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https://www.readbyqxmd.com/read/28229966/extra-oviductal-expression-of-oviductal-glycoprotein-1-in-mouse-detection-in-testis-epididymis-and-ovary
#1
Saniya Laheri, Deepak Modi, Purvi Bhatt
Oviductal glycoprotein 1 (OVGP1), also called oviductin, is an oviduct-specific protein and is suggested to play a role in fertilization. Traditionally, Ovgp1 has been shown to be exclusively expressed by the oviduct; however, recent studies have demonstrated its expression in some cancers. This observation led us to hypothesize that Ovgp1 might have some extra-oviductal expression. In the current study, we evaluated the mRNA and protein expression of Ovgp1 in normal reproductive tissues of male and female mice...
March 2017: Journal of Biosciences
https://www.readbyqxmd.com/read/28229942/dissecting-the-role-of-the-elongation-factor-1a-isoforms-in-hepatocellular-carcinoma-cells-by-liposome-mediated-delivery-of-sirnas
#2
Rossella Farra, Bruna Scaggiante, Chiara Guerra, Gabriele Pozzato, Mario Grassi, Fabrizio Zanconati, Francesca Perrone, Cinzia Ferrari, Francesco Trotta, Gabriele Grassi, Barbara Dapas
Eukaryotic elongation factor 1A (eEF1A), a protein involved in protein synthesis, has two major isoforms, eEF1A1 and eEF1A2. Despite the evidences of their involvement in hepatocellular carcinoma (HCC), the quantitative contribution of each of the two isoforms to the disease is unknown. We depleted the two isoforms by means of siRNAs and studied the effects in three different HCC cell lines. Particular care was dedicated to select siRNAs able to target each of the two isoform without affecting the other one...
February 13, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28228471/novel-layers-of-rna-polymerase-iii-control-affecting-trna-gene-transcription-in-eukaryotes
#3
REVIEW
Ewa Leśniewska, Magdalena Boguta
RNA polymerase III (Pol III) transcribes a limited set of short genes in eukaryotes producing abundant small RNAs, mostly tRNA. The originally defined yeast Pol III transcriptome appears to be expanding owing to the application of new methods. Also, several factors required for assembly and nuclear import of Pol III complex have been identified recently. Models of Pol III based on cryo-electron microscopy reconstructions of distinct Pol III conformations reveal unique features distinguishing Pol III from other polymerases...
February 2017: Open Biology
https://www.readbyqxmd.com/read/28225755/intragenic-dna-methylation-prevents-spurious-transcription-initiation
#4
Francesco Neri, Stefania Rapelli, Anna Krepelova, Danny Incarnato, Caterina Parlato, Giulia Basile, Mara Maldotti, Francesca Anselmi, Salvatore Oliviero
In mammals, DNA methylation occurs mainly at CpG dinucleotides. Methylation of the promoter suppresses gene expression, but the functional role of gene-body DNA methylation in highly expressed genes has yet to be clarified. Here we show that, in mouse embryonic stem cells, Dnmt3b-dependent intragenic DNA methylation protects the gene body from spurious RNA polymerase II entry and cryptic transcription initiation. Using different genome-wide approaches, we demonstrate that this Dnmt3b function is dependent on its enzymatic activity and recruitment to the gene body by H3K36me3...
February 22, 2017: Nature
https://www.readbyqxmd.com/read/28223400/distal-cpg-islands-can-serve-as-alternative-promoters-to-transcribe-genes-with-silenced-proximal-promoters
#5
Shrutii Sarda, Avinash Das, Charles Vinson, Sridhar Hannenhalli
DNA methylation at the promoter of a gene is presumed to render it silent, yet, a sizable fraction of genes with methylated proximal-promoters exhibit elevated expression. Here, we show, through extensive analysis of the methylome and transcriptome in 34 tissues, that in many such cases, transcription is initiated by a distal upstream CpG island (CGI) located several kilobases away that functions as an alternative promoter. Specifically, such genes are expressed precisely when the neighboring CGI remains unmethylated, but remain silenced otherwise...
