Long intergenic rna gene. Medical search. Frequent questions

Therefore, diverse cellular compartments orchestrated by multiple environment-driving factors make the mechanisms underlying asthma extraordinary complex and unclear, particularly with respect to long noncoding RNAs (lncRNAs). (researchsquare.com)
lncRNAs have been reported to possess multiple functions including regulation of gene expression, transcriptional activation and silencing of genes and thus play critical roles in a diversity of cellular process [ 14 , 15 ]. (researchsquare.com)
The recent identification of MYC-regulated long noncoding RNAs (lncRNAs) expands our knowledge of the role of lncRNAs in MYC functions. (oncotarget.com)
Of the various members of noncoding RNAs, long noncoding RNAs (lncRNAs) are characterized by their size (larger than 200 nucleotides). (oncotarget.com)
Recently, many studies have revealed versatile functions of lncRNAs in gene expression modulation through various routes such as transcriptional, posttranscriptional, posttranslational and epigenetic regulation [ 10 , 11 ]. (oncotarget.com)
Less clear is whether intergenic lncRNAs commonly regulate transcription by modulating chromatin at genomically distant loci. (ox.ac.uk)
Although some key flowering responsive genes have been identified in spinach, non-coding RNA molecules like long non-coding RNAs (lncRNAs) were not investigated yet. (biomedcentral.com)
The GO and KEGG analyses carried out on the cis target gene of lncRNAs showed that the lncRNAs play an important role in the regulation of flowering spinach. (biomedcentral.com)
Network analysis pinpointed several well-known flowering-related genes such as ELF , COL1 , FLT , and FPF1 and also some putative TFs like MYB, WRKY, GATA, and MADS-box that are important regulators of flowering in spinach and could be potential targets for lncRNAs. (biomedcentral.com)
This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach. (biomedcentral.com)
ncRNAs with more than 200 nucleotides are considered as lncRNAs, which originate from intronic and exonic regions of protein-coding genes in both sense and antisense strands, as well as from the intergenic regions [ 21 ]. (biomedcentral.com)
MicroRNAs (miRNAs) are the most altered subset of ncRNAs, followed by long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs). (ersjournals.com)
Mitophagy and long non-coding RNAs (lncRNAs) play pivotal roles in tumorigenesis, development, and drug resistance. (biomedcentral.com)
Long noncoding RNAs (lncRNAs) are a class of endogenous, non-protein coding RNAs that are highly linked to various cellular functions and pathological process. (biomedcentral.com)
Unlike miRNAs whose central function is to restrain mRNA translation by inducing degradation, lncRNAs can act as numerous roles to exert their functions by directly or indirectly interacting with DNA, RNA or protein, even can encode some short peptides (Fig. 3 a-d) [ 6 ]. (biomedcentral.com)

Based on the nucleotide sequence information of transcripts, we identified 819 novel transcriptionally active regions (nTARs) and revised 906 incorrectly predicted gene models, including revisions of exon-intron structure, gene orientation and sequencing errors. (biomedcentral.com)
Sequence data of the revised genome annotation including several hundreds of novel transcripts, improved gene models and candidate genes for alternative splicing have been made accessible in a comprehensive database. (biomedcentral.com)
After investigating single-guide RNA targeting rules for effective transcriptional activation, demonstrating multiplexed activation of 10 genes simultaneously, and upregulating long intergenic noncoding RNA transcripts, the research team decided to undertake a large-scale screen. (genengnews.com)
A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, including mRNA, the various classes of non-coding RNA, and small RNA. (jcvi.org)
We assembled the sequences from deep RNA sequencing experiments by the Genotype-Tissue Expression (GTEx) project, to create a new catalog of human genes and transcripts, called CHESS. (biomedcentral.com)
These include 224 novel protein-coding genes and 116,156 novel transcripts. (biomedcentral.com)
Single nucleotide polymorphisms with cis-regulatory effects on long non-coding transcripts in human primary monocytes. (scilifelab.se)
We use these engineered Cas9 activation complexes to investigate sgRNA targeting rules for effective transcriptional activation, demonstrate multiplexed activation of 10 genes simultaneously, and upregulate long intergenic non-coding RNA (lincRNA) transcripts. (cdc.gov)
Gene expression analyses using NGS platforms were carried out in the vegetative and reproductive tissues such as shoot, root, mature leaf, ﬂower bud, young pod, seed and nodule by various groups which resulted in identification of several tissue-specific transcripts. (intechopen.com)
Overall, small RNAs tended to align with CAGE (cap-analysis of gene expression) tags, which mark the 5' ends of capped, long RNA transcripts. (inra.fr)
Strand-specific RNAseq data show a nearly full transcription of both plastomic strands and detect C-to-U RNA-editing sites at both sense and antisense transcripts. (biomedcentral.com)
Strand-specific RNA libraries have the advantage of allowing for the discrimination of sense and antisense transcripts [ 17 ]. (biomedcentral.com)
We took advantage of this to (1) investigate the full transcription capability of both plastomic strands, (2) estimate the relative number of plastid coding and antisense transcripts, and (3) identify plastid C-to-U RNA-editing sites separately at sense and antisense transcripts in conifers. (biomedcentral.com)
In addition, they discovered that the intergenic sequences of TICs were processed via the same standard eukaryotic splicing machinery that removes introns from RNA transcripts. (cshlpress.com)
In a current model, Pol V synthesizes scaffold transcripts that interact with ARGONAUTE4-bound small RNAs, which recruits the methylation machinery to the target DNA [ 3 ]. (biomedcentral.com)

