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Versatile Applications Of Transcriptional Pulsing To Study Mrna Turnover In Mammalian Cells, Chyi-Ying A Chen, Yukiko Yamashita, Tsung-Cheng Chang, Akio Yamashita, Wenmiao Zhu, Zhenping Zhong, Ann-Bin Shyu
Versatile Applications Of Transcriptional Pulsing To Study Mrna Turnover In Mammalian Cells, Chyi-Ying A Chen, Yukiko Yamashita, Tsung-Cheng Chang, Akio Yamashita, Wenmiao Zhu, Zhenping Zhong, Ann-Bin Shyu
Journal Articles
Development of transcriptional pulsing approaches using the c-fos and Tet-off promoter systems greatly facilitated studies of mRNA turnover in mammalian cells. However, optimal protocols for these approaches vary for different cell types and/or physiological conditions, limiting their widespread application. In this study, we have further optimized transcriptional pulsing systems for different cell lines and developed new protocols to facilitate investigation of various aspects of mRNA turnover. We apply the Tet-off transcriptional pulsing strategy to investigate ARE-mediated mRNA decay in human erythroleukemic K562 cells arrested at various phases of the cell cycle by pharmacological inhibitors. This application facilitates studies of the …
Computational Identification And Functional Validation Of Regulatory Motifs In Cartilage-Expressed Genes, Sherri R Davies, Li-Wei Chang, Debabrata Patra, Xiaoyun Xing, Karen Posey, Jacqueline Hecht, Gary D Stormo, Linda J Sandell
Computational Identification And Functional Validation Of Regulatory Motifs In Cartilage-Expressed Genes, Sherri R Davies, Li-Wei Chang, Debabrata Patra, Xiaoyun Xing, Karen Posey, Jacqueline Hecht, Gary D Stormo, Linda J Sandell
Journal Articles
Chondrocyte gene regulation is important for the generation and maintenance of cartilage tissues. Several regulatory factors have been identified that play a role in chondrogenesis, including the positive transacting factors of the SOX family such as SOX9, SOX5, and SOX6, as well as negative transacting factors such as C/EBP and delta EF1. However, a complete understanding of the intricate regulatory network that governs the tissue-specific expression of cartilage genes is not yet available. We have taken a computational approach to identify cis-regulatory, transcription factor (TF) binding motifs in a set of cartilage characteristic genes to better define the transcriptional regulatory …
Selective Repression Of Retinoic Acid Target Genes By Rip140 During Induced Tumor Cell Differentiation Of Pluripotent Human Embryonal Carcinoma Cells, Kelly C. Heim, Kristina A. White, Dexin Deng, Craig R. Tomlinson, Jason Moore, Sarah Freemantle, Michael Spinella
Selective Repression Of Retinoic Acid Target Genes By Rip140 During Induced Tumor Cell Differentiation Of Pluripotent Human Embryonal Carcinoma Cells, Kelly C. Heim, Kristina A. White, Dexin Deng, Craig R. Tomlinson, Jason Moore, Sarah Freemantle, Michael Spinella
Dartmouth Scholarship
The use of retinoids as anti-cancer agents has been limited due to resistance and low efficacy. The dynamics of nuclear receptor coregulation are incompletely understood. Cell-and context-specific activities of nuclear receptors may be in part due to distinct coregulator complexes recruited to distinct subsets of target genes. RIP140 (also called NRIP1) is a ligand-dependent corepressor that is inducible with retinoic acid (RA). We had previously shown that RIP140 limits RA induced tumor cell differentiation of embryonal carcinoma; the pluriopotent stem cells of testicular germ cell tumors. This implies that RIP140 represses key genes required for RA-mediated tumor cell differentiation. Identification …
Agrobacterium Para/Mind-Like Virc1 Spatially Coordinates Early Conjugative Dna Transfer Reactions, Krishnamohan Atmakuri, Eric Cascales, Oliver T Burton, Lois M Banta, Peter J Christie
Agrobacterium Para/Mind-Like Virc1 Spatially Coordinates Early Conjugative Dna Transfer Reactions, Krishnamohan Atmakuri, Eric Cascales, Oliver T Burton, Lois M Banta, Peter J Christie
Journal Articles
Agrobacterium tumefaciens translocates T-DNA through a polar VirB/D4 type IV secretion (T4S) system. VirC1, a factor required for efficient T-DNA transfer, bears a deviant Walker A and other sequence motifs characteristic of ParA and MinD ATPases. Here, we show that VirC1 promotes conjugative T-DNA transfer by stimulating generation of multiple copies per cell of the T-DNA substrate (T-complex) through pairwise interactions with the processing factors VirD2 relaxase, VirC2, and VirD1. VirC1 also associates with the polar membrane and recruits T-complexes to cell poles, the site of VirB/D4 T4S machine assembly. VirC1 Walker A mutations abrogate T-complex generation and polar recruitment, …
