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https://www.readbyqxmd.com/read/29346292/isoform-sequencing-and-state-of-art-applications-for-unravelling-complexity-of-plant-transcriptomes
#1
REVIEW
Dong An, Hieu X Cao, Changsheng Li, Klaus Humbeck, Wenqin Wang
Single-molecule real-time (SMRT) sequencing developed by PacBio, also called third-generation sequencing (TGS), offers longer reads than the second-generation sequencing (SGS). Given its ability to obtain full-length transcripts without assembly, isoform sequencing (Iso-Seq) of transcriptomes by PacBio is advantageous for genome annotation, identification of novel genes and isoforms, as well as the discovery of long non-coding RNA (lncRNA). In addition, Iso-Seq gives access to the direct detection of alternative splicing, alternative polyadenylation (APA), gene fusion, and DNA modifications...
January 18, 2018: Genes
https://www.readbyqxmd.com/read/29344139/nls-rar%C3%AE-is-a-novel-transcriptional-factor
#2
Kai-Ling Jiang, Liang Zhong, Xiao-Qun Yang, Peng-Peng Ma, Hui Wang, Xin-Yu Zhu, Bei-Zhong Liu
Acute promyelocytic leukemia (APL) is characterized by the presence of the promyelocytic leukemia (PML)-retinoic acid receptor-α (RAR-α) fusion protein. PML-RARα can be cleaved by neutrophil elastase (NE) in several positions in cells in the promyelocytic stage, nuclear location signal (NLS)-negative PML and NLS-RARα may be the products of PML-RARα by NE. The function of NLS-RARα may be affected by the addition of NLS, which would alter its localization in cells, as the role of NLS is to identify proteins for transport to the nucleus...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29343669/direct-interaction-between-vrn1-protein-and-the-promoter-region-of-the-wheat-ft-gene
#3
Chihiro Tanaka, Takafumi Itoh, Yukimoto Iwasaki, Nobuyuki Mizuno, Shuhei Nasuda, Koji Murai
The wheat florigen gene Wheat FLOWERING LOCUS T (WFT, which is identical to VRN3) is an integrator of the vernalization, photoperiod and autonomous pathways in wheat flowering. Many studies have indicated that VERNALIZATION 1 (VRN1) directly or indirectly up-regulates WFT expression in leaves. VRN1 encodes an APETALA1/FRUITFULL-like MADS-box transcription factor that is up-regulated by vernalization and aging, leading to promotion of flowering. In this study, the VRN1 protein was expressed as a His-Tag fusion protein in Escherichia coli and used in an electrophoretic mobility shift assay (EMSA)...
January 17, 2018: Genes & Genetic Systems
https://www.readbyqxmd.com/read/29340620/delivery-of-tapasin-modified-ctl-epitope-peptide-via-cytoplasmic-transduction-peptide-induces-ctls-by-jak-stat-signaling-pathway-in-vivo
#4
Shanshan Wu, Xiaohua Chen, Yuyan Tang, Yi Zhang, Dan Li, Jie Chen, Jieling Wang, Zhenghao Tang, Guoqing Zang, Yongsheng Yu
Hepatitis B virus (HBV)-specific cytotoxic T lymphocytes (CTLs) play a vital role in viral control and clearance. Recent studies have elucidated that Tapasin, an endoplasmic reticulum chaperone, is a well-known molecule that appears to be essential in peptide-loading process. The Janus kinase/signal transducers and activators of transcription (JAK/STAT) pathway plays an important role in immune response regulation and cytokines secretion. We have previously verified that fusion protein CTP-HBcAg18-27-Tapasin could facilitate the maturation of bone marrow derived dendritic cells and enhance specific CTLs responses in vitro, which might be associated with the activation of JAK/STAT signaling pathway...
January 11, 2018: Acta Biochimica et Biophysica Sinica
https://www.readbyqxmd.com/read/29337901/transcriptional-readthrough-rnas-reflect-the-phenomenon-of-a-gene-contains-gene-s-or-gene-s-within-a-gene-in-the-human-genome-and-thus-are-not-chimeric-rnas
#5
REVIEW
Yan He, Chengfu Yuan, Lichan Chen, Mingjuan Lei, Lucas Zellmer, Hai Huang, Dezhong Joshua Liao
Tens of thousands of chimeric RNAs, i.e., RNAs with sequences of two genes, have been identified in human cells. Most of them are formed by two neighboring genes on the same chromosome and are considered to be derived via transcriptional readthrough, but a true readthrough event still awaits more evidence and trans-splicing that joins two transcripts together remains as a possible mechanism. We regard those genomic loci that are transcriptionally read through as unannotated genes, because their transcriptional and posttranscriptional regulations are the same as those of already-annotated genes, including fusion genes formed due to genetic alterations...