QIAseq Stranded RNA Library Kits use a unique protocol, which does not require actinomycin D to retain strand specificity or dUTP to ensure stranded library construction, thereby ensuring highly sensitive detection of low-expression RNA molecules with increased complexity and transcript coverage. (qiagen.com)
Because alternative RNA splicing allows different types of mRNA molecules to be created from a single gene, it generates the diversity of protein function and structure that is essential to complex organisms. (genomicglossaries.com)
RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. (genomicglossaries.com)
More specifically, antisense oligonucleotides that are useful as reagents for target validation , or as drugs, are engineered molecules that differ from natural RNA but that have a base sequence that is recognized as being complementary to a very specific mRNA sequence. (genomicglossaries.com)
Conclusions Our study successfully discovered many key noncoding RNA molecules related to pathogenesis of asthma and relevant treatment, which may provide novel biomarkers and therapeutic targets for asthmatic diagnose and therapy. (researchsquare.com)
Long intergenic non-coding RNA (LINC-RNA) molecules are critical in gene regulation via their sponging mechanism in controlling the micro-RNA molecules. (tcabse.org)
LINC-RNA molecules are usually big and are structurally unstable due to which they have not been used effectively as therapeutics. (tcabse.org)
My goal is to employ the LINC-RNA molecules as therapeutics mainly in Oncology for the suppression of genes, by stabilizing them using chemical biology approach. (tcabse.org)
Chemical biology-based strategies to stabilize the secondary structure of dynamic ceRNA molecules for detection and activation of p53 gene in colorectal cancer. (tcabse.org)
Various combinations of coding sequences and signals operate dynamically to produce multiple RNA and protein molecules from a single stretch of DNA. (huffpost.com)
MicroRNAs miRNAs are 20 22 nucleotide non-coding RNA molecules, which regulate gene expression at the post-transcriptional level, located in intergenic or intronic regions as individual or clustered genes Bartel, 2004. (tefl.co.za)

Long intergenic non-protein coding RNA 483 is a protein that in humans is encoded by the LINC00483 gene. (wikipedia.org)
What does this gene/protein do? (cancerindex.org)
What pathways are this gene/protein implicaed in? (cancerindex.org)
Highly specific and effective gene silencing of any disease can be achieved by an accurate knowledge of the target mRNA sequence and rational design of its complementary antisense agents for the downregulation of its protein message. (genomicglossaries.com)
In previous efforts to revamp CRISPR/Cas9 for gene activation purposes, scientists had tried to attach the activation domains to either end of the Cas9 protein, with limited success. (genengnews.com)
The upregulated DEGs were primarily protein‑coding genes enriched in immune and inflammation response pathways, while the downregulated DEGs were mainly coding long non‑coding (lnc)RNAs, indicating the regulatory function of USF1. (spandidos-publications.com)
MYC is a transcription factor regulating global gene expression through heterodimerization with the protein myc-associated factor X (MAX) [ 1 - 3 ]. (oncotarget.com)
For instance, the stability of MYC protein modulated by phosphorylation is regulated by promyelocytic leukemia zinc finger ( PLZF ) protein and long noncoding RNA PVT1 [ 9 , 10 ]. (oncotarget.com)
Using an integrative annotation pipeline, we assembled tissue-specific RNA-Seq libraries from 113 datasets and constructed 48 359 transcript models of protein-coding genes in eleven tissues. (jcvi.org)
Altogether, we identified 635 novel protein-coding genes, 508 novel transcribed regions, 5178 non-coding RNAs, and 35 846 small RNA loci that were formerly unannotated. (jcvi.org)
The Long Intergenic Non-protein Coding RNA 2412 (LINC02412) gene is located on chr12:93174365 -93181831 at 12q22. (empiregenomics.com)
The Long Intergenic Non-protein Coding RNA 2264 (LINC02264) gene is located on chr4:117834357 -117869947 at 4q26. (empiregenomics.com)
Among them, 52 were derived from six retrotransposon long terminal repeats loci in the B. cinerea genome, 13 were from intergenic regions of 10 loci, and eight were mapped to five protein-coding genes. (genomeweb.com)
During the Human Genome Project, most efforts to estimate and annotate genes focused on protein-coding genes, i.e., regions of the genome that are transcribed into RNA and then translated into proteins. (biomedcentral.com)
Of these regions, 60% were annotated as intergenic, which implies that they do not overlap with protein-coding genes. (scilifelab.se)
Out of the lncRNA regions regulated by cis-acting regulatory SNPs, 20% (n = 52) were co-regulated with the closest protein coding gene. (scilifelab.se)
Many intergenic long noncoding RNA (lncRNA) loci regulate the expression of adjacent protein coding genes. (ox.ac.uk)
Distally, it preferentially targets active promoters and regulates expression of neural differentiation genes, in part through physical association with the POU3F3 protein. (ox.ac.uk)
Cas9 nuclease can be converted into an RNA-guided DNA binding protein (dCas9) via inactivation of its two catalytic domains 12 , 13 and then fused to transcription activation domains. (cdc.gov)
Different regions of RNA and DNA join together to encode protein products. (huffpost.com)
Individual non-coding RNAs dwarf the number of protein-coding genes, and include classes that are well understood as well as classes for which the nature, extent and functional roles are obscure. (inra.fr)
Members of an extensive class of both small RNAs and CAGE tags were distributed across internal exons of annotated protein coding and non-coding genes, sometimes crossing exon-exon junctions. (inra.fr)
The 'one gene, one protein' rule has been fundamental to molecular biology. (cshlpress.com)
By contrast, many protein-coding genes transcribed by Pol II contain in their gene bodies exclusively CG methylation that is independent of small RNAs and Pol IV/Pol V activities. (biomedcentral.com)

Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. (genomicglossaries.com)
Programmable DNA binding proteins have emerged as an exciting platform for engineering synthetic transcription factors for modulating endogenous gene expression 5 - 11 . (cdc.gov)
These dCas9-activator fusions targeted to the promoter region of endogenous genes can then modulate gene expression 7 - 11 . (cdc.gov)
Although the current generation of dCas9-based transcription activators is able to achieve up-regulation of some endogenous loci, the magnitude of transcriptional up-regulation achieved by individual single-guide RNAs (sgRNAs) 12 typically ranges from low to ineffective 8 - 11 . (cdc.gov)
Finally, a lncRNA prognostic signature-related competing endogenous RNA (ceRNA) network was constructed. (biomedcentral.com)
By contrast, a CRP4-GFP fusion gene under the control of a CRP4 promoter fragment acquires CG and non-CG methylation in the CRP coding region in leaves similar to the silent endogenous CRP4 gene. (biomedcentral.com)

The Kim lab is particularly interested in the role of micro-RNAs (miRNA) and long intergenic non-coding RNAs (lincRNAs). (umaine.edu)
Before coming to Case Western Reserve University, Khalil authored a paper that identified more than 3,300 novel genes in human cells, referred to as long intergenic non-coding RNAs (lincRNAs). (case.edu)

Noncoding RNAs (ncRNAs) direct a remarkable number of diverse functions in development and disease through their regulation of transcription, RNA processing and translation. (nature.com)
In recent years, noncoding RNAs (ncRNAs), especially microRNAs, long noncoding RNAs and circular RNAs, have been found to be associated with abnormalities of the ASMCs. (ersjournals.com)
This review highlights findings concerning noncoding RNAs (ncRNAs) in asthmatic ASMCs so far and proposes a schematic diagram that helps us to better understand how ncRNAs are involved in pathophysiological behavioural changes in asthmatic ASMCs. (ersjournals.com)
Many noncoding RNAs (ncRNAs) have been identified in asthmatic ASMCs in recent years [ 5 ]. (ersjournals.com)

Moreover, 5′- and 3′-UTR sequences of 4378 genes have been retrieved and alternatively spliced variants of 69 genes have been identified. (biomedcentral.com)
Unlike pseudogenes arising from gene duplication, which often retain the original regulatory elements required for gene expression (promoters/enhancers), retrogenes lack regulatory sequences, and therefore their only chance of becoming expressed is when they integrate in proximity of some other gene's promoter (rather unlikely, although not impossible) [3,4]. (pandasthumb.org)
A. Retrotransposed pseudogenes: starting from the original gene (the coding sequences are in black, the non-coding introns in gray, and the promoter element is indicated by the large arrow upstream of the gene), transcription generates a primary mRNA (black and gray broken line), from which the introns are excised by RNA splicing. (pandasthumb.org)
As a result, the transcript generated from this vector does not correspond precisely to the selected non-coding RNA gene, but contains some additional sequences both upstream and downstream. (vectorbuilder.kr)

