19,625 results match your criteria function protein-coding


LINC00857 promotes cell proliferation and migration in colorectal cancer by interacting with YTHDC1 and stabilizing SLC7A5.

Oncol Lett 2021 Aug 2;22(2):578. Epub 2021 Jun 2.

Department of Gastrointestinal Surgery, Chenzhou No. 1 People's Hospital, Chenzhou, Hunan 423000, P.R. China.

Colorectal cancer (CRC) is one of the most lethal malignances in humans. Hence, it is of great significance to identify regulatory molecules in CRC progression. Accumulating evidence has demonstrated that long non-coding RNAs (lncRNAs) are involved in cancer malignancy. Read More

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Gene Instability-Related lncRNA Prognostic Model of Melanoma Patients via Machine Learning Strategy.

J Oncol 2021 25;2021:5582920. Epub 2021 May 25.

Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, Liaoning, China.

Background: Melanoma is a common tumor characterized by a high mortality rate in its late stage. After metastasis, current treatment methods are relatively ineffective. Many studies have shown that long noncoding RNA (lncRNA) may participate in gene mutation and genomic instability in cancer. Read More

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Functional examination of lncRNAs in allotetraploid Gossypium hirsutum.

BMC Genomics 2021 Jun 13;22(1):443. Epub 2021 Jun 13.

College of Agriculture and Biotechnology, Zhejiang University, 210058, Hangzhou, Zhejiang, China.

Background: An evolutionary model using diploid and allotetraploid cotton species identified 80 % of non-coding transcripts in allotetraploid cotton as being uniquely activated in comparison with its diploid ancestors. The function of the lncRNAs activated in allotetraploid cotton remain largely unknown.

Results: We employed transcriptome analysis to examine the relationship between the lncRNAs and mRNAs of protein coding genes (PCGs) in cotton leaf tissue under abiotic stresses. Read More

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Assessment of a complete and classified platelet proteome from genome-wide transcripts of human platelets and megakaryocytes covering platelet functions.

Sci Rep 2021 Jun 11;11(1):12358. Epub 2021 Jun 11.

Department of Biochemistry, CARIM, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.

Novel platelet and megakaryocyte transcriptome analysis allows prediction of the full or theoretical proteome of a representative human platelet. Here, we integrated the established platelet proteomes from six cohorts of healthy subjects, encompassing 5.2 k proteins, with two novel genome-wide transcriptomes (57. Read More

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Serotonin transporter untranslated regions influence mRNA abundance and protein expression.

Gene Rep 2020 Mar 29;18. Epub 2019 Oct 29.

Division of Gastroenterology & Hepatology, University of Illinois at Chicago, Chicago, IL, United States of America.

The serotonin transporter (SERT, SLC6A4) is a Na-dependent transporter that regulates the availability of serotonin (5-HT, 5-hydroxytryptamine), a key neurotransmitter and hormone in the brain and the intestine. The human SERT gene consists of two alternate promoters that drive expression of an identical SERT protein. However, there are different mRNA transcript variants derived from these two promoters that differ in their 5' untranslated region (5'UTR), which is the region of the mRNA upstream from the protein-coding region. Read More

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The impact of codon choice on translation process in Saccharomyces cerevisiae: folding class, protein function and secondary structure.

Authors:
Daniele Santoni

J Theor Biol 2021 Jun 7;526:110806. Epub 2021 Jun 7.

Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council of Italy, Via dei Taurini 19, Rome 00185, Italy. Electronic address:

The genetic code consists in a set of rules used by living organisms to translate genomic information, contained in genes, into proteins; every amino acid is coded by a set of nucleotide triplets or codons. We refer to codon choice as the choice of a given codon, among the synonymous available ones, to code a given amino acid occurrence. The aim of this work is to shed light on the pivotal role that codon choice plays in regulating the timing of translation process, through patterns of low and high translation efficiency codons. Read More

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Global investigation of estrogen-responsive genes regulating lipid metabolism in the liver of laying hens.