January 16, 2018: Genes
https://www.readbyqxmd.com/read/29337690/molecular-determinants-of-drosophila-immunophilin-fkbp39-nuclear-localization
#6
Marek Orłowski, Katarzyna Popławska, Joanna Pieprzyk, Aleksandra Szczygieł-Sommer, Anna Więch, Mirosław Zarębski, Aneta Tarczewska, Jurek Dobrucki, Andrzej Ożyhar
FK506-binding proteins (FKBPs) belong to a distinct class of immunophilins that interact with immunosuppressants. They use their peptidyl-prolyl isomerase (PPIase) activity to catalyse the cis-trans conversion of prolyl bonds in proteins during protein-folding events. FKBPs also act as a unique group of chaperones. The Drosophila melanogaster peptidylprolyl cis-trans isomerase FK506-binding protein of 39 kDa (FKBP39) is thought to act as a transcriptional modulator of gene expression in 20-hydroxyecdysone and juvenile hormone signal transduction...
June 27, 2017: Biological Chemistry
https://www.readbyqxmd.com/read/29335788/over-expression-of-a-grafting-responsive-gene-from-hickory-increases-abiotic-stress-tolerance-in-arabidopsis
#7
R M Saravana Kumar, Guocun Ji, Haipeng Guo, Liang Zhao, Bingsong Zheng
A grafting response gene CcPIP1;2 was cloned from hickory plant, further functional characterization of the gene for water transport activity and abiotic stress tolerances were carried out through heterologous expression in Xenopus and Arabidopsis. Plasma membrane intrinsic proteins (PIPs) are multifunctional channel proteins belonging to the membrane intrinsic protein (MIP) family. In this study, a grafting-responsive gene from hickory (CcPIP1;2) was cloned and functionally characterized. Application of non-selective water inhibitors (HgCl2 and phloretin) led to the death of grafted hickory plants at 30 days after grafting (DAG)...
January 15, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29334975/molecular-characterization-of-duck-enteritis-virus-ul41-protein
#8
Tianqiong He, Mingshu Wang, Xuelian Cao, Anchun Cheng, Ying Wu, Qiao Yang, Mafeng Liu, Dekang Zhu, Renyong Jia, Shun Chen, Kunfeng Sun, Xinxin Zhao, Xiaoyue Chen
BACKGROUND: Duck enteritis virus (DEV) belongs to the subfamily Alphaherpesvirinae, and information on the DEV UL41 gene is limited. METHODS: The DEV UL41 gene was cloned into the pET32a(+) vector and expressed in a prokaryotic expression system. Antiserum was raised against a bacterially expressed UL41-His fusion protein for further experiments. Transcription was quantified and UL41 protein expression levels were determined in DEV-infected cells at different time points by RT-qPCR and western blotting, respectively...
January 15, 2018: Virology Journal
https://www.readbyqxmd.com/read/29334492/anti-il-10-mediated-enhancement-of-antitumor-efficacy-of-a-dendritic-cell-targeting-mip3%C3%AE-gp100-vaccine-in-the-b16f10-mouse-melanoma-model-is-dependent-on-type-i-interferons
#9
James T Gordy, Kun Luo, Brian Francica, Charles Drake, Richard B Markham
The chemokine MIP3α (CCL20) binds to CCR6 on immature dendritic cells. Vaccines fusing MIP3α to gp100 have been shown to be effective in therapeutically reducing melanoma tumor burden and prolonging survival in a mouse model. Other studies have provided evidence that interleukin-10 (IL-10) neutralizing antibodies (αIL-10) enhance immunologic melanoma therapies by modulating the tolerogenic tumor microenvironment. In the current study, we have utilized the B16F10 syngeneic mouse melanoma model to demonstrate for the first time that a therapy neutralizing IL-10 enhances the antitumor efficacy of a MIP3α-gp100 DNA vaccine, leading to significantly smaller tumors, slower growing tumors, and overall increases in mouse survival...
January 12, 2018: Journal of Immunotherapy
https://www.readbyqxmd.com/read/29330352/dbf4-recruitment-by-forkhead-transcription-factors-defines-an-upstream-rate-limiting-step-in-determining-origin-firing-timing
#10
Dingqiang Fang, Armelle Lengronne, Di Shi, Romain Forey, Magdalena Skrzypczak, Krzysztof Ginalski, Changhui Yan, Xiaoke Wang, Qinhong Cao, Philippe Pasero, Huiqiang Lou
Initiation of eukaryotic chromosome replication follows a spatiotemporal program. The current model suggests that replication origins compete for a limited pool of initiation factors. However, it remains to be answered how these limiting factors are preferentially recruited to early origins. Here, we report that Dbf4 is enriched at early origins through its interaction with forkhead transcription factors Fkh1 and Fkh2. This interaction is mediated by the Dbf4 C terminus and was successfully reconstituted in vitro...
