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Alternative splicing

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https://www.readbyqxmd.com/read/28943376/evolution-of-the-alternative-aqp2-gene-acquisition-of-a-novel-protein-coding-sequence-in-dolphins
#1
Takushi Kishida, Miwa Suzuki, Asuka Takayama
Taxon-specific de novo protein-coding sequences are thought to be important for taxon-specific environmental adaptation. A recent study revealed that bottlenose dolphins acquired a novel isoform of aquaporin 2 generated by alternative splicing (alternative AQP2), which helps dolphins to live in hyperosmotic seawater. The AQP2 gene consists of four exons, but the alternative AQP2 gene lacks the fourth exon and instead has a longer third exon that includes the original third exon and a part of the original third intron...
September 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28942992/a-new-drosophila-octopamine-receptor-responds-to-serotonin
#2
Yi-Xiang Qi, Gang Xu, Gui-Xiang Gu, Fen Mao, Gong-Yin Ye, Weiwei Liu, Jia Huang
As the counterparts of the vertebrate adrenergic transmitters, octopamine and tyramine are important physiological regulators in invertebrates. They control and modulate many physiological and behavioral functions in insects. In this study, we reported the pharmacological properties of a new α2-adrenergic-like octopamine receptor (CG18208) from Drosophila melanogaster, named DmOctα2R. This new receptor gene encodes two transcripts by alternative splicing. The long isoform DmOctα2R-L differs from the short isoform DmOctα2R-S by the presence of an additional 29 amino acids within the third intracellular loop...
September 21, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28942592/major-splice-variants-and-multiple-polyadenylation-site-utilization-in-mrnas-encoding-human-translation-initiation-factors-eif4e1-and-eif4e3-regulate-the-translational-regulators
#3
Silvia Mrvová, Klára Frydrýšková, Martin Pospíšek, Václav Vopálenský, Tomáš Mašek
Alternative polyadenylation is an important and pervasive mechanism that generates heterogeneous 3'-termini of mRNA and is considered an important regulator of gene expression. We performed bioinformatics analyses of ESTs and the 3'-UTRs of the main transcript splice variants of the translational initiation factor eIF4E1 and its family members, eIF4E2 and eIF4E3. This systematic analysis led to the prediction of new polyadenylation signals. All identified polyadenylation sites were subsequently verified by 3'RACE of transcripts isolated from human lymphoblastic cell lines...
September 23, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28942291/t-homoeolog-specific-plasma-membrane-protein-3-nt-t-pmp3-2-in-polyploid-nicotiana-tabacum-shows-conserved-alternative-splicing-derived-from-extant-nicotiana-tomentosiformis-parent
#4
Kumkum Kumari, Vidya Jegadeeson, S Suji, Gayatri Venkataraman, Ajay Parida
Abiotic stress induced plasma membrane protein 3 (PMP3) genes occur as multigene families in plants, coding for hydrophobic proteins. Group I PMP3s code for shorter ORFs while Group II PMP3s code for proteins with C-terminal extensions. Allotetraploid Nicotiana tabacum (SSTT; 2n = 48) derives its parentage from extant ancestors related to Nicotiana sylvestris (SS) and Nicotiana tomentosiformis (TT). Polyploidization triggers complex genetic and epigenetic changes, often leading to homoeolog-specific retention or loss of function, sub-functionalization or neo-functionalization...
September 18, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28941705/severe-dcm-phenotype-of-patient-harboring-rbm20-mutation-s635a-can-be-modeled-by-patient-specific-induced-pluripotent-stem-cell-derived-cardiomyocytes
#5
Katrin Streckfuss-Bömeke, Malte Tiburcy, Andrey Fomin, Xiaojing Luo, Wener Li, Claudia Fischer, Cemil Özcelik, Andreas Perrot, Samuel Sossalla, Jan Haas, Ramon Oliveira Vidal, Sabine Rebs, Sara Khadjeh, Benjamin Meder, Stefan Bonn, Wolfgang A Linke, Wolfram-Hubertus Zimmermann, Gerd Hasenfuss, Kaomei Guan
The ability to generate patient-specific induced pluripotent stem cells (iPSCs) provides a unique opportunity for modeling heart disease in vitro. In this study, we generated iPSCs from a patient with dilated cardiomyopathy (DCM) caused by a missense mutation S635A in RNA-binding motif protein 20 (RBM20) and investigated the functionality and cell biology of cardiomyocytes (CMs) derived from patient-specific iPSCs (RBM20-iPSCs). The RBM20-iPSC-CMs showed abnormal distribution of sarcomeric α-actinin and defective calcium handling compared to control-iPSC-CMs, suggesting disorganized myofilament structure and altered calcium machinery in CMs of the RBM20 patient...