BMC Genomics 2021 Jun 9;22(1):428. Epub 2021 Jun 9.

College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.

Background: Estrogen plays an essential role in female development and reproductive function. In chickens, estrogen is critical for lipid metabolism in the liver. The regulatory molecular network of estrogen in chicken liver is poorly understood. Read More

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LINC01116 boosts the progression of pituitary adenoma via regulating miR-744-5p/HOXB8 pathway.

Mol Cell Endocrinol 2021 Jun 4:111350. Epub 2021 Jun 4.

Neurosurgery Department, the Third Affiliated Hospital of Sun Yat-sen University, No.600 Tianhe Road, Guangzhou, 510630, Guangdong, China. Electronic address:

Pituitary adenoma (PA) is one of the common intracranial tumors. In order to optimize status quo, seeking out potential biomarkers for pituitary adenoma diagnosis and treatment is urgent and important. Long non-coding RNAs (lncRNAs) have been related with progression of various cancers. Read More

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Annotation of snoRNA abundance across human tissues reveals complex snoRNA-host gene relationships.

Genome Biol 2021 Jun 4;22(1):172. Epub 2021 Jun 4.

Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4 K8, Canada.

Background: Small nucleolar RNAs (snoRNAs) are mid-size non-coding RNAs required for ribosomal RNA modification, implying a ubiquitous tissue distribution linked to ribosome synthesis. However, increasing numbers of studies identify extra-ribosomal roles of snoRNAs in modulating gene expression, suggesting more complex snoRNA abundance patterns. Therefore, there is a great need for mapping the snoRNome in different human tissues as the blueprint for snoRNA functions. Read More

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Tensin 1 (TNS1) is a modifier gene for low body mass index (BMI) in homozygous [F508del]CFTR patients.

Physiol Rep 2021 Jun;9(11):e14886

The Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.

Cystic fibrosis (CF) is a life-limiting autosomal recessive genetic disease caused by variants in the CFTR gene, most commonly by the [F508del] variant. Although CF is a classical Mendelian disease, genetic variants in several modifier genes have been associated with variation of the clinical phenotype for pulmonary and gastrointestinal function and urogenital development. We hypothesized that whole genome sequencing of a well-phenotyped CF populations might identify novel variants in known, or hitherto unknown, modifier genes. Read More

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A systematic review of long non-coding RNAs with a potential role in breast cancer.

Mutat Res 2021 Jan-Jun;787:108375. Epub 2021 Apr 16.

BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia; Core Member of UNSW Data Science Hub, The University of New South Wales (UNSW Sydney), Sydney, NSW, 2052, Australia; Health Data Analytics Program Leader, AI-enabled Processes (AIP) Research Centre, Macquarie University, Sydney, 2109, Australia. Electronic address:

The human transcriptome contains many non-coding RNAs (ncRNAs), which play important roles in gene regulation. Long noncoding RNAs (lncRNAs) are an important class of ncRNAs with lengths between 200 and 200,000 bases. Unlike mRNA, lncRNA lacks protein-coding features, specifically, open-reading frames, and start and stop codons. Read More

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Transcriptome wide analysis of long non-coding RNA-associated ceRNA regulatory circuits in psoriasis.

J Cell Mol Med 2021 Jun 2. Epub 2021 Jun 2.

Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China.

Long non-coding RNAs (lncRNAs) play critical roles in regulating immune-associated diseases and chronic inflammatory disorders. Here, we found that lncRNAs involve in the pathogenesis of psoriasis through integrative analysis of RNA-seq data sets from a psoriasis cohort. Then, lncRNA-protein-coding genes (PCGs) co-expression network analysis demonstrated that lncRNAs extensively interact with IFN-γ signalling pathway-associated genes. Read More

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Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation.

BMC Genomics 2021 Jun 2;22(1):403. Epub 2021 Jun 2.

Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea.

