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https://www.readbyqxmd.com/read/28327570/puf60-variants-cause-a-syndrome-of-id-short-stature-microcephaly-coloboma-craniofacial-cardiac-renal-and-spinal-features
#1
Karen J Low, Morad Ansari, Rami Abou Jamra, Angus Clarke, Salima El Chehadeh, David R FitzPatrick, Mark Greenslade, Alex Henderson, Jane Hurst, Kory Keller, Paul Kuentz, Trine Prescott, Franziska Roessler, Kaja K Selmer, Michael C Schneider, Fiona Stewart, Katrina Tatton-Brown, Julien Thevenon, Magnus D Vigeland, Julie Vogt, Marjolaine Willems, Jonathan Zonana, D D D Study, Sarah F Smithson
PUF60 encodes a nucleic acid-binding protein, a component of multimeric complexes regulating RNA splicing and transcription. In 2013, patients with microdeletions of chromosome 8q24.3 including PUF60 were found to have developmental delay, microcephaly, craniofacial, renal and cardiac defects. Very similar phenotypes have been described in six patients with variants in PUF60, suggesting that it underlies the syndrome. We report 12 additional patients with PUF60 variants who were ascertained using exome sequencing: six through the Deciphering Developmental Disorders Study and six through similar projects...
March 22, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28325844/the-sole-lsm-complex-in-cyanidioschyzon-merolae-associates-with-pre-mrna-splicing-and-mrna-degradation-factors
#2
Kirsten A Reimer, Martha R Stark, Lisbeth Carolina Aguilar, Sierra R Stark, Robert D Burke, Jack Moore, Richard P Fahlman, Calvin K Yip, Haruko Kuroiwa, Marlene Oeffinger, Stephen D Rader
Proteins of the Sm and Sm-like (LSm) families, referred to collectively as (L)Sm proteins, are found in all three domains of life, and are known to promote a variety of RNA processes such as base-pair formation, unwinding, RNA degradation, and RNA stabilization. In eukaryotes, (L)Sm proteins have been studied, inter alia, for their role in pre-mRNA splicing. In many organisms, the LSm proteins form two distinct complexes, one consisting of LSm1-7 that is involved in mRNA degradation in the cytoplasm, and the other consisting of LSm2-8 that binds spliceosomal U6 snRNA in the nucleus...
March 21, 2017: RNA
https://www.readbyqxmd.com/read/28302904/pharmacological-inhibition-of-the-spliceosome-subunit-sf3b-triggers-ejc-independent-nmd
#3
Teresa Carvalho, Sandra Martins, José Rino, Sérgio Marinho, Maria Carmo-Fonseca
Spliceostatin A, meayamycin, and pladienolide B are small molecules that target the SF3b subunit of spliceosomal U2 snRNP. These compounds are attracting much attention as tools to manipulate splicing and potential anti-cancer drugs. We investigated the effects of these inhibitors on mRNA transport and stability in human cells. Upon splicing inhibition unspliced pre-mRNAs accumulated in the nucleus, particularly within enlarged nuclear speckles. Yet, a small fraction of the pre-mRNA molecules were exported to the cytoplasm...
March 16, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28300534/identification-of-a-small-molecule-inhibitor-that-stalls-splicing-at-an-early-step-of-spliceosome-activation
#4
Anzhalika Sidarovich, Cindy L Will, Maria M Anokhina, Javier Ceballos, Sonja Sievers, Dmitry E Agafonov, Timur Samatov, Penghui Bao, Berthold Kastner, Henning Urlaub, Herbert Waldmann, Reinhard Lührmann
Small molecule inhibitors of pre-mRNA splicing are important tools for identifying new spliceosome assembly intermediates, allowing a finer dissection of spliceosome dynamics and function. Here, we identified a small molecule that inhibits human pre-mRNA splicing at an intermediate stage during conversion of pre-catalytic spliceosomal B complexes into activated B(act) complexes. Characterization of the stalled complexes (designated B(028)) revealed that U4/U6 snRNP proteins are released during activation before the U6 Lsm and B-specific proteins, and before recruitment and/or stable incorporation of Prp19/CDC5L complex and other B(act) complex proteins...
