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LincPRKD: A long intergenic noncoding rna Activated in Gastric Cancer

GASTRO HEP ADVANCES 2025年第5期4卷 100618-100618页

作者： Ravillah, Durgadevi Keerthy, Komal Singh, Salendra Kresak, Adam Guda, Kishore Blum, Andrew E. Case Western Reserve Univ Sch Med Case Comprehens Canc Ctr Div Gen Med Sci Oncol Cleveland OH USA Case Western Reserve Univ Digest Hlth Res Inst Sch Med Cleveland OH USA Cleveland Clin Fdn Lerner Res Inst Ctr Immunotherapy & Precis Immuno Oncol Cleveland OH USA Case Western Reserve Univ Sch Med Dept Pathol Cleveland OH USA Northeast Ohio Vet Affairs Healthcare Syst Div Gastroenterol Cleveland OH USA

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Lack of association of a genetic variant in the long intergenic noncoding rna (linc01080) with Alzheimer's disease and amnestic mild cognitive impairment in Han Chinese

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INTErnaTIONAL JOUrnaL OF NEUROSCIENCE 2015年第6期125卷 419-423页

作者： Luo, Xin Zhu, Jianzhong Cheng, Zaohuo Zhang, Feng Zhang, Guofu Yuan, Jianmin Jin, Chunhui Nanjing Med Univ Wuxi Mental Hlth Ctr Wuxi 214151 Jiangsu Peoples R China

Alzheimer's disease (AD) is a complex neurodegenerative disorder that is the most common form of dementia in the elderly and is characterized by progressive memory loss and cognitive dysfunction. Although the pathogenetic mechanism of AD is still unknown, genetic variants play a critical role in the pathogenesis of AD. Increasing evidence has suggested that noncoding rnas (ncrnas) may be associated with the development of AD. A previous study analyzing human single-nucleotide polymorphisms (SNPs) of long intergenic noncoding rna (lincrna) at the genome level indicated that a genetic variant, rs7990916, in the lincrna 01080 (linc01080) may play an important role in the physiology and pathophysiology of the human brain. To determine whether this SNP alters the risk for sporadic AD (SAD) or amnestic mild cognitive impairment (aMCI) susceptibility, we conducted a case control study in a Han Chinese population with 106 SAD patients, 67 aMCI patients, and 179 healthy controls. Using the LDR-PCR genotyping method, we found no significant difference in allele or genotype frequency in the SNP rs7990916 between patients and controls (p > 0.05). Our results do not support previous findings, suggesting that further studies by using large-scale association analyses are warranted in Han Chinese populations.

关键词： Alzheimer's disease amnestic mild cognitive impairment long intergenic noncoding rna single-nucleotide polymorphism association

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long intergenic noncoding rna (lincrna) Discovery from Non-Strand-Specific rna-Seq Data

Long Intergenic Noncoding RNA (lincRNA) Discovery from Non-S...

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作者： A. A. Golicz

long noncoding rnas (lncrnas) are transcripts over 200 base pairs in length without discernible protein coding potential. long intergenic noncoding rnas (lincrnas) constitute a subset of lncrnas, which do not overlap protein coding genes. Here we describe a detailed pipeline for lincrna discovery from publicly available non-stranded rna-Seq datasets. The pipeline presented can be applied to any plant species for which rna-Seq data and a reference genome sequence are available. less

关键词： rna-seq Genome Annotation Statistical Calculation Genome-Wide Association Study StringTie HISAT Python Programming Language Oryza sativa Transcriptome lincrna long intergenic noncoding rna

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LINC24065 is a monoallelically expressed long intergenic noncoding rna located in the cattle DLK1-DIO3 cluster

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JOUrnaL OF GENETICS 2019年第1期98卷 30-30页

作者： Zhang, Cui Xu, Da Chen, Weina Li, Junliang Gao, Qinghua Li, Shijie Hebei Agr Univ Dept Biochem & Mol Biol Coll Life Sci Baoding 071001 Peoples R China Hebei Univ Coll Tradit Chinese Med Baoding 071000 Peoples R China Hebei Acad Sci Inst Microbiol Baoding 071051 Peoples R China