Background: The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of 16 strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that help it to survive in the cold environment. Read More

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Amplified Fragments of an Autosome-Borne Gene Constitute a Significant Component of the W Sex Chromosome of (Reptilia, Lacertidae).

Genes (Basel) 2021 May 20;12(5). Epub 2021 May 20.

Institute of Molecular and Cellular Biology SB RAS, Acad. Lavrentiev Ave. 8/2, 630090 Novosibirsk, Russia.

Heteromorphic W and Y sex chromosomes often experience gene loss and heterochromatinization, which is frequently viewed as their "degeneration". However, the evolutionary trajectories of the heterochromosomes are in fact more complex since they may not only lose but also acquire new sequences. Previously, we found that the heterochromatic W chromosome of a lizard (Lacertidae) is decondensed and thus transcriptionally active during the lampbrush stage. Read More

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Genome-Wide Identification of Barley Long Noncoding RNAs and Analysis of Their Regulatory Interactions during Shoot and Grain Development.

Int J Mol Sci 2021 May 11;22(10). Epub 2021 May 11.

Department of Functional Genomics, Plant Breeding and Acclimatization Institute-National Research Institute, 05-870 Błonie, Radzików, Poland.

Long noncoding RNAs (lncRNAs) are a class of RNA molecules with gene regulatory functions in plant development and the stress response. Although the number of lncRNAs identified in plants is rapidly increasing, very little is known about their role in barley development. In this study, we performed global identification of barley lncRNAs based on 53 RNAseq libraries derived from nine different barley tissues and organs. Read More

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Comparative analysis of de novo genomes reveals dynamic intra-species divergence of NLRs in pepper.

BMC Plant Biol 2021 May 31;21(1):247. Epub 2021 May 31.

Plant Immunity Research Center, Plant Genomics and Breeding Institute, Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.

Background: Peppers (Capsicum annuum L.) containing distinct capsaicinoids are the most widely cultivated spices in the world. However, extreme genomic diversity among species represents an obstacle to breeding pepper. Read More

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The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions.

BMC Plant Biol 2021 May 31;21(1):248. Epub 2021 May 31.

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization At College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Background: Paphiopedilum is the largest genus of slipper orchids. Previous studies showed that the phylogenetic relationships of this genus are not well resolved, and sparse taxon sampling documented inverted repeat (IR) expansion and small single copy (SSC) contraction of the chloroplast genomes of Paphiopedilum.

Results: Here, we sequenced, assembled, and annotated 77 plastomes of Paphiopedilum species (size range of 152,130 - 164,092 bp). Read More

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The holobiont transcriptome of teneral tsetse fly species of varying vector competence.

BMC Genomics 2021 May 31;22(1):400. Epub 2021 May 31.

Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, 26505, USA.

Background: Tsetse flies are the obligate vectors of African trypanosomes, which cause Human and Animal African Trypanosomiasis. Teneral flies (newly eclosed adults) are especially susceptible to parasite establishment and development, yet our understanding of why remains fragmentary. The tsetse gut microbiome is dominated by two Gammaproteobacteria, an essential and ancient mutualist Wigglesworthia glossinidia and a commensal Sodalis glossinidius. Read More

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First Complete Mitochondrial Genome of a Tanaidacean Crustacean ().

Zoolog Sci 2021 Jun;38(3):267-272

Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa 277-8564, Japan.

We present a complete mitochondrial genomic sequence for the tanaidacean (Richardson, 1899); this is the first complete mitogenome reported from the order Tanaidacea. The mitogenome is 13,988 bp long and contains 13 protein coding and two ribosomal RNA genes (as is typical for animal mitogenomes), and 21 of 22 transfer RNAs; we did not detect an isoleucine transfer RNA (trnI) gene. The gene order differed markedly from the hypothetical ground pattern for Pancrustacea; only four clusters (trnM + nad2; trnC + trnY + cox1 + trnL2 + cox2; trnD + atp8 + atp6 + cox3; trnH + nad4 + nad4l) ancestrally present were retained. Read More

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The Role of Long Non-coding RNAs in Sepsis-Induced Cardiac Dysfunction.