March 16, 2017: ELife
https://www.readbyqxmd.com/read/28296713/whole-exome-sequencing-identifies-recurrent-sf3b1-r625-mutation-and-comutation-of-nf1-and-kit-in-mucosal-melanoma
#5
Jennifer D Hintzsche, Nicholas T Gorden, Carol M Amato, Jihye Kim, Kelsey E Wuensch, Steven E Robinson, Allison J Applegate, Kasey L Couts, Theresa M Medina, Keith R Wells, Joshua A Wisell, Martin D McCarter, Neil F Box, Yiqun G Shellman, Rene C Gonzalez, Karl D Lewis, John J Tentler, Aik Choon Tan, William A Robinson
Mucosal melanomas are a rare subtype of melanoma, arising in mucosal tissues, which have a very poor prognosis due to the lack of effective targeted therapies. This study aimed to better understand the molecular landscape of these cancers and find potential new therapeutic targets. Whole-exome sequencing was performed on mucosal melanomas from 19 patients and 135 sun-exposed cutaneous melanomas, with matched peripheral blood samples when available. Mutational profiles were compared between mucosal subgroups and sun-exposed cutaneous melanomas...
March 14, 2017: Melanoma Research
https://www.readbyqxmd.com/read/28296343/a-genome-wide-sirna-screen-for-regulators-of-tumor-suppressor-p53-activity-in-human-non-small-lung-cancer-cells-identifies-components-of-the-rna-splicing-machinery-as-targets-for-anticancer-treatment
#6
Ellen Siebring-van Olst, Maxime Blijlevens, Renee X de Menezes, Ida H van der Meulen-Muileman, Egbert F Smit, Victor W van Beusechem
Reinstating wild-type tumor suppressor p53 activity could be a valuable option for the treatment of cancer. To contribute to development of new treatment options for non-small cell lung cancer (NSCLC), we performed genome-wide siRNA screens for determinants of p53 activity in NSCLC cells. We identified many genes not previously known to be involved in regulating p53 activity. Silencing p53 pathway inhibitor genes was associated with loss of cell viability. The largest functional gene cluster influencing p53 activity was mRNA splicing...
March 13, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28285769/mutations-in-the-spliceosome-component-cwc27-cause-retinal-degeneration-with-or-without-additional-developmental-anomalies
#7
Mingchu Xu, Yajing Angela Xie, Hana Abouzeid, Christopher T Gordon, Alessia Fiorentino, Zixi Sun, Anna Lehman, Ihab S Osman, Rachayata Dharmat, Rosa Riveiro-Alvarez, Linda Bapst-Wicht, Darwin Babino, Gavin Arno, Virginia Busetto, Li Zhao, Hui Li, Miguel A Lopez-Martinez, Liliana F Azevedo, Laurence Hubert, Nikolas Pontikos, Aiden Eblimit, Isabel Lorda-Sanchez, Valeria Kheir, Vincent Plagnol, Myriam Oufadem, Zachry T Soens, Lizhu Yang, Christine Bole-Feysot, Rolph Pfundt, Nathalie Allaman-Pillet, Patrick Nitschké, Michael E Cheetham, Stanislas Lyonnet, Smriti A Agrawal, Huajin Li, Gaëtan Pinton, Michel Michaelides, Claude Besmond, Yumei Li, Zhisheng Yuan, Johannes von Lintig, Andrew R Webster, Hervé Le Hir, Peter Stoilov, Jeanne Amiel, Alison J Hardcastle, Carmen Ayuso, Ruifang Sui, Rui Chen, Rando Allikmets, Daniel F Schorderet
Pre-mRNA splicing factors play a fundamental role in regulating transcript diversity both temporally and spatially. Genetic defects in several spliceosome components have been linked to a set of non-overlapping spliceosomopathy phenotypes in humans, among which skeletal developmental defects and non-syndromic retinitis pigmentosa (RP) are frequent findings. Here we report that defects in spliceosome-associated protein CWC27 are associated with a spectrum of disease phenotypes ranging from isolated RP to severe syndromic forms...
