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polypyrimidine tract

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https://www.readbyqxmd.com/read/29752441/ptbp3-contributes-to-the-metastasis-of-gastric-cancer-by-mediating-cav1-alternative-splicing
#1
Xin Liang, Weixia Chen, Haiyang Shi, Xiangyu Gu, Yueqi Li, Yingxue Qi, Ke Xu, Aiguang Zhao, Jianwen Liu
Polypyrimidine tract-binding protein 3 (PTBP3) is an essential RNA-binding protein with roles in RNA splicing, 3' end processing and translation. Although increasing evidence implicates PTBP3 in several cancers, its role in gastric cancer metastasis remains poorly explored. In this study, we found that PTBP3 was upregulated in the gastric cancer tissues of patients with lymph node metastasis. Patients with high PTBP3 expression levels had significantly shorter survival than those with low PTBP3 expression. Overexpression/knockdown of PTBP3 expression had no effect on proliferation, whereas it regulated migration and invasion in vitro...
May 11, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29748555/ptbp1-enhances-mir-101-guided-ago2-targeting-to-mcl1-and-promotes-mir-101-induced-apoptosis
#2
Jia Cui, William J Placzek
Myeloid cell leukemia 1 (MCL1) is a key anti-apoptotic protein belonging to the BCL-2 protein family. To preserve normal cellular homeostasis, cells must maintain strict control over MCL1 expression. Overexpression of MCL1 has been identified as a key contributor to tumorigenesis, and further enables resistance to a number of anti-cancer chemotherapies. Thus, there is an ongoing interest to develop selective MCL1 inhibitors. In order to better target MCL1, it is essential to understand the molecular mechanisms that regulate MCL1 expression in cells...
May 10, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29709556/goldclip-gel-omitted-ligation-dependent-clip
#3
Jiaqi Gu, Ming Wang, Yang Yang, Ding Qiu, Yiqun Zhang, Jinbiao Ma, Yu Zhou, Gregory J Hannon, Yang Yu
Protein-RNA interaction networks are essential to understand gene regulation control. Identifying binding sites of RNA-binding proteins (RBPs) by the UV-crosslinking and immunoprecipitation (CLIP) represents one of the most powerful methods to map protein-RNA interactions in vivo. However, the traditional CLIP protocol is technically challenging, which requires radioactive labeling and suffers from material loss during PAGE-membrane transfer procedures. Here we introduce a super-efficient CLIP method (GoldCLIP) that omits all gel purification steps...
April 27, 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29695138/organ-specific-micrornas-mir122-137-and-206-contribute-to-tissue-characteristics-and-carcinogenesis-by-regulating-pyruvate-kinase-m1-2-pkm-expression
#4
Kohei Taniguchi, Nobuhiko Sugito, Haruka Shinohara, Yuki Kuranaga, Yosuke Inomata, Kazumasa Komura, Kazuhisa Uchiyama, Yukihiro Akao
Pyruvate kinase is known as the glycolytic enzyme catalyzing the final step in glycolysis. In mammals, two different forms of it exist, i.e., pyruvate kinase M1/2 ( PKM ) and pyruvate kinase L/R ( PKLR ). Also, PKM has two isoforms, i.e., PKM1 and PKM2 . These genes have tissue-specific distribution. Namely, PKM1 is distributed in high-energy-demanding organs, such as brain and muscle. Also, PKM2 is distributed in various other organs, such as the colon. On the other hand, PKLR is distributed in liver and red blood cells (RBCs)...
April 24, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29592812/discovery-of-physiological-and-cancer-related-regulators-of-3-utr-processing-with-kapac
#5
Andreas J Gruber, Ralf Schmidt, Souvik Ghosh, Georges Martin, Andreas R Gruber, Erik van Nimwegen, Mihaela Zavolan
3' Untranslated regions (3' UTRs) length is regulated in relation to cellular state. To uncover key regulators of poly(A) site use in specific conditions, we have developed PAQR, a method for quantifying poly(A) site use from RNA sequencing data and KAPAC, an approach that infers activities of oligomeric sequence motifs on poly(A) site choice. Application of PAQR and KAPAC to RNA sequencing data from normal and tumor tissue samples uncovers motifs that can explain changes in cleavage and polyadenylation in specific cancers...