Leading the charge in the RNA revolution is a class of ncRNAs that are synthesized at active enhancers, called enhancer RNAs (eRNAs). (nature.com)
A particularly important novelty highlighted by the Genome Biology paper is the unexpected and burgeoning role of so-called "non-coding" RNAs ( ncRNAs ) in all aspects of genome function. (huffpost.com)
Cells transcribe many functional ncRNAs from so-called "intergenic" regions that had no functional importance according to the genocentric theory. (huffpost.com)
NcRNAs such as those involved in RNA interference can be independently inherited, and can also direct chromatin modification and DNA methylation see [7, 8] RNA Inheritance of Acquired Characters , and Nucleic Acid Invaders from Food Confirmed , SiS 63). (i-sis.org.uk)

Promoter region motif analysis indicated that ETV5 has more binding motifs and genes than USF1 itself for USF1‑regulated DEGs, indicating that USF1 may indirectly modulate gene expression by regulating ETV5 expression in Huh7 cells. (spandidos-publications.com)

To understand how the immune system is being modulated by these factors the role of non-coding RNAs (ncRNA) were investigated. (umaine.edu)
In this regards, they can be separated into small non-coding RNA (small ncRNA) and lncRNA. (biomedcentral.com)

From their structural studies, the MIT team realized that two small loops of the RNA guide poke out from the Cas9 complex and could be better points of attachment because they allow the activation domains to have more flexibility in recruiting transcription machinery. (genengnews.com)
Each gene showed at least a twofold boost in transcription, and for many genes, the researchers found multiple orders of magnitude increase in activation. (genengnews.com)
Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. (nature.com)
Dali is transcribed downstream of the Pou3f3 transcription factor gene and its depletion disrupts the differentiation of neuroblastoma cells. (ox.ac.uk)
We have long been puzzled by these findings because it is then unclear whether plastomic rearrangements affect plastid gene transcription. (biomedcentral.com)
In the January issue of the journal Genome Research, two teams of scientists describe a widespread phenomenon in the human genome called transcription-induced chimerism (TIC), where two adjacent genes produce a single, fused RNA transcript. (cshlpress.com)
The work has implications for drug development, as well as for understanding mechanisms underlying gene evolution, transcription regulation, and genomic organization. (cshlpress.com)
For RNA polymerase II-mediated transcription, the start site is typically in the 3' region of the promoter while the termination site is within the polyA signal sequence. (vectorbuilder.kr)
Unlike CG methylation in gene bodies, which does not dramatically affect Pol II transcription, combined CG and non-CG methylation in CRP coding regions is likely to contribute to gene silencing in leaves because loss of this methylation in synergid cells is associated with CRP gene expression. (biomedcentral.com)

This comparison identified 32 SNPs in loci from genome-wide association studies that displayed a strong association signal with allele-specific expression of non-coding RNAs in monocytes, with p-values ranging from 6.7×10(-7) to 9.5×10(-89). (scilifelab.se)

The AAV non-coding RNA expression vector uses an RNA polymerase II promoter to drive the expression of the user-selected non-coding RNA gene. (vectorbuilder.kr)

We successfully employed deep sequencing RNA-Seq data in combination with an elaborate bioinformatics strategy in order to identify novel genes, incorrect gene models and mechanisms of transcript processing in the corn anthracnose fungus C. graminicola . (biomedcentral.com)

Transcriptome analysis has been utilized extensively to identify non-coding RNAs such as miRNAs and long intergenic non-coding (LINC) RNAs. (intechopen.com)
Several steps must occur before miRNAs can act, including the action of many enzymes, such as RNA polymerase II, Drosha, Exportin 5, Dicer and Argonaute Ago. (tefl.co.za)

In addition, we annotated various classes of non-coding RNA including microRNA, long intergenic RNA, small nucleolar RNA, natural antisense transcript, small nuclear RNA, and small RNA using published datasets and in-house analytic results. (jcvi.org)