March 6, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28276456/principal-components-analysis-based-unsupervised-feature-extraction-applied-to-gene-expression-analysis-of-blood-from-dengue-haemorrhagic-fever-patients
#8
Y-H Taguchi
Dengue haemorrhagic fever (DHF) sometimes occurs after recovery from the disease caused by Dengue virus (DENV), and is often fatal. However, the mechanism of DHF has not been determined, possibly because no suitable methodologies are available to analyse this disease. Therefore, more innovative methods are required to analyse the gene expression profiles of DENV-infected patients. Principal components analysis (PCA)-based unsupervised feature extraction (FE) was applied to the gene expression profiles of DENV-infected patients, and an integrated analysis of two independent data sets identified 46 genes as critical for DHF progression...
March 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28273088/depletion-of-arabidopsis-sc35-and-sc35-like-serine-arginine-rich-proteins-affects-the-transcription-and-splicing-of-a-subset-of-genes
#9
Qingqing Yan, Xi Xia, Zhenfei Sun, Yuda Fang
Serine/arginine-rich (SR) proteins are important splicing factors which play significant roles in spliceosome assembly and splicing regulation. However, little is known regarding their biological functions in plants. Here, we analyzed the phenotypes of mutants upon depleting different subfamilies of Arabidopsis SR proteins. We found that loss of the functions of SC35 and SC35-like (SCL) proteins cause pleiotropic changes in plant morphology and development, including serrated leaves, late flowering, shorter roots and abnormal silique phyllotaxy...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28263986/tdrd6-mediates-early-steps-of-spliceosome-maturation-in-primary-spermatocytes
#10
Müge Akpınar, Mathias Lesche, Grigorios Fanourgakis, Jun Fu, Konstantinos Anasstasiadis, Andreas Dahl, Rolf Jessberger
Tudor containing protein 6 (TDRD6) is a male germ line-specific protein essential for chromatoid body (ChB) structure, elongated spermatid development and male fertility. Here we show that in meiotic prophase I spermatocytes TDRD6 interacts with the key protein arginine methyl transferase PRMT5, which supports splicing. TDRD6 also associates with spliceosomal core protein SmB in the absence of RNA and in an arginine methylation dependent manner. In Tdrd6-/- diplotene spermatocytes PRMT5 association with SmB and arginine dimethylation of SmB are much reduced...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28258160/a-new-cis-acting-motif-is-required-for-the-axonal-smn-dependent-anxa2-mrna-localization
#11
Khalil Rihan, Etienne Antoine, Thomas Maurin, Barbara Bardoni, Rémy Bordonné, Johann Soret, Florence Rage
Spinal muscular atrophy (SMA) is caused by mutations and/or deletions of the survival motor neuron gene (SMN1). Besides its function in the biogenesis of spliceosomal snRNPs, SMN might possess a motor neuron specific role and could function in the transport of axonal mRNAs and in the modulation of local protein translation. Accordingly, SMN colocalizes with axonal mRNAs of differentiated NSC-34 motor neuron-like cells. We recently showed that SMN depletion gives rise to a decrease in the axonal transport of the mRNAs encoding Annexin A2 (Anxa2)...
March 3, 2017: RNA
https://www.readbyqxmd.com/read/28257432/alternate-splicing-of-transcripts-shape-macrophage-response-to-mycobacterium-tuberculosis-infection
#12
Haroon Kalam, Mary F Fontana, Dhiraj Kumar
Transcriptional reprogramming of macrophages upon Mycobacterium tuberculosis (Mtb) infection is widely studied; however, the significance of alternate splicing (AS) in shaping cellular responses to mycobacterial infections is not yet appreciated. Alternate splicing can influence transcript stability or structure, function and localization of corresponding proteins thereby altering protein stoichiometry and physiological consequences. Using comprehensive analysis of a time-series RNA-seq data obtained from human macrophages infected with virulent or avirulent strains of Mtb, we show extensive remodeling of alternate splicing in macrophage transcriptome...