long noncoding rnas (lncrnas) are important regulators of biological processes, and regulate genomic imprinting in cis and/or trans to induce monoallelic expression with parent-origin-specific pattern. DLK1-DIO3 domain is one of the largest imprinted clusters in mammals, and maternally expressed noncoding rnas of this region is related to the pluripotency of the embryonic stem cells. Previously, we sequenced the cDNA of two maternally expressed noncoding rnas, MEG8 and MEG9, and mapped a lncrna (LINC24061) between the two genes in the cattle DLK1-DIO3 domain on chromosome 21. In this study, we identified LINC24065, a novel long intergenic noncoding rna (lincrna), which was also located between MEG8 and MEG9. We identified four variants of LINC24065 (LINC24065-v1, LINC24065-v2, LINC24065-v3 and LINC24065-v4) that were a result of alternative splicing from 18 exons. LINC24065-v1 and LINC24065-v2 showed tissue-specific expression patterns in adult bovine tissues, and LINC24065-v3 and LINC24065-v4 were detected in all eight analysed tissues (heart, liver, spleen, lung, kidney, skeletal muscle, adipose and brain). Using single-nucleotide polymorphism (SNP)-based method, LINC24065 was identified to have monoallelic expression in adult tissues, suggesting that it is imprinted in cows. These results provide a foundation for further investigation about whether LINC24065 plays a role in regulating imprinting of the DLK1-DIO3 domain.

关键词： long intergenic noncoding rna cattle LNC24065 gene monoallelic expression spliced variants

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Functional Implications of rna Splicing for Human long intergenic noncoding rnas

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EVOLUTIONARY BIOINFORMATICS 2014年第2014期10卷 219-228页

作者： Chen, Feng-Chi Pan, Chia-Lin Lin, Hsuan-Yu Natl Hlth Res Inst Inst Populat Hlth Sci Zhunan Taiwan Natl Chiao Tung Univ Dept Biol Sci & Technol Hsinchu City Taiwan China Med Univ Dept Dent Taipei Taiwan

long intergenic noncoding rnas (lincrnas) have been suggested as playing important roles in human gene regulation. The majority of annotated human lincrnas include multiple exons and are alternatively spliced. However, the connections between alternative rna splicing (AS) and the functions/regulations of lincrnas have remained elusive. In this study, we compared the sequence evolution and biological features between single-exonic lincrnas and multi-exonic lincrnas (SELs and MELs, respectively) that were present only in the hominoids (hominoid-specific) or conserved in primates (primate-conserved). The MEL exons were further classified into alternatively spliced exons (ASEs) and constitutively spliced exons (CSEs) for evolutionary analyses. Our results indicate that SELs and MELs differed significantly from each other. Firstly, in hominoid-specific lincrnas, MELs (both CSEs and ASEs) evolved slightly more rapidly than SELs, which evolved approximately at the neutral rate. In primate-conserved lincrnas, SELs and ASEs evolved slightly more slowly than CSEs and neutral sequences. The evolutionary path of hominid-specific lincrnas thus seemed to have diverged from that of their more ancestral counterparts. Secondly, both of the exons and transcripts of SELs were significantly longer than those of MELs, and this was probably because SEL transcripts were more resistant to rna splicing than MELs. Thirdly, SELs were physically closer to coding genes than MELs. Fourthly, SELs were more widely expressed in human tissues than MELs. These results suggested that SELs and MELs represented two biologically distinct groups of genes. In addition, the SEL-MEL and ASE-CSE differences implied that splicing might be important for the functionality or regulations of lincrnas in primates.

关键词： long intergenic noncoding rna alternative splicing sequence evolution gene regulation

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Genome-wide identification and characterization of long intergenic noncoding rnas in the regenerative flatworm Macrostomum lignano

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GENOMICS 2020年第2期112卷 1273-1281页

作者： Azlan, Azali Halim, Mardani Abdul Azzam, Ghows Univ Sains Malaysia Sch Biol Sci George Town 11800 Malaysia Univ Sains Malaysia USM RIKEN Int Ctr Ageing Sci URICAS George Town 11800 Malaysia

The free-living flatworm Macrostoma lignano (M. lignano) is an emerging model organism for aging and regeneration research. long intergenic non-coding rnas (lincrnas) have important roles in many biological processes such as aging, stem cell maintenance and differentiation. However, to date, there is no systematic identification of lincrnas in M. lignano. By using public rna-seq data, we identified a total of 2547 lincrna transcripts in M. lignano genome. We discovered that M. lignano lincrnas shared many characteristics with other species such as shorter in length, lower GC content, and lower in expression compared to protein-coding genes. Unlike protein-coding genes, M. lignano lincrnas showed higher tendency to be expressed in temporal and region-specific fashion. Additionally, co-expression network analysis and functional enrichment suggest that M. lignano lincrnas have potential roles in regeneration. This study will provide important resources and pave the way for investigations on non-coding genes involved in aging and regeneration.