September 20, 2017: Journal of Molecular and Cellular Cardiology
https://www.readbyqxmd.com/read/28941457/intracellular-localization-of-apoptotic-endonuclease-endog-and-splice-variants-of-telomerase-catalytic-subunit-htert
#6
D D Zhdanov, V S Pokrovsky, E V Orlova, V S Orlova, M V Pokrovskaya, S S Aleksandrova, N N Sokolov
The activity of telomerase catalytic subunit hTERT (human telomerase reverse transcriptase) can be regulated by alternative splicing of its mRNA. The mechanism of hTERT splicing is not understood in detail. Apoptotic endonuclease EndoG is known to participate in this process. In the present work, the intracellular colocalization and mRNA levels of EndoG and hTERT splice-variants in normal and apoptotic cancer cells were studied. We found that the development of apoptosis increased the expression of EndoG and changed the ratio of hTERT splice-variants, which decreased the telomerase activity in the cells...
August 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/28939666/the-e2a-splice-variant-e47-regulates-the-differentiation-of-projection-neurons-via-p57-kip2-during-cortical-development
#7
Sabrina Pfurr, Yu-Hsuan Chu, Christian Bohrer, Franziska Greulich, Robert Beattie, Könül Mammadzada, Miriam Hils, Sebastian J Arnold, Verdon Taylor, Kristina Schachtrup, N Henriette Uhlenhaut, Christian Schachtrup
During corticogenesis, distinct classes of neurons are born from progenitor cells located in the ventricular and subventricular zones, from where they migrate towards the pial surface to assemble into highly organized layer-specific circuits. However, the precise and coordinated transcriptional network activity defining neuronal identity is still not understood. Here, we show that genetic depletion of the basic helix-loop-helix (bHLH) transcription factor E2A splice variant E47 increased the number of Tbr1-positive deep layer and Satb2-positive upper layer neurons at E14...
September 22, 2017: Development
https://www.readbyqxmd.com/read/28939043/neuroligin-induced-presynaptic-differentiation-through-slm2-mediated-splicing-modifications-of-neurexin-in-cerebellar-cultures
#8
Yuji Sato, Satoko Suzuki, Yoko Iijima, Takatoshi Iijima
Neurexins (NRXs) and neuroligins (NLs) play important roles in synapse specification. The alternatively spliced segment 4 (AS4) of NRX genes (Nrxn) is a critical element in selective trans-synaptic interactions. However, the role of splicing of NRXs and NLs in synapse specification is not fully understood. To investigate the exact role of splice-dependent NRX-NL interaction in the specification of glutamatergic and gamma-aminobutyric acid (GABA)-ergic synapses in the cerebellum, we evaluated the synaptogenic receptor activity of NL1/2/3 isoforms in a neuron-fibroblast co-culture system, in which the Nrxn AS4 segments are manipulated using SLM2, a selective and dominant regulator of AS4 splicing...
September 19, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28938739/sequence-variants-of-khdrbs1-as-high-penetrance-susceptibility-risks-for-primary-ovarian-insufficiency-by-mis-regulating-mrna-alternative-splicing
#9
Binbin Wang, Lin Li, Ying Zhu, Wei Zhang, Xi Wang, Beili Chen, Tengyan Li, Hong Pan, Jing Wang, Kehkooi Kee, Yunxia Cao
STUDY QUESTION: Does a novel heterozygous KHDRBS1 variant, identified using whole-exome sequencing (WES) in two patients with primary ovarian insufficiency (POI) in a pedigree, cause defects in mRNA alternative splicing? SUMMARY ANSWER: The heterozygous variant of KHDRBS1 was confirmed to cause defects in alternative splicing of many genes involved in DNA replication and repair. WHAT IS KNOWN ALREADY: Studies in mice revealed that Khdrbs1 deficient females are subfertile, which manifests as delayed sexual maturity and significantly reduced numbers of secondary and pre-antral follicles...
