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3' utr intron

Subhajit Giri, Tufan Naiya, Zaffar Equbal, Charulata Savant Sankhla, Shyamal Kumar Das, Kunal Ray, Jharna Ray
BACKGROUND: Primary Dystonia is a common movement disorder manifested by dystonic symptoms only. DYT6, a major genetic factor, plays a significant role in primary pure dystonia pathogenesis. In this study we analyzed THAP1 (DYT 6) gene in primary pure dystonia patients, which has been widely studied in other populations but not in Indians. METHODS: The study cohort contained 227 index primary pure dystonia patients with the involvement of cervical region and 254 neurologically control individuals collected from East Indian population...
November 29, 2016: Neuroscience Letters
Raffaele Ferrari, Yunpeng Wang, Jana Vandrovcova, Sebastian Guelfi, Aree Witeolar, Celeste M Karch, Andrew J Schork, Chun C Fan, James B Brewer, Parastoo Momeni, Gerard S Schellenberg, William P Dillon, Leo P Sugrue, Christopher P Hess, Jennifer S Yokoyama, Luke W Bonham, Gil D Rabinovici, Bruce L Miller, Ole A Andreassen, Anders M Dale, John Hardy, Rahul S Desikan
BACKGROUND: Clinical, pathological and genetic overlap between sporadic frontotemporal dementia (FTD), Alzheimer's disease (AD) and Parkinson's disease (PD) has been suggested; however, the relationship between these disorders is still not well understood. Here we evaluated genetic overlap between FTD, AD and PD to assess shared pathobiology and identify novel genetic variants associated with increased risk for FTD. METHODS: Summary statistics were obtained from the International FTD Genomics Consortium, International PD Genetics Consortium and International Genomics of AD Project (n>75 000 cases and controls)...
November 29, 2016: Journal of Neurology, Neurosurgery, and Psychiatry
Martino Colombo, Evangelos D Karousis, Joël Bourquin, Rémy Bruggmann, Oliver Mühlemann
Besides degrading aberrant mRNAs that harbor a premature translation termination codon (PTC), nonsense-mediated mRNA decay (NMD) also targets many seemingly "normal" mRNAs that encode for full-length proteins. To identify a bona fide set of such endogenous NMD targets in human cells, we applied a meta-analysis approach in which we combined transcriptome profiling of knockdowns and rescues of the three NMD factors UPF1, SMG6 and SMG7. We provide evidence that this combinatorial approach identifies NMD-targeted transcripts more reliably than previous attempts that focused on inactivation of single NMD factors...
November 18, 2016: RNA
David K Kranzhöfer, Ralf Gilsbach, Björn A Grüning, Rolf Backofen, Thomas G Nührenberg, Lutz Hein
BACKGROUND: Cardiomyocytes undergo major changes in DNA methylation during maturation and transition to a non-proliferative state after birth. 5'-hydroxylation of methylated cytosines (5hmC) is not only involved in DNA loss of CpG methylation but is also thought to be an epigenetic mark with unique distribution and functions. Here, we sought to get insight into the dynamics of 5'-hydroxymethylcytosine in newborn and adult cardiomyocytes. METHODS: Cardiomyocyte nuclei from newborn and adult C57BL/6 mice were purified by flow cytometric sorting...
2016: PloS One
Weiqian Yan, Beisha Tang, Xiaoxia Zhou, Lifang Lei, Kai Li, Qiying Sun, Qian Xu, Xinxiang Yan, Jifeng Guo, Zhenhua Liu
Mutations in TMEM230 were identified as a genetic factor for Parkinson's disease (PD) with typical clinical symptoms and Lewy bodies in a North American population, and a highly prevalent TMEM230 mutation, c.550_552delTAGinsCCCGGG (p.*184ProGlyext*5), was found in 7 Chinese families. In the present study, we investigated the prevalence of TMEM230 mutations in a large cohort of Chinese PD patients and healthy controls individuals from mainland China. We sequenced all exons and exon-intron boundaries of TMEM230 in Chinese Han population including 1235 patients with PD and 1252 healthy control individuals...
October 11, 2016: Neurobiology of Aging
Yuxin Yin, James H Lan, David Nguyen, Nicole Valenzuela, Ping Takemura, Yung-Tsi Bolon, Brianna Springer, Katsuyuki Saito, Ying Zheng, Tim Hague, Agnes Pasztor, Gyorgy Horvath, Krisztina Rigo, Elaine F Reed, Qiuheng Zhang
BACKGROUND: Unambiguous HLA typing is important in hematopoietic stem cell transplantation (HSCT), HLA disease association studies, and solid organ transplantation. However, current molecular typing methods only interrogate the antigen recognition site (ARS) of HLA genes, resulting in many cis-trans ambiguities that require additional typing methods to resolve. Here we report high-resolution HLA typing of 10,063 National Marrow Donor Program (NMDP) registry donors using long-range PCR by next generation sequencing (NGS) approach on buccal swab DNA...