关键词： Macrostomum lignano long intergenic noncoding rna Regeneration Transcriptome

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Genome-Wide Analysis of Human SNPs at long intergenic noncoding rnas

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HUMAN MUTATION 2013年第2期34卷 338-344页

作者： Chen, Geng Qiu, Chengxiang Zhang, Qipeng Liu, Bing Cui, Qinghua Peking Univ Sch Basic Med Sci Dept Biomed Informat Beijing 100191 Peoples R China Chinese Acad Sci LIAMA Ctr Computat Med Natl Lab Pattern Recognit Inst Automat Beijing 100190 Peoples R China Peking Univ Inst Syst Biomed Beijing 100191 Peoples R China Peking Univ MOE Key Lab Mol Cardiovasc Sci Beijing 100191 Peoples R China

long intergenic noncoding rnas (lincrnas) represent a large portion of the noncoding genes in mammals and other eukaryotes but remains among the least well-understood of genetic factors to date. Here, we systematically analyzed the human SNPs of lincrnas at a genome level. We found a significantly lower SNP density in lincrna regions than both their upstream and downstream flanking regions. Functional regions show lower SNP density than other regions in lincrnas. We revealed that lincrnas with higher expression levels and broader expression spectrum have significantly lower SNP density. Moreover, we identified lincrnas that are under recent positive selection and revealed that these lincrnas show distinct SNP density, expression level, and tissue specificity. Importantly, we identified a genetic variant (rs7990916:T>C) under recent positive selection at a brain-specific lincrna that significantly affects the structure of normal brain. Analysis of brain magnetic resonance images showed that individuals with CC genotype have significant bigger regional gray matter volume than individuals with TT genotype. Moreover, the genotype of this SNP shows different distribution in normal elders, mild cognitive impairment, and Alzheimer disease subjects, suggesting that this lincrna may have a role in physiology and pathophysiology of human brain.

关键词： long intergenic noncoding rna SNP Alzheimer disease brain

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linc-UBC1 physically associates with polycomb repressive complex 2 (PRC2) and acts as a negative prognostic factor for lymph node metastasis and survival in bladder cancer

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BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE 2013年第10期1832卷 1528-1537页

作者： He, Wang Cai, Qingqing Sun, Fenyong Zhong, Guangzheng Wang, Pei Liu, Hongyan Luo, Junhua Yu, Hao Huang, Jian Lin, Tianxin Sun Yat Sen Mem Hosp Dept Urol Guangzhou Guangdong Peoples R China Sun Yat Sen Univ Ctr Canc Dept Internal Med Guangzhou 510275 Guangdong Peoples R China Tongji Univ Dept Lab Shanghai Peoples Hosp 10 Hospitatal 10 Shanghai 200092 Peoples R China Gaozhou Hosp Dept Med Ultrason Maoming Peoples R China Sun Yat Sen Univ Lin Bai Xin Res Ctr Sun Yat Sen Mem Hosp Guangzhou 510275 Guangdong Peoples R China

Objectives: The human genome encodes many long intergenic noncoding rnas (lincrnas). However, their biological functions, molecular mechanisms and prognostic values associated with bladder cancer remain to be elucidated. Here we investigated a lincrna termed linc-UBC1 (Up-regulated in bladder cancer 1) and evaluated its prognostic value in bladder cancer patients. Materials and methods: Expression of linc-UBC1 was evaluated by quantitative reverse transcription PCR (qRT-PCR) in 102 bladder cancer tissue samples and normal adjacent tissues. The functions of linc-UBC1 on cell proliferation, migration, invasion, colony formation, tumorigenicity and metastatic potential were evaluated by knockdown strategy in vitro and in vivo. rna immunoprecipitation (RIP) was performed to confirm that linc-UBC1 physically associates with EZH2 and SUZ12, core components of polycomb repressive complex 2 (PRO). Chromatin immunoprecipitation (ChIP) was conducted to examine histone modification status. Results: qRT-PCR confirmed that linc-UBC1 expression is up-regulated in 60 cases (58.8%) in bladder cancer tissues compared with normal adjacent tissues, and its overexpression correlates with lymph node metastasis and poor survival. Further functional analysis demonstrated that knockdown of linc-UBC1 attenuates bladder cancer cell proliferation, motility, invasion, colony formation ability, tumorigenicity and metastatic potential. Importantly, the inhibitory effect of linc-UBC1 on cell proliferation was also observed in primary bladder cancer cells obtained from patients. RIP and ChIP assay confirmed that linc-UBC1 physically associates with PRO complex and regulates histone modification status of target genes. Conclusions: Frequently overexpressed linc-UBC1 physically associates with PRC2 complex, and acts as a negative prognostic factor for lymph node metastasis and survival in bladder cancer. (C) 2013 Elsevier B.V. All rights reserved.