To date, small RNAs have been identified in various fungi and oomycetes, but data has been inconclusive as to whether they regulate host-pathogen interaction. (genomeweb.com)
Many small RNAs, including the previously described promoter-associated small RNAs, appeared to possess cap structures. (inra.fr)
Supplying synthetic promoter-associated small RNAs corresponding to the c-MYC transcriptional start site reduced MYC messenger RNA abundance. (inra.fr)
The studies presented here expand the catalogue of cellular small RNAs and demonstrate a biological impact for at least one class of non-canonical small RNAs. (inra.fr)
Small RNAs including short-interfering (si)RNAs and piRNAs, and long RNAs such as long intergenic noncoding (linc)RNAs can direct histone modifications and cytosine methylation. (i-sis.org.uk)
This pattern of methylation is mediated in part by small RNAs and two specialized RNA polymerases, termed Pol IV and Pol V, in a process called RNA-directed DNA methylation. (biomedcentral.com)
In leaves, the CRP genes are silent and their coding regions contain dense, transposon-like methylation in CG, CHG and CHH contexts, which depends partly on the Pol IV/Pol V pathway and small RNAs. (biomedcentral.com)
Plants have evolved a complex transcriptional machinery for generating and using small RNAs that guide DNA cytosine methylation at homologous regions of the genome. (biomedcentral.com)

QIAseq Stranded RNA Library Kits provide a superior method for generating Illumina compatible RNA-seq libraries from total RNA or mRNA enriched samples. (qiagen.com)
For applications such as gene expression, fusion gene or mutation detection, QIAseq Stranded mRNA Select Kits include an optimized mRNA enrichment protocol with all the reagents and components required to build high-quality RNA-seq libraries. (qiagen.com)
More than half of all human genes are alternatively spliced, so it is expected that alternative pre- mRNA splicing will be responsible for the identification of more than 90 percent of all human proteins. (genomicglossaries.com)
High- fidelity mRNA amplification for gene profiling. (genomicglossaries.com)
RNA-like oligonucleotides that are complementary to a portion of a target mRNA molecule. (genomicglossaries.com)
A complementary RNA sequence that binds to a naturally occurring (sense) mRNA molecule, thus blocking its translation. (genomicglossaries.com)
MiRNA usually binds directly to the 3′-untranslated region (3′-UTR) of target gene mRNA through the RNA-induced silencing complex (RISC) [ 15 , 16 ]. (ersjournals.com)
Further demonstrating that expressed CRP genes lack gene body methylation, a CRP4-GFP fusion gene under the control of the constitutive 35 S promoter remains unmethylated in leaves and is transcribed to produce a translatable mRNA. (biomedcentral.com)

Through the genome-wide regulation of gene expression, MYC is involved in diverse cellular processes including cell growth, cell cycle, apoptosis, angiogenesis, cell differentiation and genomic instability [ 4 ]. (oncotarget.com)
Achieving systematic, genome-scale perturbations within intact biological systems is important for elucidating gene function and epigenetic regulation. (cdc.gov)

Pol IV is needed to produce the small RNA trigger for methylation whereas Pol V acts downstream of small RNA biogenesis to facilitate de novo methylation of genomic DNA at the small RNA-targeted site. (biomedcentral.com)

Future studies should investigate gene-by-environment interactions and employ functional imaging to understand how salience network structure translates to psychiatric disorder risk. (nature.com)
These conservation-based methods, however, depend critically on the assumption that genomic elements are present at orthologous locations and maintain similar functional roles over relatively long evolutionary time periods. (biorxiv.org)
One of the recent examples was a 2003 paper by Hirotsune and colleagues in Nature, which reported that alteration of the pattern of expression of a purported mouse pseudogene (i.e. an apparently inactivated, non-functional gene, part of the so-called "junk DNA") results unexpectedly in the modification of the activity of its functional counterpart, leading to a series of dramatic developmental defects. (pandasthumb.org)
A third, more rare instance is that of functional genes losing their function in certain lineages, but not others ("unitary" pseudogenes - a classic example is the independent inactivation of the gene for vitamin C synthesis in primates and guinea pigs). (pandasthumb.org)
Note that the number of pseudogenes in the human genome (20,000 or so at the latest count, many of them crippled viral elements) is comparable to that of our functional genes - an impressive amount. (pandasthumb.org)

Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)
By integrating these two datasets, 16 overlapped genes were detected, including downregulated lncRNA‑NEAT1 and upregulated TF‑ETV5. (spandidos-publications.com)

Long non-coding RNA LINC00926 regulates WNT10B signaling pathway thereby altering inflammatory gene expression in PTSD. (nih.gov)
University of California, Riverside researchers this month reported the discovery that a fungal pathogen known to infect a wide variety of vegetable and fruit crops is capable of hijacking a plant's RNA interference pathway to suppress host immunity, thereby enhancing its virulence. (genomeweb.com)
Gene pathway analysis using the 689 DEG identified important cancer pathways such as remodeling of the extracellular matrix and epithelial-mesenchymal transition. (bvsalud.org)
Pathway analysis of the identified genes showed their involvement in cellular development, molecular transport, RNA trafficking, cell-to-cell signaling and interaction, cellular growth and proliferation. (frontiersin.org)
Long noncoding RNA NALT1-induced gastric cancer invasion and metastasis via NOTCH signaling pathway. (nih.gov)
Key components of the RNA-directed DNA methylation pathway include two functionally diversified RNA polymerase II (Pol II)-related RNA polymerases called Pol IV and Pol V [ 1 ]. (biomedcentral.com)