March 28, 2018: Genome Biology
https://www.readbyqxmd.com/read/29512730/ptbp1-knockdown-in-renal-cell-carcinoma-inhibits-cell-migration-invasion-and-angiogenesis-in-vitro-and-metastasis-in-vivo-via-the-hypoxia-inducible-factor-1%C3%AE-pathway
#6
Haixia Shan, Pingfu Hou, Meng Zhang, Liantao Li, Yu Pan, Fang Chen, Tao Jiang, Jin Bai, Junnian Zheng
Polypyrimidine tract-binding protein 1 (PTBP1), a heterogeneous nuclear ribonucleoprotein, is a multi-functional RNA-binding protein. PTBP1 participates in a number of biological processes, including maintaining cell structure and motility, immunity, protein metabolism and the cell cycle. The present study aimed to investigate the association between PTBP1 expression and the prognosis and clinicopathological characteristics of patients with renal cell cancer (RCC). The potential mechanism of action of PTBP1 in the metastasis of RCC was also investigated...
March 2, 2018: International Journal of Oncology
https://www.readbyqxmd.com/read/29415650/conservation-of-polypyrimidine-tract-binding-proteins-and-their-putative-target-rnas-in-several-storage-root-crops
#7
Kirtikumar R Kondhare, Amit Kumar, David J Hannapel, Anjan K Banerjee
BACKGROUND: Polypyrimidine-tract binding proteins (PTBs) are ubiquitous RNA-binding proteins in plants and animals that play diverse role in RNA metabolic processes. PTB proteins bind to target RNAs through motifs rich in cytosine/uracil residues to fine-tune transcript metabolism. Among tuber and root crops, potato has been widely studied to understand the mobile signals that activate tuber development. Potato PTBs, designated as StPTB1 and StPTB6, function in a long-distance transport system by binding to specific mRNAs (StBEL5 and POTH1) to stabilize them and facilitate their movement from leaf to stolon, the site of tuber induction, where they activate tuber and root growth...
February 7, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29415469/circsmarca5-inhibits-migration-of-glioblastoma-multiforme-cells-by-regulating-a-molecular-axis-involving-splicing-factors-srsf1-srsf3-ptb
#8
Davide Barbagallo, Angela Caponnetto, Matilde Cirnigliaro, Duilia Brex, Cristina Barbagallo, Floriana D'Angeli, Antonio Morrone, Rosario Caltabiano, Giuseppe Maria Barbagallo, Marco Ragusa, Cinzia Di Pietro, Thomas Birkballe Hansen, Michele Purrello
Circular RNAs (circRNAs) have recently emerged as a new class of RNAs, highly enriched in the brain and very stable within cells, exosomes and body fluids. To analyze their involvement in glioblastoma multiforme (GBM) pathogenesis, we assayed the expression of twelve circRNAs, physiologically enriched in several regions of the brain, through real-time PCR in a cohort of fifty-six GBM patient biopsies and seven normal brain parenchymas. We focused on hsa_circ_0001445 (circSMARCA5): it was significantly downregulated in GBM biopsies as compared to normal brain tissues ( p -value < 0...
February 6, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29373718/the-aberrant-splicing-of-baf45d-links-splicing-regulation-and-transcription-in-glioblastoma
#9
Guillermo Aldave, Marisol Gonzalez-Huarriz, Angel Rubio, Juan Pablo Romero, Datta Ravi, Belén Miñana, Mar Cuadrado-Tejedor, Ana García-Osta, Roeland Verhaak, Enric Xipell, Naiara Martinez-Vélez, Arlet Acanda de la Rocha, Montserrat Puigdelloses, Marc García-Moure, Miguel Marigil, Jaime Gállego Pérez-Larraya, Oskar Marín-Bejar, Maite Huarte, Maria Stella Carro, Roberto Ferrarese, Cristobal Belda-Iniesta, Angel Ayuso, Ricardo Prat-Acín, Fernando Pastor, Ricardo Díez-Valle, Sonia Tejada, Marta M Alonso
Background: Glioblastoma, the most aggressive primary brain tumor, is a genetically heterogeneous tumor. Alternative spicing (AS) plays a key role in numerous pathologies, including cancer. The objective of our study was to determine whether aberrant AS could play a role in the malignant phenotype of glioma and to understand the mechanism underlying its aberrant regulation. Methods: We obtained surgical samples from patients with glioblastoma who underwent 5-aminolevulinic fluorescence-guided surgery...
January 24, 2018: Neuro-oncology
https://www.readbyqxmd.com/read/29346433/vault-rnas-partially-induces-drug-resistance-of-human-tumor-cells-mcf-7-by-binding-to-the-rna-dna-binding-protein-psf-and-inducing-oncogene-gage6
#10
Jianjun Chen, Hui OuYang, Xuemei An, Shixi Liu
BACKGROUND: Vault is the largest nonicosahedral cytosolic nucleoprotein particle, which is widely involved in induction of chemoresistance and lead to failure in long-term chemotherapy. Vault contains three different major vault proteins (MVPs) and four vault RNAs paralogues (vtRNAs, vtRNA1-1, vtRNA1-2, vtRNA1-3 and vtRNA2-1). Disruption of the MVPs do not induce hypersensitivity while expression of vtRNAs contributes to cells' drug resistance, indicates that vtRNAs, but not MVPs play an important role in causing drug resistance...