关键词： long intergenic noncoding rna linc-UBC1 Prognostic factor Bladder cancer Polycomb repressive complex 2

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long noncoding rna (lincrna), a new paradigm in gene expression control

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FUNCTIONAL & INTEGRATIVE GENOMICS 2017年第2-3期17卷 135-143页

作者： Deniz, Emre Erman, Batu Acibadem Univ Fac Arts & Sci Dept Mol Biol & Genet Istanbul Turkey Sabanci Univ Fac Engn & Nat Sci Mol Biol Genet & Bioengn Program Istanbul Turkey

long intergenic non-coding rnas (lincrnas) are defined as rna transcripts that are longer than 200 nucleotides. By definition, these rnas must not have open reading frames that encode proteins. Many of these transcripts are encoded by rna polymerase II, are spliced, and are poly-adenylated. This final fact indicates that there is a trove of information about lincrnas in databases such as the Gene Expression Omnibus (GEO), which is a repository for rnaseq and microarray data. Recent experiments indicate that there are upwards of 15,000 lincrnas encoded by the human genome. The term "intergenic" refers to the identification of these transcripts from regions of the genome that do not contain protein-encoding genes. These regions coincide with what was once labeled as the "junk DNA" portions of our genomes, which, upon careful examination by whole genome rna sequencing experiments, clearly encode rna transcripts. Lincrnas also contain promoter- or enhancer-associated rnas that are gene proximal and can be either in the sense or antisense orientation, relative to the protein-coding gene with which they are associated. In this review, we describe the functions of lincrnas playing roles in biological processes such as gene expression control, scaffold formation, and epigenetic control.

关键词： long intergenic noncoding rna Gene expression Chromatin Chromatin-modifying complexes

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The role of long noncoding rnas in cancer metastasis

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Journal of Cancer Metastasis and Treatment 2018年第1期4卷 237-259页

作者： Christine Parsons Alexis M.Tayoun Benjamin D.Benado Gabriel Ragusa Rose F.Dorvil Elizabeth A.Rourke Kaitlyn O’Connor Irene G.Reed Angela Alexander Lian Willetts Maryam Habibian Brian D.Adams School of Medicine UConn HealthFarmingtonCT 06030USA Department of RNA Sciences The Brain Institute of AmericaGrotonCT 06340USA Department of Biology and Environmental Sciences University of New HavenWest HavenCT 06516USA Department of Biology University of Saint JosephWest HartfordCT 06117USA Department of Breast Medical Oncology MD Anderson Cancer CenterHoustonTX 77030USA Cumming School of Medicine University of CalgaryCalgaryAB T2N 1N4Canada Department of Chemistry Stanford UniversityStanfordCA 94305USA Investigative Medicine Program Yale University Medical SchoolNew HavenCT 06520USA

Signaling pathways are tightly controlled systems that regulate the appropriate timing of gene expression required for the differentiation of cells down a particular lineage essential for proper tissue ***,apoptosis and metabolic pathways are just a few examples of the signaling pathways that require fine-tuning,so as to control the proper development of a particular tissue type or organ *** estimated 70%of the genome is actively transcribed,only 2%of which codes for known protein-coding *** noncoding rnas(lncrnas)in particular,are a large and diverse class of rnas>200 nucleotides in length,and not translated into *** are essential transcriptional and post-transcriptional regulators that control the expression of genes in a spatial,temporal,and cell context-dependent *** aberrant expression of lncrnas is therefore linked with a number of chronic diseases including cardiac dysfunction,diabetes,and *** this review,we highlight the specific role lncrnas have in promoting the metastatic cascade across a number of epithelial cancer models.

关键词： long noncoding rna long intergenic noncoding rna microrna competitive endogenous rna breast cancer brain cancer lung cancer prostate cancer metastasis therapeutics

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