-function mutations in several zinc cluster ...
Zhang Zengdi Z Department of Developmental Genetics, Nanjing Medical University, Nanjing, Jiangsu 210029, - - 2013
Medulloblastoma is the most common malignant pediatric brain tumor. Some are thought to originate from cerebellar granule neuron progenitors (CGNPs) that fail to undergo normal cell cycle exit and differentiation. The contribution of microRNAs to the initiation and progression of medulloblastoma remains poorly understood. Increased expression of the miR-183∼96∼182 cluster ...
Cisse Ibrahim I - - 2013
Transcription is reported to be spatially compartmentalized in nuclear transcription factories with clusters of RNA Polymerase II (Pol II). However, little is known about when these foci assemble or their relative stability. We developed a quantitative single-cell approach to characterize protein spatiotemporal organization, with single-molecule sensitivity in live eukaryotic cells. ...
Yin Chuan - - 2013
Hepatocyte nuclear factor-4α (HNF4α) is a dominant transcriptional regulator of hepatocyte differentiation and hepatocellular carcinogenesis. A previous study from this laboratory demonstrated striking suppression of hepatocellular carcinoma (HCC) by HNF4α, although the mechanisms by which HNF4α reverses HCC malignancy are largely unknown. Herein, we demonstrated that HNF4α administration to HCC ...
Heinrich Eva-Marie - - 2013
MicroRNAs are small non-coding RNAs that regulate gene expression. Although all seven members of the miR-17-92a cluster originate from one primary transcript they are differentially expressed suggesting the presence of posttranscriptional regulation. By RNA pulldown and mass spectrometry we identified SND1, a known regulator of edited RNAs, interacting with pre-miR-92a ...
Gao Feng - - 2013
Wheat seeds can be released from a dormant state by after-ripening; however, the underlying molecular mechanisms are still mostly unknown. We previously identified transcriptional programmes involved in the regulation of after-ripening-mediated seed dormancy decay in wheat (Triticum aestivum L.). Here, we show that seed dormancy maintenance and its release by ...
Manzardo A M - - 2013
We examined miRNA expression from RNA isolated from the frontal cortex (Broadman area 9) of 9 alcoholics (6 males, 3 females, mean age 48 years) and 9 matched controls using both the Affymetrix GeneChip miRNA 2.0 and Human Exon 1.0 ST Arrays to further characterize genetic influences in alcoholism and ...
Zhou Mingliang - - 2013
MicroRNAs (miRNAs) have been identified to play important functions during osteoblast proliferation, differentiation, and apoptosis. The miR-17~92 cluster is highly conserved in all vertebrates. Loss-of-function of the miR-17-92 cluster results in smaller embryos and immediate postnatal death of all animals. Germline hemizygous deletions of MIR17HG are accounted for microcephaly, short ...
Chen Ron A-J - - 2013
RNA polymerase transcription initiation sites are largely unknown in C. elegans. The initial 5' end of most protein-coding transcripts are removed by trans-splicing, and non-coding initiation sites have not been investigated. We characterized the landscape of RNA Pol II transcription initiation, identifying 73,500 distinct clusters of initiation. Bidirectional transcription is ...
Zhang Zhonghui - - 2013
Small molecules (SM) can greatly enhance the efficiency of iPS cell generation, but the mechanisms by which they act have not been fully explored. We show here that a SM cocktail (NaB, PD03259, SB431542) significantly promotes iPS cell generation from human fibroblasts, and NaB is more potent than the other ...
Brown Raquel M - - 2013
The gonadotropin surge is the essential trigger to stimulate ovulation and luteinization of ovarian follicles. While the hormone signals from the brain that initiate ovulation are known, the specific targets which regulate this process are not well known. In this report, we assess the suitability of the Rhox homeobox gene ...
Sung Chang Ohk - - 2013
AIMS: Sarcomatoid carcinoma (SC) is considered to be a result of the sarcomatoid change of epithelial carcinoma. However, epithelial-mesenchymal transition (EMT) in SC has been insufficiently studied. METHODS: We evaluated the expression patterns of EMT-related phenotypic markers with transcription factors in 27 SCs originating from various organs, and we investigated ...
Liu Xiangyang - - 2013
Mining the genome sequence of Burkholderia thailandensis MSMB43 revealed a cryptic biosynthetic gene cluster resembling that of FR901464 (4), a prototype spliceosome inhibitor produced by Pseudomonas sp. No. 2663. Transcriptional analysis revealed a cultivation condition in which a regulatory gene of the cryptic gene cluster is adequately expressed. Consequently, three ...
Toubiana Mylène - - 2013
TLR- and MyD88-related sequences have been previously investigated in Mytibase and then in new transcript reads obtained by Illumina technology from the mussel, Mytilus galloprovincialis. Based on full cds and domain organizations of virtual translations, we identified 23 Toll-like receptors (TLRs) and 3 MyD88 adaptors. MgTLRs can be arranged in ...
Gu Yang Y Department of Obstetrics and Gynecology, Louisiana State University Health Sciences Center-Shreveport, LA 71130, - - 2013
To determine placental microRNA (miRNA) expression at different gestational age, total RNA from six first and six third trimester placentas was isolated. miRNA expression was analyzed by Affymetrix miRNA microarray, and miRNA clusters were identified by web-based programs MirClust and miRGen Cluster. qRT-PCR was carried out to validate miRNA expression, ...
Kumar Premlata P Department of Biochemistry, North Texas March of Dimes Birth Defects Center, University of Texas Southwestern Medical Center, Dallas, Texas, - - 2013
Mononuclear cytotrophoblasts of the human placenta proliferate rapidly, subsequently fuse, and differentiate to form multinucleated syncytiotrophoblast with induction of aromatase (hCYP19A1) and chorionic gonadotropin (hCGβ) expression. Using microarray analysis, we identified members of the miR-17~92 cluster and its paralogs, miR-106a~363 and miR-106b~25, that are significantly downregulated upon syncytiotrophoblast differentiation. Interestingly, ...
Dassi Erik - - 2013
Little is known regarding the post-transcriptional networks that control gene expression in eukaryotes. Additionally, we still need to understand how these networks evolve, and the relative role played in them by their sequence-dependent regulatory factors, non-coding RNAs (ncRNAs) and RNA-binding proteins (RBPs). Here, we used an approach that relied on ...
Valentino Carlo C Department of Pathology, University of Arizona College of Medicine, Tucson, 85724, - - 2013
Abnormalities of the MYC oncogene on chromosome 8 are characteristic of Burkitt lymphoma and other aggressive B-cell lymphomas, including diffuse large B-cell lymphoma (DLBCL). We recently described a colorimetric in situ hybridization (CISH) method for detecting extra copies of the MYC gene in DLBCL and the frequent occurrence of excess ...
Baumgarten Anna - - 2013
BACKGROUND: The transcription factor TWIST1 has been described to regulate the microRNA (miR)-199/214 cluster. Genetic disruption of TWIST1 resulted in a cachectic phenotype and early death of the knock-out mice. This might be connected to the activity of the ubiquitin-proteasome-system (UPS), as miR-199a has been suggested to regulate the ubiquitin ...
Hollensen Anne Kruse - - 2013
MicroRNAs (miRNAs) are ubiquitous regulators of gene expression that contribute to almost any cellular process. Methods for managing of miRNA activity are attracting increasing attention in relation to diverse experimental and therapeutic applications. DNA-encoded miRNA inhibitors expressed from plasmid or virus-based vectors provide persistent miRNA suppression and options of tissue-directed ...
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