2016: PloS One
Chen Yang, Jing Ye, Xiumei Li, Xiaoxiao Gao, Kaifa Zhang, Lei Luo, Jianping Ding, Yunhai Zhang, Yunsheng Li, Hongguo Cao, Yinghui Ling, Xiaorong Zhang, Ya Liu, Fugui Fang
Female pubertal development is tightly controlled by complex mechanisms, including neuroendocrine and epigenetic regulatory pathways. Specific gene expression patterns can be influenced by DNA methylation changes in the hypothalamus, which can in turn regulate timing of puberty onset. In order to understand the relationship between DNA methylation changes and gene expression patterns in the hypothalamus of pubertal goats, whole-genome bisulfite sequencing and RNA-sequencing analyses were carried out. There was a decline in DNA methylation levels in the hypothalamus during puberty and 268 differentially methylated regions (DMR) in the genome, with differential patterns in different gene regions...
2016: PloS One
Gesine Lühken, Stefan Krebs, Sophie Rothammer, Julia Küpper, Boro Mioč, Ingolf Russ, Ivica Medugorac
BACKGROUND: The mode of inheritance of horn status in sheep is far more complex than a superficial analysis might suggest. Observations, which were mostly based on crossbreeding experiments, indicated that the allele that results in horns is dominant in males and recessive in females, and some authors even speculated about the involvement of more than two alleles. However, all recent genome-wide association analyses point towards a very strong effect of a single autosomal locus on ovine chromosome 10, which was narrowed down to a putatively causal insertion polymorphism in the 3'-untranslated region of the relaxin/insulin-like family peptide receptor 2 gene (RXFP2)...
October 19, 2016: Genetics, Selection, Evolution: GSE
Sujata Chakraborty, Matteo Vatta, Linda L Bachinski, Ralf Krahe, Stephen Dlouhy, Shaochun Bai
Myotonic dystrophy types 1 (DM1) and 2 (DM2) are autosomal dominant, microsatellite repeat expansion disorders that affect muscle function. Myotonic dystrophy type 1 is caused by CTG repeat expansion in the 3' UTR region of the DMPK gene. Patients with DM2 have expansion of CCTG repeats in intron 1 of the CNBP gene. In this unit, we review and discuss the clinical phenotypes, genetic mutations causing the diseases, and the molecular diagnostic approaches and tools that are used to determine repeat sizes in DM1/2...
October 11, 2016: Current Protocols in Human Genetics
Kensuke Ninomiya, Mutsuhito Ohno, Naoyuki Kataoka
Localization of mRNA in neuronal cells is a critical process for spatiotemporal regulation of gene expression. Cytoplasmic localization of mRNA is often conferred by transport elements in 3' untranslated region (UTR). Activity-regulated cytoskeleton-associated protein (arc) mRNA is one of the localizing mRNAs in neuronal cells, and its localization is mediated by dendritic targeting element (DTE). As arc mRNA has introns in its 3' UTR, it was thought that arc mRNA is a natural target of nonsense-mediated mRNA decay (NMD)...
November 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Mengmeng Lu, Konstantin V Krutovsky, C Dana Nelson, Tomasz E Koralewski, Thomas D Byram, Carol A Loopstra
BACKGROUND: Loblolly pine (Pinus taeda L.) is one of the most widely planted and commercially important forest tree species in the USA and worldwide, and is an object of intense genomic research. However, whole genome resequencing in loblolly pine is hampered by its large size and complexity and a lack of a good reference. As a valid and more feasible alternative, entire exome sequencing was hence employed to identify the gene-associated single nucleotide polymorphisms (SNPs) and to genotype the sampled trees...
September 13, 2016: BMC Genomics
Kshitij Srivastava, Eunah Lee, Eric Owens, Pairaya Rujirojindakul, Willy A Flegel
BACKGROUND: Scianna (SC) blood group system comprises two antithetical antigens, Sc1 and Sc2, and five additional antigens. The antigens reside on a glycoprotein encoded by the erythroblast membrane-associated protein (ERMAP) gene. For the common ERMAP alleles, we determined the full-length nucleotide sequence that encodes the Scianna glycoprotein. STUDY DESIGN AND METHODS: Blood donor samples from five populations were analyzed including 20 African Americans, 10 Caucasians, 10 Thai, five Asians, and five Hispanics for a total of 100 chromosomes...
September 9, 2016: Transfusion
Alejandra Young, Uma Dandekar, Calvin Pan, Avery Sader, Jie J Zheng, Richard A Lewis, Debora B Farber
Ocular albinism type 1 (OA), caused by mutations in the OA1 gene, encodes a G-protein coupled receptor, OA1, localized in melanosomal membranes of the retinal pigment epithelium (RPE). This disorder is characterized by both RPE macro-melanosomes and abnormal decussation of ganglion cell axons at the brain's optic chiasm. We demonstrated previously that Oa1 specifically activates Gαi3, which also signals in the Oa1 transduction pathway that regulates melanosomal biogenesis. In this study, we screened the human Gαi3 gene, GNAI3, in DNA samples from 26 patients who had all clinical characteristics of OA but in whom a specific mutation in the OA1 gene had not been found, and in 6 normal control individuals...