2018: PloS One
https://www.readbyqxmd.com/read/29235465/molecular-basis-of-differential-3-splice-site-sensitivity-to-anti-tumor-drugs-targeting-u2-snrnp
#11
Luisa Vigevani, André Gohr, Thomas Webb, Manuel Irimia, Juan Valcárcel
Several splicing-modulating compounds, including Sudemycins and Spliceostatin A, display anti-tumor properties. Combining transcriptome, bioinformatic and mutagenesis analyses, we delineate sequence determinants of the differential sensitivity of 3' splice sites to these drugs. Sequences 5' from the branch point (BP) region strongly influence drug sensitivity, with additional functional BPs reducing, and BP-like sequences allowing, drug responses. Drug-induced retained introns are typically shorter, displaying higher GC content and weaker polypyrimidine-tracts and BPs...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29219070/predicting-human-splicing-branchpoints-by-combining-sequence-derived-features-and-multi-label-learning-methods
#12
Wen Zhang, Xiaopeng Zhu, Yu Fu, Junko Tsuji, Zhiping Weng
BACKGROUND: Alternative splicing is the critical process in a single gene coding, which removes introns and joins exons, and splicing branchpoints are indicators for the alternative splicing. Wet experiments have identified a great number of human splicing branchpoints, but many branchpoints are still unknown. In order to guide wet experiments, we develop computational methods to predict human splicing branchpoints. RESULTS: Considering the fact that an intron may have multiple branchpoints, we transform the branchpoint prediction as the multi-label learning problem, and attempt to predict branchpoint sites from intron sequences...
December 1, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29187406/ptbp3-mediated-regulation-of-zeb1-mrna-stability-promotes-epithelial-mesenchymal-transition-in-breast-cancer
#13
Pingfu Hou, Lin Li, Fang Chen, Yansu Chen, Hui Liu, Jingjing Li, Jin Bai, Junnian Zheng
The RNA polypyrimidine tract-binding protein PTBP3 is a little studied paralog of PTBP1, which has oncogenic properties. In this study, we demonstrate that PTBP3 induces epithelial-mesenchymal transition (EMT) in breast tumor cells and promotes their invasive growth and metastasis. Elevated expression of PTBP3 associated significantly with lymph node metastasis, advanced histology grade, TNM stage, and poor 5-year overall survival of patients. In human mammary epithelial cells, PTBP3 overexpression was sufficient to induce EMT and to enhance cell migration, invasion, and cancer stem-like cell properties...
January 15, 2018: Cancer Research
https://www.readbyqxmd.com/read/29186814/alternative-splicing-of-l-type-ca-v-1-2-calcium-channels-implications-in-cardiovascular-diseases
#14
REVIEW
Zhenyu Hu, Mui Cheng Liang, Tuck Wah Soong
L-type Cav1.2 calcium channels are the major pathway for Ca2+ influx to initiate the contraction of smooth and cardiac muscles. Alteration of Cav1.2 channel function has been implicated in multiple cardiovascular diseases, such as hypertension and cardiac hypertrophy. Alternative splicing is a post-transcriptional mechanism that expands Cav1.2 channel structures to modify function, pharmacological and biophysical property such as calcium/voltage-dependent inactivation (C/VDI), or to influence its post-translational modulation by interacting proteins such as Galectin-1...