October 1, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28938650/genomic-variants-link-to-hepatitis-c-racial-disparities
#10
Matthew M Yeh, Sarag Boukhar, Benjamin Roberts, Nairanjana Dasgupta, Sayed S Daoud
Chronic liver diseases are one of the major public health issues in United States, and there are substantial racial disparities in liver cancer-related mortality. We previously identified racially distinct alterations in the expression of transcripts and proteins of hepatitis C (HCV)-induced hepatocellular carcinoma (HCC) between Caucasian (CA) and African American (AA) subgroups. Here, we performed a comparative genome-wide analysis of normal vs. HCV+ (cirrhotic state), and normal adjacent tissues (HCCN) vs...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28937654/genome-wide-analysis-of-cca1-like-proteins-in-soybean-and-functional-characterization-of-gmmyb138a
#11
Shaomin Bian, Donghao Jin, Ruihua Li, Xin Xie, Guoli Gao, Weikang Sun, Yuejia Li, Lulu Zhai, Xuyan Li
Plant CIRCADIAN CLOCK ASSOCIATED1 (CCA1)-like proteins are a class of single-repeat MYELOBLASTOSIS ONCOGENE (MYB) transcription factors generally featured by a highly conserved motif SHAQK(Y/F)F, which play important roles in multiple biological processes. Soybean is an important grain legume for seed protein and edible vegetable oil. However, essential understandings regarding CCA1-like proteins are very limited in soybean. In this study, 54 CCA1-like proteins were identified by data mining of soybean genome...
September 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28935704/the-splicing-co-factor-barricade-tat-sf1-is-required-for-cell-cycle-and-lineage-progression-in-drosophila-neural-stem-cells
#12
Monika K Abramczuk, Thomas R Burkard, Vivien Rolland, Victoria Steinmann, Peter Duchek, Yanrui Jiang, Sebastian Wissel, Heinrich Reichert, Juergen A Knoblich
Stem cells need to balance self-renewal and differentiation for correct tissue development and homeostasis. Defects in this balance can lead to developmental defects or tumor formation. In recent years, mRNA splicing has emerged as one important mechanism regulating cell fate decisions. Here we address the role of the evolutionary conserved splicing co-factor Barricade (Barc)/Tat-SF1/CUS2 in Drosophila neural stem cell (neuroblast) lineage formation. We show that Barc is required for the generation of neurons during Drosophila brain development by ensuring correct neural progenitor proliferation and differentiation...
September 21, 2017: Development
https://www.readbyqxmd.com/read/28934506/clip-seq-analysis-of-multi-mapped-reads-discovers-novel-functional-rna-regulatory-sites-in-the-human-transcriptome
#13
Zijun Zhang, Yi Xing
Crosslinking or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-seq/RIP-seq reads are short, existing computational tools focus on uniquely mapped reads, while reads mapped to multiple loci are discarded. We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectation-maximization algorithm to assign multi-mapped reads and calls peaks combining uniquely and multi-mapped reads. To demonstrate the utility of CLAM, we applied it to a wide range of public CLIP-seq/RIP-seq datasets involving numerous splicing factors, microRNAs and m6A RNA methylation...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934498/widespread-intra-dependencies-in-the-removal-of-introns-from-human-transcripts
#14
Seong Won Kim, Allison J Taggart, Claire Heintzelman, Kamil J Cygan, Caitlin G Hull, Jing Wang, Barsha Shrestha, William G Fairbrother
Research into the problem of splice site selection has followed a reductionist approach focused on how individual splice sites are recognized. Early applications of information theory uncovered an inconsistency. Human splice signals do not contain enough information to explain the observed fidelity of splicing. Here, we conclude that introns do not necessarily contain 'missing' information but rather may require definition from neighboring processing events. For example, there are known cases where an intronic mutation disrupts the splicing of not only the local intron but also adjacent introns...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934490/number-of-inadvertent-rna-targets-for-morpholino-knockdown-in-danio-rerio-is-largely-underestimated-evidence-from-the-study-of-ser-arg-rich-splicing-factors
#15
Marine Joris, Marie Schloesser, Denis Baurain, Marc Hanikenne, Marc Muller, Patrick Motte
Although the involvement of Ser/Arg-rich (SR) proteins in RNA metabolism is well documented, their role in vertebrate development remains elusive. We, therefore, elected to take advantage of the zebrafish model organism to study the SR genes' functions using the splicing morpholino (sMO) microinjection and the programmable site-specific nucleases. Consistent with previous research, we revealed discrepancies between the mutant and morphant phenotypes and we show that these inconsistencies may result from a large number of unsuspected inadvertent morpholino RNA targets...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934393/neurofibromatosis-type-1-alternative-splicing-is-a-key-regulator-of-ras-erk-signaling-and-learning-behaviors-in-mice
#16
Hieu T Nguyen, Melissa N Hinman, Xuan Guo, Alok Sharma, Hiroyuki Arakawa, Guangbin Luo, Hua Lou
Appropriate activation of the Ras/extracellular signal-regulated kinase (ERK) protein signaling cascade within the brain is crucial for optimal learning and memory. One key regulator of this cascade is the Nf1 Ras GTPase activating protein (RasGAP), which attenuates Ras/ERK signaling by converting active Ras is bound to guanosine triphosphate, activating Ras into inactive Ras is bound to guanosine diphosphate, inactivating Ras. A previous study using embryonic stem cells and embryonic stem cell-derived neurons indicated that Nf1 RasGAP activity is modulated by the highly regulated alternative splicing of Nf1 exon 23a...