January 12, 2018: Genes & Development
https://www.readbyqxmd.com/read/29330284/novel-intergenically-spliced-chimera-nfatc3-pla2g15-is-associated-with-aggressive-t-all-biology-and-outcome
#11
Jonathan Bond, Christine Tran Quang, Guillaume Hypolite, Mohamed Belhocine, Aurélie Bergon, Gaëlle Cordonnier, Jacques Ghysdael, Elizabeth Macintyre, Nicolas Boissel, Salvatore Spicuglia, Vahid Asnafi
Leukemias are frequently characterized by the expression of oncogenic fusion chimeras that normally arise due to chromosomal rearrangements. Intergenically-spliced chimeric RNAs (ISCs) are transcribed in the absence of structural genomic changes, and aberrant ISC expression is now recognized as a potential driver of cancer. To better understand these potential oncogenic drivers, high-throughput RNA-sequencing (RNA-seq) was performed on T-acute lymphoblastic leukemia (T-ALL) patient specimens (n=24) and candidate T-ALL-related ISCs were identified (n=55; a median of 4 per patient)...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29328472/combined-analysis-of-gene-expression-and-genome-binding-profiles-identified-potential-therapeutic-targets-of-ciclopirox-in-ewing-sarcoma
#12
Baisheng Yuan, Wei Ji, Haipeng Xia, Jianmin Li
Ciclopirox (CPX) is a synthetic antifungal drug that is mainly used to treat dermatomycoses. The aim of the present study was to determine whether CPX could influence Ewing sarcoma progression. The present study suggested that CPX treatment may inhibit Ewing sarcoma (ES) progression through Ewing sarcoma breakpoint region 1‑Friend leukemia integration 1 (EWS‑FLI1), a common fusion transcript structure in patients with ES. To determine the underlying mechanisms of ES progression, cross analysis was conducted on three high‑throughput genome or transcript me datasets from the Gene Expression Omnibus...
January 10, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29327718/epithelioid-fibrous-histiocytoma-molecular-characterization-of-alk-fusion-partners-in-23-cases
#13
Brendan C Dickson, David Swanson, George S Charames, Christopher Dm Fletcher, Jason L Hornick
Epithelioid fibrous histiocytoma is a rare and distinctive cutaneous neoplasm. Most cases harbor ALK rearrangement and show ALK overexpression, which distinguish this neoplasm from conventional cutaneous fibrous histiocytoma and variants. SQSTM1 and VCL have previously been shown to partner with ALK in one case each of epithelioid fibrous histiocytoma. The purpose of this study was to examine a large cohort of epithelioid fibrous histiocytomas by next-generation sequencing to characterize the nature and prevalence of ALK fusion partners...
January 12, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29327716/genomic-heterogeneity-of-alk-fusion-breakpoints-in-non-small-cell-lung-cancer
#14
Jason N Rosenbaum, Ryan Bloom, Jason T Forys, Jeff Hiken, Jon R Armstrong, Julie Branson, Samantha McNulty, Priya D Velu, Kymberlie Pepin, Haley Abel, Catherine E Cottrell, John D Pfeifer, Shashikant Kulkarni, Ramaswamy Govindan, Eric Q Konnick, Christina M Lockwood, Eric J Duncavage
In lung adenocarcinoma, canonical EML4-ALK inversion results in a fusion protein with a constitutively active ALK kinase domain. Evidence of ALK rearrangement occurs in a minority (2-7%) of lung adenocarcinoma, and only ~60% of these patients will respond to targeted ALK inhibition by drugs such as crizotinib and ceritinib. Clinically, targeted anti-ALK therapy is often initiated based on evidence of an ALK genomic rearrangement detected by fluorescence in situ hybridization (FISH) of interphase cells in formalin-fixed, paraffin-embedded tissue sections...
January 12, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29327709/insm1-expression-and-its-diagnostic-significance-in-extraskeletal-myxoid-chondrosarcoma
#15
Akihiko Yoshida, Naohiro Makise, Susumu Wakai, Akira Kawai, Nobuyoshi Hiraoka
Extraskeletal myxoid chondrosarcoma is a rare subtype of sarcoma that affects the soft tissue and bones in middle-aged and elderly adults. Its diagnosis can be challenging, with the differential diagnoses including a wide variety of mesenchymal tumors. The line of differentiation of extraskeletal myxoid chondrosarcoma has been controversial, but recent evidence suggests a neuroendocrine phenotype. INSM1 is a zinc-finger transcription factor that plays a pivotal role in neuroendocrine differentiation, and has been proposed as a promising immunohistochemical marker of neuroendocrine carcinoma...
