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3' utr intron

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)...
September 23, 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...
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
Chengsheng Zhang, Chao Feng, Jing Wang, Fanyu Kong, Wenxiu Sun, Fenglong Wang
Polygalacturonase inhibiting proteins (PGIPs) are major defensive proteins produced by plant cell walls that play a crucial role in pathogen resistance by reducing polygalacturonase (PG) activity. In the present study, a novel PGIP gene was isolated from tobacco (Nicotiana tabacum), hereafter referred as NtPGIP. A full-length NtPGIP cDNA of 1,412 bp with a 186 bp 5'-untranslated region (UTR), and 209 bp 3'-UTR was cloned from tobacco, NtPGIP is predicted to encode a protein of 338 amino acids. The NtPGIP sequence from genomic DNA showed no introns and sequence alignments of NtPGIP's deduced amino acid sequence showed high homology with known PGIPs from other plant species...
May 2016: Heliyon
Xiaomeng Ma, Long Guan, Junli Xuan, Huihua Wang, Zehu Yuan, Mingming Wu, Ruizao Liu, Caiye Zhu, Caihong Wei, Fuping Zhao, Lixin Du, Li Zhang
Our previous genome-wide association study in sheep revealed that OAR3-84073899.1 (SNP31) in intron 8 of the CAMKMT gene was significantly associated with post-weaning gain at the genomic level. Herein, we performed a replication study to investigate single nucleotide polymorphisms (SNPs) within the CAMKMT gene exons, and 1000 bp of the 5'- and 3'-intranslated regions (UTRs) and their associations with growth traits in Ujumqin sheep. Five SNPs were identified through DNA pool sequencing technology: SNP26 in the 5'-UTR, SNP06 in exon 5, SNP07 in exon 8 and SNP27 and SNP28 in the 3'-UTR...
October 2016: Animal Genetics
Guang Yang, Hongqin Xu, Huiping Zhang, Qiong Yu, Yanhua Wu, Jieping Shi, Wenwang Rao, Yueyue You, Changgui Kou, Yaqin Yu
OBJECTIVE: The purpose of this study was to explore the association between single nucleotide polymorphisms (SNPs) in the phospholipase A2 (PLA2), group XIIA gene (PLA2G12A) and schizophrenia. METHODS: This study included 1,063 schizophrenia patients and 1,103 healthy controls from a Han Chinese Population in Northeast China. Four tagSNPs (rs11728699 in intron 1, synonymous rs2285714 in exon 3, rs3087494 in the 3' UTR, and rs7694620 in the downstream region) in PLA2G12A were selected, and they were genotyped by the MALDI-TOF-MS technology...
2016: PloS One
Namarta Kalia, Aarti Sharma, Manpreet Kaur, Sukhdev Singh Kamboj, Jatinder Singh
Mannose binding lectin (MBL) is a liver derived protein which plays an important role in innate immunity. Mannose binding lectin gene 2 (MBL2) polymorphisms are reported to be associated with various diseases. In spite of being exhaustively studied molecule, no attempt has been made till date to comprehensively and systematically analyze the SNPs of MBL2 gene. The present study was carried out to identify and prioritize the SNPs of MBL2 gene for further genotyping and functional studies. To predict the possible impact of SNPs on MBL structure and function SNP data obtained from dbSNP database were analyzed using various bioinformatics tools...
2016: SpringerPlus
Patricia Moreno, Esther Garcia-Rosado, Juan J Borrego, M Carmen Alonso
Fish interferons are cytokines involved in its resistance to viral infections by inducing the transcription of several interferon-induced genes, such as isg15. The aim of the present study was the genetic characterization of the European sea bass isg15 gene, describing the regulatory motifs found in its sequence. In addition, an in vivo analysis of transcription in response to betanodavirus (RGNNV genotype) and poly I:C has been performed. The analysis of the resulting sequences showed that sea bass isg15 gene is composed of two exons and a single 276-bp intron located at the 5'-UTR region...
August 2016: Fish & Shellfish Immunology
Cheng Guo, Matthew Spinelli, Man Liu, Qingshun Q Li, Chun Liang
Alternative polyadenylation has been recognized as a key contributor of gene expression regulation by generating different transcript isoforms with altered 3' ends. Although polyadenylation is well known for marking the end of a 3' UTR, an increasing number of studies have reported previously less-addressed polyadenylation events located in other parts of genes in many eukaryotic organisms. These other locations include 5' UTRs, introns and coding sequences (termed herein as non-3UTR), as well as antisense and intergenic polyadenlation...
2016: Scientific Reports
Chiung-Chyi Shen, Wen-Yu Cheng, Ming-Tsang Chiao, Yea-Jiuan Liang, Tsuo-Fei Mao, Bai-Shuan Liu
The expression levels of different vascular endothelial growth factor A (VEGF) isoforms are associated with the angiogenesis and the patient's prognoses in human cancers. Ribosomes specifically scan from 5' to 3' CUG initiation codon in the long 5'-untranslated region (5'-UTR) of the VEGF mRNA, resulting in the generation of high mol wt VEGF isoform [call large VEGF (L-VEGF)]. Alternative splicing of VEGF mRNA transcripts results in several isoforms with distinct properties that are dependent up their exon compositions...
2016: Current Neurovascular Research
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