March 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28255022/molecular-features-of-early-onset-adult-myelodysplastic-syndrome
#13
Cassandra M Hirsch, Bartlomiej P Przychodzen, Tomas Radivoyevitch, Bhumika Patel, Swapna Thota, Michael J Clemente, Yasunobu Nagata, Thomas LaFramboise, Hetty Carraway, Aziz Nazha, Mikkael A Sekeres, Hideki Makishima, Jaroslaw P Maciejewski
Myelodysplastic syndromes are typically diseases of older adults. Early onset patients may have distinct molecular and clinical features or reflect a demographic continuum. The identification of differences between early onset patients and those diagnosed at a traditional age has the potential to advance understanding of the pathogenesis of myelodysplasia and may lead to formation of distinct morphologic subcategories. We studied a cohort of 634 patients with various subcategories of myelodysplastic syndrome and secondary acute myeloid leukemia, stratifying based on age at presentation and clinical parameters...
March 2, 2017: Haematologica
https://www.readbyqxmd.com/read/28254838/the-7sk-snrnp-associates-with-the-little-elongation-complex-to-promote-snrna-gene-expression
#14
Sylvain Egloff, Patrice Vitali, Michael Tellier, Raoul Raffel, Shona Murphy, Tamás Kiss
The 7SK small nuclear RNP (snRNP), composed of the 7SK small nuclear RNA (snRNA), MePCE, and Larp7, regulates the mRNA elongation capacity of RNA polymerase II (RNAPII) through controlling the nuclear activity of positive transcription elongation factor b (P-TEFb). Here, we demonstrate that the human 7SK snRNP also functions as a canonical transcription factor that, in collaboration with the little elongation complex (LEC) comprising ELL, Ice1, Ice2, and ZC3H8, promotes transcription of RNAPII-specific spliceosomal snRNA and small nucleolar RNA (snoRNA) genes...
March 2, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28250049/diabetic-polyneuropathy-sensory-neurons-nuclear-structure-and-spliceosome-alterations-a-role-for-cwc22
#15
Masaki Kobayashi, Ambika Chandrasekhar, Chu Cheng, Jose A Martinez, Hilarie Ng, Cristiane de la Hoz, Douglas W Zochodne
Unique deficits in the function of adult sensory neurons as part of their early neurodegeneration might account for progressive polyneuropathy during chronic diabetes mellitus. Here, we provide structural and functional evidence for aberrant pre-mRNA splicing in a chronic type 1 model of experimental diabetic polyneuropathy (DPN). Cajal bodies (CBs), unique nuclear substructures involved in RNA splicing, increased in number in diabetic sensory neurons, but their expected colocalization with survival motor neuron (SMN) proteins was reduced - a mislocalization described in motor neurons of spinal muscular atrophy...
March 1, 2017: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28246447/transcriptomic-comparison-of-primary-bovine-horn-core-carcinoma-culture-and-parental-tissue-at-early-stage
#16
Sharadindu Shil, R S Joshi, C G Joshi, A K Patel, Ravi K Shah, Namrata Patel, Subhash J Jakhesara, Sumana Kundu, Bhaskar Reddy, P G Koringa, D N Rank
AIM: Squamous cell carcinoma or SCC of horn in bovines (bovine horn core carcinoma) frequently observed in Bos indicus affecting almost 1% of cattle population. Freshly isolated primary epithelial cells may be closely related to the malignant epithelial cells of the tumor. Comparison of gene expression in between horn's SCC tissue and its early passage primary culture using next generation sequencing was the aim of this study. MATERIALS AND METHODS: Whole transcriptome sequencing of horn's SCC tissue and its early passage cells using Ion Torrent PGM were done...