Dynamics Of A Minimal Model Of Interlocked Positive And Negative Feedback Loops Of Transcriptional Regulation By Camp-Response Element Binding Proteins, Hao Song, Paul Smolen, Evyatar Av-Ron, Douglas A Baxter, John H Byrne
Dynamics Of A Minimal Model Of Interlocked Positive And Negative Feedback Loops Of Transcriptional Regulation By Camp-Response Element Binding Proteins, Hao Song, Paul Smolen, Evyatar Av-Ron, Douglas A Baxter, John H Byrne
Journal Articles
cAMP-response element binding (CREB) proteins are involved in transcriptional regulation in a number of cellular processes (e.g., neural plasticity and circadian rhythms). The CREB family contains activators and repressors that may interact through positive and negative feedback loops. These loops can be generated by auto- and cross-regulation of expression of CREB proteins, via CRE elements in or near their genes. Experiments suggest that such feedback loops may operate in several systems (e.g., Aplysia and rat). To understand the functional implications of such feedback loops, which are interlocked via cross-regulation of transcription, a minimal model with a positive and negative loop …
Oocyte Cytoplasmic Maturation: A Key Mediator Of Oocyte And Embryo Developmental Competence., A J Watson
Oocyte Cytoplasmic Maturation: A Key Mediator Of Oocyte And Embryo Developmental Competence., A J Watson
Obstetrics & Gynaecology Publications
Efforts have intensified to successfully mature and inseminate oocytes in vitro and then culture ensuing embryos to transferable stages from a large number of mammalian species. Success varies, but generally even for the most successful species it is only possible to obtain a maximum of a 40 to 50% development of zygotes to the blastocyst stage. Reduced oocyte developmental competence is suggested as a primary reason for the reduced potential of in vitro-produced embryos. The vast majority of in vitro-matured oocytes are meiotically competent; however, many do not attain an optimal oocyte diameter before insemination. Variations in oocyte in vitro …
Aldosterone-Induced Sgk1 Relieves Dot1a-Af9-Mediated Transcriptional Repression Of Epithelial Na+ Channel Alpha, Wenzheng Zhang, Xuefeng Xia, Mary Rose Reisenauer, Timo Rieg, Florian Lang, Dietmar Kuhl, Volker Vallon, Bruce C Kone
Aldosterone-Induced Sgk1 Relieves Dot1a-Af9-Mediated Transcriptional Repression Of Epithelial Na+ Channel Alpha, Wenzheng Zhang, Xuefeng Xia, Mary Rose Reisenauer, Timo Rieg, Florian Lang, Dietmar Kuhl, Volker Vallon, Bruce C Kone
Journal Articles
Aldosterone plays a major role in the regulation of salt balance and the pathophysiology of cardiovascular and renal diseases. Many aldosterone-regulated genes--including that encoding the epithelial Na+ channel (ENaC), a key arbiter of Na+ transport in the kidney and other epithelia--have been identified, but the mechanisms by which the hormone modifies chromatin structure and thus transcription remain unknown. We previously described the basal repression of ENaCalpha by a complex containing the histone H3 Lys79 methyltransferase disruptor of telomeric silencing alternative splice variant a (Dot1a) and the putative transcription factor ALL1-fused gene from chromosome 9 (Af9) as well as the release …
Genome Sequence Of Fusobacterium Nucleatum Subspecies Polymorphum - A Genetically Tractable Fusobacterium, Sandor E Karpathy, Xiang Qin, Jason Gioia, Huaiyang Jiang, Yamei Liu, Joseph F Petrosino, Shailaja Yerrapragada, George E Fox, Susan Kinder Haake, George M Weinstock, Sarah K Highlander
Genome Sequence Of Fusobacterium Nucleatum Subspecies Polymorphum - A Genetically Tractable Fusobacterium, Sandor E Karpathy, Xiang Qin, Jason Gioia, Huaiyang Jiang, Yamei Liu, Joseph F Petrosino, Shailaja Yerrapragada, George E Fox, Susan Kinder Haake, George M Weinstock, Sarah K Highlander
Journal Articles
Fusobacterium nucleatum is a prominent member of the oral microbiota and is a common cause of human infection. F. nucleatum includes five subspecies: polymorphum, nucleatum, vincentii, fusiforme, and animalis. F. nucleatum subsp. polymorphum ATCC 10953 has been well characterized phenotypically and, in contrast to previously sequenced strains, is amenable to gene transfer. We sequenced and annotated the 2,429,698 bp genome of F. nucleatum subsp. polymorphum ATCC 10953. Plasmid pFN3 from the strain was also sequenced and analyzed. When compared to the other two available fusobacterial genomes (F. nucleatum subsp. nucleatum, and F. nucleatum subsp. vincentii) 627 open reading frames unique …