Huh7 cells that overexpress USF1 were used with whole transcriptome profiling through RNA sequencing and chromatin immunoprecipitation (ChIP) sequencing methods to investigate the downstream targets of USF1. (spandidos-publications.com)

Fig. 1: Molecular features that define enhancer RNAs. (nature.com)
Schoenfelder, S. & Fraser, P. Long-range enhancer-promoter contacts in gene expression control. (nature.com)
The cis-regulatory SNPs that were significantly associated with allele-specific expression of long non-coding RNAs were enriched to enhancer regions marked for active or bivalent, poised chromatin by histone modifications. (scilifelab.se)

An annotated genomic sequence of the corn anthracnose fungus Colletotrichum graminicola has been published previously, but correct identification of gene models by means of automated gene annotation remains a challenge. (biomedcentral.com)
Comparative analysis of RNA-Seq data and the genome sequence did not provide evidence for RNA editing in C. graminicola . (biomedcentral.com)
87(5): 1663-1667] Specifically, the investigators started by priming whole cerebellar RNA with a synthetic oligonucleotide containing a T7 RNA polymerase promoter sequence. (genomicglossaries.com)
RNA which contains an intron sequence that has an enzyme- like catalytic activity. (genomicglossaries.com)
Meanwhile, two plant defense marker genes, which do not contain target sites for the fungal sRNAs, were highly upregulated, leading the researchers to conclude that suppression of some but not all genes is a result of sequence-specific sRNA interaction and not cell death within infected lesions. (genomeweb.com)
Over the last two decades, several laboratories have used a wide range of techniques encompassing expressed sequence tag (EST) analysis, serial analysis of gene expression (SAGE), microarray and next-generation sequencing (NGS) technologies for analysing the chickpea transcriptomes. (intechopen.com)
We retrieved OC-related RNA sequence, copy number variation, somatic mutation, and clinicopathological information from The Cancer Genome Atlas database and mitophagy-related gene sets from the Reactome database. (biomedcentral.com)
RNA-directed DNA methylation results in a characteristic modification pattern that is typified by methylation of cytosines in all sequence contexts (CG, CHG and CHH, where H is A, T or C) within the region of small RNA-DNA sequence homology [ 4 ]. (biomedcentral.com)
The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS. (bvsalud.org)

Downstream genes, including lncRNA‑NEAT1 and TF‑ETV5, may also have potential functions in the regulated network by USF1 and have potential functions in the progression of HCC. (spandidos-publications.com)

Here, we report both genomically local and distal RNA-dependent roles of Dali, a conserved central nervous system expressed intergenic lncRNA. (ox.ac.uk)
These results demonstrate, for the first time, that a single intergenic lncRNA controls the activity and methylation of genomically distal regulatory elements to modulate large-scale transcriptional programmes. (ox.ac.uk)

This SNP mapped to a locus on chromosome 5q35.2 harboring genes involved in neuronal development and regeneration. (nature.com)
Sorek's team unraveled an interesting gene fusion event involving genes called PIP5K1A and PSD4, which reside side by side on human chromosome 1. (cshlpress.com)
These genes produce a fusion product that, during the course of evolution, inserted into a different location in the human genome (chromosome 10), becoming a new gene that is actively transcribed in a variety of tissues. (cshlpress.com)

The role of HMT gene variants in prostate cancer remains unknown. (cancerindex.org)
Concretely, genome-wide association studies have detected numerous asthma-associated gene variants, while few of them (less than 10%) can be explained to contribute to the risk of asthma [ 10 ]. (researchsquare.com)
Genome-wide association studies (GWAS) attempt to link genetic variants to nearby genes, relying on standard catalogs of human genes. (biomedcentral.com)
Many software packages that analyze RNA sequencing (RNA-seq) experiments, which measure gene expression, rely on a database of known genes and cannot measure genes or splice variants unless they are included in the database. (biomedcentral.com)
We additionally performed exome-sequencing analysis in 960 individuals to investigate rare variants in candidate genes. (frontiersin.org)
We performed additional in silico analyses to identify more evidence for the associated variants and genes in relation to the plasma MPO-DNA complex levels. (frontiersin.org)

QIAseq Stranded RNA Library Kits are intended for molecular biology applications. (qiagen.com)
However, molecular genetics quickly introduced difficulties with the theory of atomistic genes aligned like beads on a string. (huffpost.com)
The basic issue is that molecular genetics has made it impossible to provide a consistent, or even useful, definition of the term "gene. (huffpost.com)