2016: PloS One
Chul H Kim, Eun K Lee, Yoen J Choi, Hye J An, Hyung O Chung, Dae E Park, Byung C Ghim, Byung P Yu, Jong Bhak, Hae Y Chung
DNA methylation plays major roles in many biological processes, including aging, carcinogenesis, and development. Analyses of DNA methylation using next-generation sequencing offer a new way to profile and compare methylomes across the genome in the context of aging. We explored genomewide DNA methylation and the effects of short-term calorie restriction (CR) on the methylome of aged rat kidney. Whole-genome methylation of kidney in young (6 months old), old (25 months old), and OCR (old with 4-week, short-term CR) rats was analyzed by methylated DNA immunoprecipitation and next-generation sequencing (MeDIP-Seq)...
August 25, 2016: Aging Cell
Nicolau Brito da Cunha, Aulus Estevão Anjos de Deus Barbosa, Renato Goulart de Almeida, William Farias Porto, Mariana Rocha Maximiano, Luana Cristina Silva Álvares, Cassia Beatriz Rodrigues Munhoz, Chesterton Ulysses Orlando Eugênio, Antônio Américo Barbosa Viana, Octavio Luiz Franco, Simoni Campos Dias
Cyclotides are multifunctional plant cyclic peptides containing 28-37 amino acid residues and a pattern of three disulfide bridges, forming a motif known as the cyclic cystine knot. Due to their high biotechnological potential, the sequencing and characterization of cyclotide genes are crucial not only for cloning and establishing heterologous expression strategies, but also to understand local plant evolution in the context of host-pathogen relationships. Here, two species from the Brazilian Cerrado, Palicourea rigida (Rubiaceae) and Pombalia lanata (A...
August 23, 2016: Biopolymers
B L Huang, X K Zhang, Y Y Li, D Y Li, M Y Ma, D T Cai, W H Wu, B Q Huang
Eruca vesicaria subsp sativa is one of the most tolerant Cruciferae species to drought, and dehydration-responsive element-binding protein 2A (DREB2A) is involved in responses to salinity, heat, and particularly drought. In this study, a gene encoding EvDREB2A was cloned and characterized in E. vesicaria subsp sativa. The full-length EvDREB2A cDNA sequence contained a 388-bp 5'-untranslated region (UTR), a 348-bp 3'-UTR, and a 1002-bp open reading frame that encoded 334 amino acid residues. The theoretical isoelectric point of the EvDREB2A protein was 4...
2016: Genetics and Molecular Research: GMR
Aiti Vizzini, Angela Bonura, Valeria Longo, Maria Antonietta Sanfratello, Daniela Parrinello, Matteo Cammarata, Paolo Colombo
The diversification of cellular functions is one of the major characteristics of multicellular organisms which allow cells to modulate their gene expression, leading to the formation of transcripts and proteins with different functions and concentrations in response to different stimuli. CAP genes represent a widespread family of proteins belonging to the cysteine-rich secretory protein, antigen 5 and pathogenesis-related 1 superfamily which, it has been proposed, play key roles in the infection process and the modulation of immune responses in host animals...
September 2016: Molecular Immunology
Jianquan Guo, Yu Mei, Kai Li, Xuemei Huang, Huanjie Yang
Celastrol has potential application for the treatment of prostate cancer. However it causes autophagy as a protective response in prostate and other types of cancers, thus unveiling the underlying mechanisms may benefit its future application. In the present study, we demonstrate that the miR-17-92a cluster plays a negative role in celastrol induced-autophagy. Dissection of miR-17-92a cluster revealed the role of miR-17 seed family (miR-20a and miR-17) in autophagy inhibition in the context of prostate cancer cells...
September 16, 2016: Biochemical and Biophysical Research Communications
Katharina Ilm, Steffen Fuchs, Giridhar Mudduluru, Ulrike Stein
Metastasis is a multistep molecular network process, which is lethal for more than 90% of the cancer patients. Understanding the regulatory functions of metastasis-inducing molecules is in high demand for improved therapeutic cancer approaches. Thus, we studied the post-transcriptional regulation of the crucial carcinogenic and metastasis-mediating molecule metastasis associated in colon cancer 1 (MACC1). In silico analysis revealed MACC1 as a potential target of miR-218, a tumor suppressor miRNA. Expression of these two molecules inversely correlated in colorectal cancer (CRC) cell lines...
July 23, 2016: Oncotarget
Di Wang, Shaowu Li, Jingzhuang Zhao, Hongbai Liu, Tongyan Lu, Jiasheng Yin
Hepcidin, an antimicrobial peptide, plays a crucial role in innate immune system of teleost fish. As a cysteine-rich peptide, hepcidin possesses a dual function including iron regulation and innate immunity. In the present study, a full-length hepcidin cDNA (HtHep) was cloned and characterized by RT-PCR and RACE techniques from taimen (Hucho taimen, Pallas), which is a type of rare, precious and cold-water fish species in China. The cDNA contains an open reading frame (ORF) of 267 bp encoding 88 amino acid (aa), with 170 bp located in the 5(') untranslated region (UTR) and 151 bp in the 3' UTR...
September 2016: Fish & Shellfish Immunology
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