Front Cardiovasc Med 2021 10;8:684348. Epub 2021 May 10.

Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China.

Sepsis is a syndrome with life-threatening organ dysfunction induced by a dysregulated host response to infection. The heart is one of the most commonly involved organs during sepsis, and cardiac dysfunction, which is usually indicative of an extremely poor clinical outcome, is a leading cause of death in septic cases. Despite substantial improvements in the understanding of the mechanisms that contribute to the origin and responses to sepsis, the prognosis of sepsis-induced cardiac dysfunction (SICD) remains poor and its molecular pathophysiological changes are not well-characterized. Read More

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Long Noncoding RNA LINC01410 Suppresses Tumorigenesis and Enhances Radiosensitivity in Neuroblastoma Cells Through Regulating miR-545-3p/HK2 Axis.

Onco Targets Ther 2021 18;14:3225-3238. Epub 2021 May 18.

Department of Laboratory, People's Hospital of Rizhao, Rizhao, 276800, Shandong, People's Republic of China.

Background: Abnormal expression of long noncoding RNAs (lncRNAs) was often involved in tumorigenesis and radiosensitivity of various cancers. The aim of this study was to explore the biological function and regulatory mechanism of lncRNA long intergenic non-protein coding RNA 1410 (LINC01410) in tumorigenesis and radiosensitivity of neuroblastoma (NB).

Methods: The expression of LINC01410, microRNA-329-3p (miR-545-3p) and hexokinase 2 (HK2) was detected by quantitative real-time polymerase chain reaction (qRT-PCR). Read More

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Identification of novel variants and the genotype-phenotype relationship in patients with Okur-Chung neurodevelopmental syndrome: a case report and systematic literature review.

J Int Med Res 2021 May;49(5):3000605211017063

Department of Children's Neuroendocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University Guangzhou, P. R. China.

germline variants of the casein kinase 2α subunit (CK2α) gene () have been reported in individuals with the congenital neuropsychiatric disorder Okur-Chung neurodevelopmental syndrome (OCNS). Here, we report on two unrelated children with OCNS and review the literature to explore the genotype-phenotype relationship in OCNS. Both children showed facial dysmorphism, growth retardation, and neuropsychiatric disorders. Read More

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RiceLncPedia: a comprehensive database of rice long non-coding RNAs.

Plant Biotechnol J 2021 May 26. Epub 2021 May 26.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.

Long noncoding RNAs (lncRNAs) are referred as RNA molecules with length of at least 200 nucleotides (nt) and usually have low protein-coding potential (Chekanova 2015). In plants, emerging evidences indicate that lncRNAs function as key modulators in development and stress response at the epigenetic, transcriptional and post-transcriptional levels (Chekanova 2015; Lucero et al. 2021). Read More

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Genetic associations for two biological age measures point to distinct aging phenotypes.

Aging Cell 2021 06 26;20(6):e13376. Epub 2021 May 26.

Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA.

Biological age measures outperform chronological age in predicting various aging outcomes, yet little is known regarding genetic predisposition. We performed genome-wide association scans of two age-adjusted biological age measures (PhenoAgeAcceleration and BioAgeAcceleration), estimated from clinical biochemistry markers (Levine et al., 2018; Levine, 2013) in European-descent participants from UK Biobank. Read More

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LINC00997/miR-574-3p/CUL2 promotes cervical cancer development via the MAPK signaling.

Mol Cell Biol 2021 May 24. Epub 2021 May 24.

Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, China.

Cervical cancer (CC) is a common gynecological malignancy with high morbidity and mortality. Mounting evidence has highlighted that long noncoding RNAs are essential regulators in cancer development. Herein, long intergenic non-protein coding RNA 997 (LINC00997) was identified for study due to its high expression in CC tissues. Read More

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LINC00261: a burgeoning long noncoding RNA related to cancer.