February 21, 2017: Genome Research
https://www.readbyqxmd.com/read/28222105/stat3-cdc25a-dependent-cell-proliferation-promotes-embryonic-axis-extension-during-zebrafish-gastrulation
#6
Yinzi Liu, Diane S Sepich, Lilianna Solnica-Krezel
Cell proliferation has generally been considered dispensable for anteroposterior extension of embryonic axis during vertebrate gastrulation. Signal transducer and activator of transcription 3 (Stat3), a conserved controller of cell proliferation, survival and regeneration, is associated with human scoliosis, cancer and Hyper IgE Syndrome. Zebrafish Stat3 was proposed to govern convergence and extension gastrulation movements in part by promoting Wnt/Planar Cell Polarity (PCP) signaling, a conserved regulator of mediolaterally polarized cell behaviors...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28220113/diverse-plant-associated-pleosporalean-fungi-from-saline-areas-ecological-tolerance-and-nitrogen-status-dependent-effects-on-plant-growth
#7
Yuan Qin, Xueyu Pan, Christian Kubicek, Irina Druzhinina, Komal Chenthamara, Jessy Labbé, Zhilin Yuan
Similar to mycorrhizal mutualists, the rhizospheric and endophytic fungi are also considered to act as active regulators of host fitness (e.g., nutrition and stress tolerance). Despite considerable work in selected model systems, it is generally poorly understood how plant-associated fungi are structured in habitats with extreme conditions and to what extent they contribute to improved plant performance. Here, we investigate the community composition of root and seed-associated fungi from six halophytes growing in saline areas of China, and found that the pleosporalean taxa (Ascomycota) were most frequently isolated across samples...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28219675/tcf7l2-plays-crucial-roles-in-forebrain-development-through-regulation-of-thalamic-and-habenular-neuron-identity-and-connectivity
#8
Myungsin Lee, Jiyeon Yoon, Hobeom Song, Bumwhee Lee, Lam Tri Duc, Jaeseung Yoon, Kwanghee Baek, Hans Clevers, Yongsu Jeong
The thalamus acts as a central integrator for processing and relaying sensory and motor information to and from the cerebral cortex, and the habenula plays pivotal roles in emotive decision making by modulating dopaminergic and serotonergic circuits. These neural compartments are derived from a common developmental progenitor domain, called prosomere 2, in the caudal forebrain. Thalamic and habenular neurons exhibit distinct molecular profile, neurochemical identity, and axonal circuitry. However, the mechanisms of how their progenitors in prosomere 2 give rise to these two populations of neurons and contribute to the forebrain circuitry remains unclear...
February 17, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28218250/chromatin-remodeller-fun30-fft3-induces-nucleosome-disassembly-to-facilitate-rna-polymerase-ii-elongation
#9
Junwoo Lee, Eun Shik Choi, Hogyu David Seo, Keunsoo Kang, Joshua M Gilmore, Laurence Florens, Michael P Washburn, Joonho Choe, Jerry L Workman, Daeyoup Lee
Previous studies have revealed that nucleosomes impede elongation of RNA polymerase II (RNAPII). Recent observations suggest a role for ATP-dependent chromatin remodellers in modulating this process, but direct in vivo evidence for this is unknown. Here using fission yeast, we identify Fun30(Fft3) as a chromatin remodeller, which localizes at transcribing regions to promote RNAPII transcription. Fun30(Fft3) associates with RNAPII and collaborates with the histone chaperone, FACT, which facilitates RNAPII elongation through chromatin, to induce nucleosome disassembly at transcribing regions during RNAPII transcription...
February 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28215706/uv-irradiation-induces-a-non-coding-rna-that-functionally-opposes-the-protein-encoded-by-the-same-gene
#10
Laura Williamson, Marco Saponaro, Stefan Boeing, Philip East, Richard Mitter, Theodoros Kantidakis, Gavin P Kelly, Anna Lobley, Jane Walker, Bradley Spencer-Dene, Michael Howell, Aengus Stewart, Jesper Q Svejstrup
The transcription-related DNA damage response was analyzed on a genome-wide scale with great spatial and temporal resolution. Upon UV irradiation, a slowdown of transcript elongation and restriction of gene activity to the promoter-proximal ∼25 kb is observed. This is associated with a shift from expression of long mRNAs to shorter isoforms, incorporating alternative last exons (ALEs) that are more proximal to the transcription start site. Notably, this includes a shift from a protein-coding ASCC3 mRNA to a shorter ALE isoform of which the RNA, rather than an encoded protein, is critical for the eventual recovery of transcription...