November 24, 2017: Genes
https://www.readbyqxmd.com/read/29147905/transcriptional-regulation-of-dj-1
#15
Kazuko Takahashi-Niki, Takeshi Niki, Sanae M M Iguchi-Ariga, Hiroyoshi Ariga
DJ-1 is an oncogene and also a causative gene for familial Parkinson's disease. DJ-1 has various functions, and the oxidative status of a cysteine residue at position 106 (C106) is crucial for determination of the activation level of DJ-1.DJ-1 binds to many proteins, including various transcription factors, and acts as a coactivator or corepressor for regulating their target genes without direct binding to DNA, thereby affecting various cell functions. DJ-1-regulating transcription factors and their modified proteins are the androgen receptor and its regulatory proteins, p53; polypyrimidine tract-binding protein-associated splicing factor (PSF); Keap1, an inhibitor for nuclear factor erythroid2-related factor 2 (Nrf2); sterol regulatory element-binding protein (SREBP); Ras-responsive element-binding protein (RREB1); signal transducer and activator of transcription 1 (STAT1); and Nurr1...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29140550/lncrna-h19-interacts-with-polypyrimidine-tract-binding-protein-1-to-reprogram-hepatic-lipid-homeostasis
#16
Chune Liu, Zhihong Yang, Jianguo Wu, Li Zhang, Sangmin Lee, Dong-Ju Shin, Melanie Tran, Li Wang
H19 is an imprinted long non-coding RNA abundantly expressed in embryonic liver and repressed after birth. Here we show that H19 serves as a lipid sensor by synergizing with RNA-binding protein PTBP1 to modulate hepatic metabolic homeostasis. H19RNA interacts with PTBP1 to facilitate its association with SREBP1c mRNA and protein, leading to increased stability and nuclear transcriptional activity. H19 and PTBP1 are upregulated by fatty acids in hepatocytes and in diet-induced fatty liver, which further augments lipid accumulation...
November 15, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/29045475/association-between-rna-binding-protein-ptbp2-and-germ-cell-injury-in-an-experimentally-induced-unilateral-cryptorchidism-murine-model
#17
Xianming Dou, Jingjing Gao, Pan Gao, Dongdong Tang, Dangwei Peng, Jun Mao, Zhenyu Huang, Peng Chen, He Chen, Shengwei Ke, Chaozhao Liang, Xiansheng Zhang
RNA binding protein polypyrimidine tract binding protein 2 (Ptbp2) as a key alternative splicing regulator for male germ cell development is well established. However, its expression levels and role in cryptorchidism testes tissues has not been explored. Additionally, the molecular mechanism of heat stress impacts the correct proliferation and differentiation of germ cells is unclear. To investigate whether changes in Ptbp2 expression are correlated with heat stress-induced germ cell injury in testicular tissue, we used a murine model of intraperitoneal cryptorchidism with surgical operation...
2017: PloS One
https://www.readbyqxmd.com/read/29034946/spin-labelling-for-integrative-structure-modelling-a-case-study-of-the-polypyrimidine-tract-binding-protein-1-domains-in-complexes-with-short-rnas
#18
Christoph Gmeiner, Georg Dorn, Frédéric H T Allain, Gunnar Jeschke, Maxim Yulikov
A combined method, employing NMR and EPR spectroscopies, has demonstrated its strength in solving structures of protein/RNA and other types of biomolecular complexes. This method works particularly well when the large biomolecular complex consists of a limited number of rigid building blocks, such as RNA-binding protein domains (RBDs). A variety of spin labels is available for such studies, allowing for conventional as well as spectroscopically orthogonal double electron-electron resonance (DEER) measurements in EPR...
October 25, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28993438/architecture-and-distribution-of-introns-in-core-genes-of-four-fusarium-species
#19
Mmatshepho M Phasha, Brenda D Wingfield, Martin P A Coetzee, Quentin C Santana, Gerda Fourie, Emma T Steenkamp
Removal of introns from transcribed RNA represents a crucial step during the production of mRNA in eukaryotes. Available whole-genome sequences and expressed sequence tags (ESTs) have increased our knowledge of this process and revealed various commonalities among eukaryotes. However, certain aspects of intron structure and diversity are taxon-specific, which can complicate the accuracy of in silico gene prediction methods. Using core genes, we evaluated the distribution and architecture of Fusarium circinatum spliceosomal introns, and linked these characteristics to the accuracy of the predicted gene models of the genome of this fungus...
November 6, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28981396/cancer-specific-energy-metabolism-in-rhabdomyosarcoma-cells-is-regulated-by-microrna
#20
Nobuhiko Sugito, Kohei Taniguchi, Yuki Kuranaga, Maki Ohishi, Tomoyoshi Soga, Yuko Ito, Mitsuru Miyachi, Ken Kikuchi, Hajime Hosoi, Yukihiro Akao
Rhabdomyosarcoma (RMS) is a soft tissue sarcoma and is most frequently found in children. In RMS, there are two major subtypes, that is, embryonal RMS and alveolar RMS (ARMS). ARMS has exclusively the worse prognosis and is caused by formation of the chimeric PAX3-FOXO1 gene. Regarding cancer, the Warburg effect is known as a feature of cancer-specific metabolism. Polypyrimidine tract-binding protein 1 (PTBP1), a splicer of pyruvate kinase muscle (PKM) mRNA, is a positive regulator of cancer-specific energy metabolism...
December 2017: Nucleic Acid Therapeutics
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