January 12, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29325767/primary-synovial-sarcoma-arising-from-gingivo-buccal-sulcus-harbouring-ss18-ssx2-positive-fusion-transcript-the-1st-reported-case-in-english-literature
#16
Tanush Vig, Meera Thomas, Rekha Pai, Amit Jiwan Tirkey, Rajnikanth Janakiraman
Synovial sarcoma (SS) is a mesenchymal tumour of uncertain histiogenesis that can show dual epithelial and mesenchymal differentiation. Thought to arise predominantly in deep soft tissue of extremities, these sarcomas have shown that they can affect a wide variety of organs and sites, however intraoral mucosal SS is rarely encountered and herein the authors present possibly the second reported case of a young lady presenting with a slow growing tumour arising in the gingivo-buccal sulcus that was reported as Synovial sarcoma on biopsy and subsequently confirmed using molecular studies, tumour demonstrating SS18-SSX2 fusion transcript...
January 8, 2018: Journal of Stomatology, Oral and Maxillofacial Surgery
https://www.readbyqxmd.com/read/29325202/interfacial-mineral-fusion-and-tubule-entanglement-as-a-means-to-harden-a-bone-augmentation-material
#17
Erik A B Hughes, Sophie C Cox, Megan E Cooke, Owen G Davies, Richard L Williams, Thomas J Hall, Liam M Grover
A new bone augmenting material is reported, which is formed from calcium-loaded hydrogel-based spheres. On immersion of these spheres in a physiological medium, they become surrounded with a sheath of precipitate, which ruptures due to a build-up in osmotic pressure. This results in the formation of mineral tubes that protrude from the sphere surface. When brought into close contact with one another, these spheres become fused through the entanglement and subsequent interstitial mineralization of the mineral tubules...
January 11, 2018: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/29324704/dissection-of-myogenic-differentiation-signatures-in-chickens-by-rna-seq-analysis
#18
Tingting Li, Genxi Zhang, Pengfei Wu, Lian Duan, Guohui Li, Qiuhong Liu, Jinyu Wang
A series of elaborately regulated and orchestrated changes in gene expression profiles leads to muscle growth and development. In this study, RNA sequencing was used to profile embryonic chicken myoblasts and fused myotube transcriptomes, long non-coding RNAs (lncRNAs), and messenger RNAs (mRNAs) at four stages of myoblast differentiation. Of a total of 2484 lncRNA transcripts, 2288 were long intergenic non-coding RNAs (lincRNAs) and 198 were antisense lncRNAs. Additionally, 1530 lncRNAs were neighboring 2041 protein-coding genes (<10 kb upstream and downstream) and functionally enriched in several pathways related to skeletal muscle development that have been extensively studied, indicating that these genes may be in cis-regulatory relationships...
January 11, 2018: Genes
https://www.readbyqxmd.com/read/29323298/a-metabolic-function-of-fgfr3-tacc3-gene-fusions-in-cancer
#19
Véronique Frattini, Stefano M Pagnotta, Tala, Jerry J Fan, Marco V Russo, Sang Bae Lee, Luciano Garofano, Jing Zhang, Peiguo Shi, Genevieve Lewis, Heloise Sanson, Vanessa Frederick, Angelica M Castano, Luigi Cerulo, Delphine C M Rolland, Raghvendra Mall, Karima Mokhtari, Kojo S J Elenitoba-Johnson, Marc Sanson, Xi Huang, Michele Ceccarelli, Anna Lasorella, Antonio Iavarone
Chromosomal translocations that generate in-frame oncogenic gene fusions are notable examples of the success of targeted cancer therapies. We have previously described gene fusions of FGFR3-TACC3 (F3-T3) in 3% of human glioblastoma cases. Subsequent studies have reported similar frequencies of F3-T3 in many other cancers, indicating that F3-T3 is a commonly occuring fusion across all tumour types. F3-T3 fusions are potent oncogenes that confer sensitivity to FGFR inhibitors, but the downstream oncogenic signalling pathways remain unknown...
January 11, 2018: Nature
https://www.readbyqxmd.com/read/29323078/renal-cell-carcinoma-with-t-6-11-a-case-report-and-review-of-literature
#20
K S Jansi Prema, K S Devanathan, Anila Abraham Kurien
Renal cell carcinomas (RCCs) with t(6,11) are very rare tumours. Only a few cases have been reported so far. t(6,11) results in fusion of alpha gene and transcription factor EB (TFEB) gene resulting in the overexpression of TFEB. The specific light and immunohistochemical features help in the diagnosis of this rare type of tumor. We report a case of t(6,11) RCC in a 38-year-old female who was incidentally found to have a right renal mass. We present this case to emphasize the typical light microscopic picture of this extremely rare tumor...
October 2017: Indian Journal of Pathology & Microbiology
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