February 16, 2017: Cell
https://www.readbyqxmd.com/read/28215225/transcription-factors-in-breast-cancer-lessons-from-recent-genomic-analyses-and-therapeutic-implications
#11
E Zacksenhaus, J C Liu, Z Jiang, Y Yao, L Xia, M Shrestha, Y Ben-David
Multiplatform genomic analyses have identified 93 frequently altered genes in breast cancer. Of these, as many as 49 genes are directly or indirectly involved in transcription. These include constitutive and inducible DNA-binding transcription factors (DB-TFs, 13 genes), corepressors/coactivators (14 genes), epigenetic (10), and mediator/splicing/rRNA (3) factors. At least nine additional genes are immediate upstream regulators of transcriptional cofactors. G:profiler analysis reveals that these alterations affect cell cycle, development/differentiation, steroid hormone, and chromatin modification pathways...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28215221/targeting-chromatin-remodeling-in-inflammation-and-fibrosis
#12
J Yang, B Tian, A R Brasier
Mucosal surfaces of the human body are lined by a contiguous epithelial cell surface that forms a barrier to aerosolized pathogens. Specialized pattern recognition receptors detect the presence of viral pathogens and initiate protective host responses by triggering activation of the nuclear factor κB (NFκB)/RelA transcription factor and formation of a complex with the positive transcription elongation factor (P-TEFb)/cyclin-dependent kinase (CDK)9 and Bromodomain-containing protein 4 (BRD4) epigenetic reader...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28213523/identification-of-regions-in-the-spt5-subunit-of-dsif-that-are-involved-in-promoter-proximal-pausing
#13
Yijun Qiu, David S Gilmour
DRB-sensitivity inducing factor (DSIF(2), or Spt4/5) is a conserved transcription elongation factor that both inhibits and stimulates transcription elongation in metazoans. In Drosophila and vertebrates, DSIF together with negative elongation factor (NELF) associates with RNA polymerase II (Pol II) during early elongation and causes Pol II to pause in the promoter proximal region of genes. The mechanism of how DSIF establishes pausing is not known. We constructed Spt5 mutant forms of DSIF and tested their capacity to restore promoter proximal pausing to DSIF-depleted Drosophila nuclear extracts...
February 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28211799/increased-expression-of-long-non-coding-rna-glidr-in-prostate-cancer
#14
Yingyi Zhang, Zhe Kong, Yalong Zhang, Wenhua Huang, Hai Wu, Xuechao Wan, Yao Li
Prostate cancer (PCa) was one of the most common cancers in males in China. Long non-coding RNAs (lncRNA), a class of non-coding RNAs with more than 200 nucleotides, played key roles in the progression of prostate cancer. GLIDR, a novel long intergenic ncRNA, was found to be upregulated in tumors compared to normal tissues by using publically databases. In the clinical validation cohort, our results showed GLIDR was significantly up-regulated in prostate cancer samples and cell lines. To explore the potential functions of the GLIDR, we constructed gene co-expression networks and applied GO analysis...
February 3, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/28211089/icariin-promotes-mouse-hair-follicle-growth-by-increasing-insulin-like-growth-factor-1-expression-in-dermal-papillary-cells
#15
Y-S Su, Z-X Fan, S-E Xiao, B-J Lin, Y Miao, Z-Q Hu, H Liu
BACKGROUND: Icariin is a major flavonoid isolated from Epimedium spp. leaves (Epimedium Herba), and has multiple pharmacological functions, including anti-angiogenesis, anti-oxidant, anti-inflammatory and immunoprotective effects. AIM: To investigate whether icariin can stimulate growth of hair follicles in mice and the underlying mechanism. METHODS: In vitro, the effect of icariin on hair growth was assessed by using a vibrissae hair follicle (VHF) organ-culture model...