Cancer Cell Int 2021 May 22;21(1):274. Epub 2021 May 22.

Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshedong Road, Erqi District, Zhengzhou, 450052, China.

Long noncoding RNAs (lncRNAs), are transcripts longer than 200 nucleotides that are considered to be vital regulators of many cellular processes, particularly in tumorigenesis and cancer progression. long intergenic non-protein coding RNA 261 (LINC00261), a recently discovered lncRNA, is abnormally expressed in a variety of human malignancies, including pancreatic cancer, gastric cancer, colorectal cancer, lung cancer, hepatocellular carcinoma, breast cancer, laryngeal carcinoma, endometrial carcinoma, esophageal cancer, prostate cancer, choriocarcinoma, and cholangiocarcinoma. LINC00261 mainly functions as a tumor suppressor that regulates a variety of biological processes in the above-mentioned cancers, such as cell proliferation, apoptosis, motility, chemoresistance, and tumorigenesis. Read More

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Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors.

BMC Genomics 2021 May 22;22(1):373. Epub 2021 May 22.

Crop Diseases, Pests, and Genetics Research Unit, San Joaquin Valley Agricultural Sciences Center, USDA Agricultural Research Service, Parlier, CA, 93648, USA.

Background: Spiroplasma citri comprises a bacterial complex that cause diseases in citrus, horseradish, carrot, sesame, and also infects a wide array of ornamental and weed species. S. citri is transmitted in a persistent propagative manner by the beet leafhopper, Neoaliturus tenellus in North America and Circulifer haematoceps in the Mediterranean region. Read More

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Non-coding region variants upstream of MEF2C cause severe developmental disorder through three distinct loss-of-function mechanisms.

Am J Hum Genet 2021 06 21;108(6):1083-1094. Epub 2021 May 21.

Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK; East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK.

Clinical genetic testing of protein-coding regions identifies a likely causative variant in only around half of developmental disorder (DD) cases. The contribution of regulatory variation in non-coding regions to rare disease, including DD, remains very poorly understood. We screened 9,858 probands from the Deciphering Developmental Disorders (DDD) study for de novo mutations in the 5' untranslated regions (5' UTRs) of genes within which variants have previously been shown to cause DD through a dominant haploinsufficient mechanism. Read More

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Increased miR‑187‑3p expression after cerebral ischemia/reperfusion induces apoptosis via initiation of endoplasmic reticulum stress.

Neurosci Lett 2021 May 17;759:135947. Epub 2021 May 17.

Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, School of Basic Medical Science, Guizhou Medical University, China; Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, Guizhou, 550004, China. Electronic address:

Ischemia/reperfusion (I/R) injury induces activation of the endoplasmic reticulum stress (ERS) pathway, accompanied by an increase in apoptosis. Multiple microRNAs (miRNAs/miRs) are dysregulated during I/R and contribute to I/R-induced injury. miRNAs act as suppressors of gene expression and negatively regulate gene expression by targeting the protein-coding sequence (CDS) of specific target mRNAs. Read More

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Expression Profile of Long Noncoding RNAs and Circular RNAs in Mouse C3H10T1/2 Mesenchymal Stem Cells Undergoing Myogenic and Cardiomyogenic Differentiation.

Stem Cells Int 2021 30;2021:8882264. Epub 2021 Apr 30.

Department of Cell Biology, Medical College of Soochow University, Soochow University, Ren Ai Road 199, Suzhou Industrial Park, Suzhou 215123, China.

Background: Currently, a heterogeneous category of noncoding RNAs (ncRNA) that directly regulate the expression or function of protein-coding genes is shown to have an effect on the fate decision of stem cells. However, the detailed regulatory roles of ncRNAs in myogenic and cardiomyogenic differentiation of mouse C3H10T1/2 mesenchymal stem cells (MSCs) are far from clear.

Methods: In this study, 5-azacytidine- (5-AZA-) treated C3H10T1/2 cells were differentiated into myocyte-like and cardiomyocyte-like cells. Read More

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