October 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28934368/a-single-danio-rerio-hars-gene-encodes-both-cytoplasmic-and-mitochondrial-histidyl-trna-synthetases
#17
Ashley L Waldron, Sara Helms Cahan, Christopher S Franklyn, Alicia M Ebert
Histidyl tRNA Synthetase (HARS) is a member of the aminoacyl tRNA synthetase (ARS) family of enzymes. This family of 20 enzymes is responsible for attaching specific amino acids to their cognate tRNA molecules, a critical step in protein synthesis. However, recent work highlighting a growing number of associations between ARS genes and diverse human diseases raises the possibility of new and unexpected functions in this ancient enzyme family. For example, mutations in HARS have been linked to two different neurological disorders, Usher Syndrome Type IIIB and Charcot Marie Tooth peripheral neuropathy...
2017: PloS One
https://www.readbyqxmd.com/read/28932105/changes-in-alternative-splicing-as-pharmacodynamic-markers-for-sudemycin-d6
#18
Morgan Thurman, Jacob van Doorn, Barbara Danzer, Thomas R Webb, Stefan Stamm
OBJECTIVE: The aim of the study was to define pharmacodynamic markers for sudemycin D6, an experimental cancer drug that changes alternative splicing in human blood. METHODS: Blood samples from 12 donors were incubated with sudemycin D6 for up to 24 hours, and at several time points total RNA from lymphocytes was prepared and the pre-messenger RNA (mRNA) splicing patterns were analyzed with reverse transcription-polymerase chain reaction. RESULTS: Similar to immortalized cells, blood lymphocytes change alternative splicing due to sudemycin D6 treatment...
2017: Biomarker Insights
https://www.readbyqxmd.com/read/28931466/1-alpha-25-dihydroxyvitamin-d3-up-regulates-the-expression-of-2-types-of-human-intestinal-alkaline-phosphatase-alternative-splicing-variants-in-caco-2-cells-and-may-be-an-important-regulator-of-their-expression-in-gut-homeostasis
#19
Seiko Noda, Asako Yamada, Kanae Nakaoka, Masae Goseki-Sone
Vitamin D insufficiency is associated with a greater risk of osteoporosis and also influences skeletal muscle functions, differentiation, and development. The principal function of vitamin D in calcium homeostasis is to increase the absorption of calcium from the intestine, and the level of alkaline phosphatase (ALP) activity, a differentiation marker for intestinal epithelial cells, is regulated by vitamin D. Intestinal-type ALP is expressed at a high concentration in the brush border membrane of intestinal epithelial cells, and is known to be affected by several kinds of nutrients...
August 4, 2017: Nutrition Research
https://www.readbyqxmd.com/read/28930565/role-of-fibroblast-growth-factor-receptor-2-splicing-in-normal-and-cancer-cells
#20
Toshiyuki Ishiwata
Types 1-4 of fibroblast growth factor receptors (FGFR) are all expressed in various cancers. Because of its prominent role in carcinogenesis and cancer progression, FGFR-2, is being considered as a novel target in cancer treatment. Owing to the alternative splicing of its extracellular domain, FGFR-2 exists in two variants: IIIb and IIIc. FGFR-2 IIIb is mainly expressed in normal epithelial cells, as well as in oral mucosal, esophageal, gastric, colorectal, pancreatic, pulmonary, breast, endometrial, cervical, and prostate cancers...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
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