February 16, 2017: Clinical and Experimental Dermatology
https://www.readbyqxmd.com/read/28210955/the-effects-of-igf-1-on-tnf-%C3%AE-treated-drg-neurons-by-modulating-atf3-and-gap-43-expression-via-pi3k-akt-s6k-signaling-pathway
#16
Lei Zhang, Yaping Yue, Meishuo Ouyang, Huaxiang Liu, Zhenzhong Li
Upregulation of the pro-inflammatory cytokine tumor necrosis factor α (TNF-α) is involved in the development and progression of numerous neurological disorders. Recent reports have challenged the concept that TNF-α exhibits only deleterious effects of pro-inflammatory destruction, and have raised the awareness that it may play a beneficial role in neuronal growth and function in particular conditions, which prompts us to further investigate the role of this cytokine. Insulin-like growth factor-1 (IGF-1) is a cytokine possessing powerful neuroprotective effects in promoting neuronal survival, neuronal differentiation, neurite elongation, and neurite regeneration...
February 16, 2017: Neurochemical Research
https://www.readbyqxmd.com/read/28209164/rnf40-regulates-gene-expression-in-an-epigenetic-context-dependent-manner
#17
Wanhua Xie, Sankari Nagarajan, Simon J Baumgart, Robyn Laura Kosinsky, Zeynab Najafova, Vijayalakshmi Kari, Magali Hennion, Daniela Indenbirken, Stefan Bonn, Adam Grundhoff, Florian Wegwitz, Ahmed Mansouri, Steven A Johnsen
BACKGROUND: Monoubiquitination of H2B (H2Bub1) is a largely enigmatic histone modification that has been linked to transcriptional elongation. Because of this association, it has been commonly assumed that H2Bub1 is an exclusively positively acting histone modification and that increased H2Bub1 occupancy correlates with increased gene expression. In contrast, depletion of the H2B ubiquitin ligases RNF20 or RNF40 alters the expression of only a subset of genes. RESULTS: Using conditional Rnf40 knockout mouse embryo fibroblasts, we show that genes occupied by low to moderate amounts of H2Bub1 are selectively regulated in response to Rnf40 deletion, whereas genes marked by high levels of H2Bub1 are mostly unaffected by Rnf40 loss...
February 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/28199965/whole-exome-sequencing-identified-a-homozygous-brdt-mutation-in-a-patient-with-acephalic-spermatozoa
#18
Lin Li, Yanwei Sha, Xi Wang, Ping Li, Jing Wang, Kehkooi Kee, Binbin Wang
Acephalic spermatozoa is a very rare disorder of male infertility. Here, in a patient from from a consanguineous family, we have identified, by whole-exome sequencing, a homozygous mutation (c.G2783A, p.G928D) in the BRDT gene. The gene product, BRDT, is a testis-specific protein that is considered an important drug target for male contraception. The G928D mutation is in the P-TEFb binding domain, which mediates the interaction with transcription elongation factor and might affect the transcriptional activities of downstream genes...
February 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28199109/the-nucleotide-selectivity-at-a-pre-insertion-checkpoint-of-t7-rna-polymerase-transcription-elongation
#19
Chao E, Baogen Duan, Jin Yu
Nucleotide selection is crucial for transcription fidelity control, in particular, for viral T7 RNA polymerase (RNAP) lack of proofreading activity. It has been recognized that multiple kinetic checkpoints exist prior to full nucleotide incorporation. In this work, we implemented intensive atomistic molecular dynamics (MD) simulations to quantify how strong the nucleotide selection is at the initial checkpoint of an elongation cycle of T7 RNAP. The incoming nucleotides bind into a pre-insertion site where a critical tyrosine residue locates nearby to assist the nucleotide selection...
February 15, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28191883/loap-is-a-broadly-conserved-antiterminator-protein-that-regulates-antibiotic-gene-clusters-in-bacillus-amyloliquefaciens
#20
Jonathan R Goodson, Steven Klupt, Chengxi Zhang, Paul Straight, Wade C Winkler
A valuable resource available in the search for new natural products is the diverse microbial life that spans the planet. A large subset of these microorganisms synthesize complex specialized metabolites exhibiting biomedically important activities. A limiting step to the characterization of these compounds is an elucidation of the genetic regulatory mechanisms that oversee their production. Although proteins that control transcription initiation of specialized metabolite gene clusters have been identified, those affecting transcription elongation have not been broadly investigated...
February 13, 2017: Nature Microbiology
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