January 2017: Veterinary World
https://www.readbyqxmd.com/read/28242684/aberrant-splicing-in-maize-rough-endosperm3-reveals-a-conserved-role-for-u12-splicing-in-eukaryotic-multicellular-development
#17
Christine M Gault, Federico Martin, Wenbin Mei, Fang Bai, Joseph B Black, W Brad Barbazuk, A Mark Settles
RNA splicing of U12-type introns functions in human cell differentiation, but it is not known whether this class of introns has a similar role in plants. The maize ROUGH ENDOSPERM3 (RGH3) protein is orthologous to the human splicing factor, ZRSR2. ZRSR2 mutations are associated with myelodysplastic syndrome (MDS) and cause U12 splicing defects. Maize rgh3 mutants have aberrant endosperm cell differentiation and proliferation. We found that most U12-type introns are retained or misspliced in rgh3 Genes affected in rgh3 and ZRSR2 mutants identify cell cycle and protein glycosylation as common pathways disrupted...
February 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28222521/the-effects-of-lw-afc-on-the-hippocampal-transcriptome-in-senescence-accelerated-mouse-prone-8-strain-a-mouse-model-of-alzheimer-s-disease
#18
Jianhui Wang, Yang Liu, Xiaorui Cheng, Xiaorui Zhang, Feng Liu, Gang Liu, Shanyi Qiao, Ming Ni, Wenxia Zhou, Yongxiang Zhang, Fei Li
The senescence-accelerated mouse prone 8 (SAMP8) strain is considered a robust experimental model for developing preventative and therapeutic treatments for Alzheimer's disease (AD), a neurodegenerative disease which cannot be effectively prevented, halted, or cured. Our previous studies showed that LW-AFC, a new formula derived from the classical traditional Chinese medicinal prescription Liuwei Dihuang decoction, ameliorates cognitive deterioration in PrP-hAβPPswe/PS1ΔE9 transgenic mice and SAMP8 mice. This study aims to investigate the mechanism that mediates how LW-AFC improves cognitive deficit on the basis of the transcriptome...
2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28222336/a-two-step-approach-for-sequencing-spliceosome-related-genes-as-a-complementary-diagnostic-assay-in-mds-patients-with-ringed-sideroblasts
#19
Kamila Janusz, Mónica Del Rey, María Abáigar, Rosa Collado, David Ivars, María Hernández-Sánchez, Alberto Valiente, Cristina Robledo, Rocío Benito, María Díez-Campelo, Fernando Ramos, Alexander Kohlmann, Consuelo Del Cañizo, Jesús María Hernández-Rivas
Our study aimed to analyze the presence of mutations in SF3B1 and other spliceosome-related genes in myelodysplastic syndromes with ringed sideroblasts (MDS-RS) by combining conventional Sanger and next-generation sequencing (NGS) methods, and to determine the feasibility of this approach in a clinical setting. 122 bone marrow samples from MDS-RS patients were studied. Initially, exons 14 and 15 of the SF3B1 gene were analyzed by Sanger sequencing. Secondly, they were studied by NGS covering besides SF3B1, SRSF2, U2AF1 and ZRSR2 genes...
February 4, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28217959/anti-rnpc3-antibodies-as-a-marker-of-cancer-associated-scleroderma
#20
Ami A Shah, George Xu, Antony Rosen, Laura K Hummers, Fredrick M Wigley, Stephen J Elledge, Livia Casciola-Rosen
INTRODUCTION: Prior studies have demonstrated an increased risk of cancer-associated scleroderma in patients with RNA polymerase III (POL) autoantibodies and in patients negative for anti-centromere (CENP), anti-topoisomerase-1 (TOPO), and anti-POL antibodies (referred to as CENP/TOPO/POL (CTP)-Negative). In a recent study of 16 CTP-negative scleroderma patients with coincident cancer, we found that 25% had autoantibodies to RNPC3, a member of the minor spliceosome complex. In this investigation, we validated the relationship between anti-RNPC3 antibodies and cancer and examined the associated clinical phenotype in a large sample of scleroderma patients...
February 19, 2017: Arthritis & Rheumatology
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