Identification of PARD3 signature on PARD3 deficient H157 cell line, reconstituting the expression of PARD3 gene, with a wt and a mutant form. (nih.gov)
A biological process that is crucial for gene expression in most animal life, including humans. (genomicglossaries.com)
presents an opportunity to manipulate gene expression within the cells to treat various diseases, and acts as a powerful tool for studying gene function utilizing antisense agents to manage the diseases by regulating the expression of the specific factor that actually causes the particular disease. (genomicglossaries.com)
A gene signature based on the top screening hits, the authors added, correlated with a gene expression signature of BRAF inhibitor resistance in cell lines and patient-derived samples. (genengnews.com)
On the other hand, environmental factors have been reported to modulate epigenetic modifications and thereby affect gene expression and phenotype [ 11 , 12 ]. (researchsquare.com)
As a TF, USF1 has a bidirectional regulatory function, being able to regulate gene expression by activating or suppressing the promoter region of target genes ( 5 , 6 ). (spandidos-publications.com)
Analysis of the splicing events and RNA-Seq based expression profiles revealed the landscapes of gene structures, untranslated regions, and splicing activities to be more intricate than previously appreciated. (jcvi.org)
Monocytes were purified from white blood cells of healthy blood donors to detect cis-acting genetic variation that regulates the expression of long non-coding RNAs. (scilifelab.se)
Focusing on the intergenic regions, and using stringent analysis of the allele-specific expression data, we detected robust cis-regulatory SNPs in 258 out of 489 informative intergenic regions included in the analysis. (scilifelab.se)
In this study, our main goal was to determine these signatures, by evaluating the gene expression of paired colorectal adenoma and adenocarcinoma samples to identify novel genetic markers in association to the adenoma-adenocarcinoma stage transition. (bvsalud.org)
METHODS: Ten paired adenoma and adenocarcinoma colorectal samples were subjected to microarray gene expression analysis. (bvsalud.org)
Systematic interrogation of gene function requires the ability to perturb gene expression in a robust and generalizable manner. (cdc.gov)
The signature of our top screening hits is significantly correlated with gene expression data from clinical melanoma samples. (cdc.gov)
However, the comparative transcriptome analysis of two spinach accessions with different bolting times identified genome-wide gene expression profiling and large-scale discovery of flowering-related genes from vegetative and reproductive leaves [ 13 ]. (biomedcentral.com)
Consequently, little is known about how gene expression changes in response to genomic rearrangements in plastids. (biomedcentral.com)
We demonstrate that the expression of plastid coding genes is strongly functionally dependent among conifer species. (biomedcentral.com)
This finding indicates that plastomic rearrangement influences gene expression. (biomedcentral.com)
We also compared plastid gene expression levels among conifers and demonstrated a strong association between gene expression and plastomic rearrangements. (biomedcentral.com)
The AAV non-coding RNA expression vector is a highly efficient vehicle for in vitro and in vivo delivery of non-coding RNAs of interest. (vectorbuilder.kr)
The AAV non-coding RNA expression vector is first constructed as a plasmid in E. coli. (vectorbuilder.kr)

The results showed that USF1 significantly regulates 350 differentially expressed genes (DEGs). (spandidos-publications.com)

When Barbara McClintock and Curt Stern demonstrated simultaneously in 1931 that genetic markers of plants (maize) and animals (Drosophila) locate on visible chromosomes, the idea began to crystallize that that the genotype consisted of linear arrays of genes strung along chromosomes like "beads on a string. (huffpost.com)

To date, various genome-scale loss-of-function screening methods have been developed, including approaches employing RNA interference 1 , 2 and the RNA-guided endonuclease Cas9 from the microbial CRISPR (clustered regularly interspaced short palindromic repeat) adaptive immune system 3 , 4 . (cdc.gov)

Soon after fertilization, the vast majority of methylcytosine in sperm is converted by the Tet3 enzyme to hydroxymethylcytosine that gets lost by dilution during replication, effectively erasing cytosine methylation patterns except for a subset that is maintained, including those of some imprinted genes. (i-sis.org.uk)

This updated Arabidopsis genome annotation with a substantially increased resolution of gene models will not only further our understanding of the biological processes of this plant model but also of other species. (jcvi.org)
In order to confirm that the sRNAs suppressed their targets using their host's RNAi pathways, the investigators immunoprecipitated Argonaute 1 - the primary component of the RNA-induced silencing complex that enables RNAi - from Arabidopsis and identified the three sRNAs they have been studying in Ago1-associated fraction pulled from B. cinerea -infected plant samples but not controls. (genomeweb.com)
We performed a methylation-sensitive amplification polymorphism analysis to search for targets of RNA-directed DNA methylation in Arabidopsis thaliana and identified several members of a gene family encoding cysteine-rich peptides (CRPs). (biomedcentral.com)

Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (nih.gov)

Efforts to identify cancer-causing mutations usually focus on mutations that involve known genes, ignoring mutations that occur in other regions. (biomedcentral.com)
We analysed 8929 regions harboring genes for potential long non-coding RNA that were retrieved from data from the ENCODE project. (scilifelab.se)
These arose both from within annotated genes and from unannotated intergenic regions. (inra.fr)
When focusing on these regions, the researchers identified six TIC events (involving 3.6% of tandem gene pairs), only one of which was identified during the whole-genome survey. (cshlpress.com)

Among the nTARs, 146 share significant similarity with proteins that have been identified in other species suggesting that they are hitherto unidentified genes in C. graminicola . (biomedcentral.com)
The understanding that some gene pairs are naturally produced as fused proteins might lead, in the future, to the development of non-toxic engineered fused proteins that could be used as drugs. (cshlpress.com)

B. Duplicated pseudogenes: DNA duplication generates a more-or-less faithful copy of the original gene, including introns and, in many cases, promoter and other transcriptional regulatory elements. (pandasthumb.org)

It is unclear how the different methylation machineries distinguish between transposons and genes. (biomedcentral.com)
Here we report on a group of atypical genes that display in their coding region a transposon-like methylation pattern, which is associated with gene silencing in sporophytic tissues. (biomedcentral.com)
Methylation in the coding region is reduced, however, in the synergid cells of the female gametophyte, where the CRP genes are specifically expressed. (biomedcentral.com)
We discuss this unusual methylation pattern and its alteration in synergid cells as well as the possible retrogene origin and evolutionary significance of CRP genes that are methylated like transposons. (biomedcentral.com)
In particular, asymmetric CHH methylation is a hallmark of RNA-directed DNA methylation. (biomedcentral.com)

Results In the present study, we performed a systematic transcriptome analysis based on the deep RNA sequencing of ten asthmatic children before and after desensitization treatment. (researchsquare.com)

Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes. (genomicglossaries.com)
That is, it had demonstrated only limited success as a way to activate specific genes. (genengnews.com)

The long non-coding RNA Dali is an epigenetic regulator of neural differentiation. (ox.ac.uk)
That was the beginning of the epigenetic revolution [1] ( Epigenetic Inheritance - What Genes Remember , SiS 41). (i-sis.org.uk)

Mutations in the APC, DCC, KRAS and TP53 genes have been associated with the progression of sporadic CRC, occurring at defined pathological stages of the tumor progression and consequently modulating several genes in the corresponding signaling pathways. (bvsalud.org)
In addition, mutations in APC, KRAS and TP53 genes were investigated by DNA sequencing in paired samples of adenoma, adenocarcinoma, normal tissue, and peripheral blood from ten patients. (bvsalud.org)
In most cases, this duplicated gene will undergo crippling, inactivating mutations and turn into a pseudogene (in rarer cases, the duplicated copy will acquire new functions and become a new gene). (pandasthumb.org)

Moving forward, Khalil hopes to develop RNA-based therapeutic approaches in which cancer cells can be targeted without affecting neighboring healthy cells. (case.edu)

By the conventional view, if genes are the only important actors, then these surprisingly abundant "intergenic" repeats must constitute " junk DNA " and be " ultimate parasites " in the genome. (huffpost.com)

Wendell Read just sent me notice of a new paper in Genome Biology linking transposable elements, long intergenic non-coding RNAs, and cell type. (huffpost.com)

The research team based their work on their analysis (published earlier this year) of the structure formed when Cas9 binds to the guide RNA and its target DNA. (genengnews.com)
It was also demonstrated that USF1 directly binds to the promoter region of 2,492 genes, which may be involved in the viral progression and cell proliferation pathways. (spandidos-publications.com)
In summary, the results demonstrated that USF1 binds to the promoter region of thousands of genes and affects a large part of DEGs indirectly. (spandidos-publications.com)

Functionally related genes are commonly found in clusters and are likely co-transcribed as operons [ 10 ]. (biomedcentral.com)

The silencing was abolished, however, when the target genes carried a synonymously mutated version of the relevant" B. cinerea sRNA. (genomeweb.com)
Although the plants showed normal morphology and development in the absence of pathogen challenge, even though the target genes were suppressed, all three displayed "enhanced susceptibility" to infection upon introduction of B. cinerea . (genomeweb.com)

In this first GWAS and exome-sequencing analysis of NETs levels, we found several genes that were associated with NETs. (frontiersin.org)

This screen was designed to identify genes that confer resistance to a melanoma drug called PLX-4720. (genengnews.com)

A better gene list may also help to explain the genetic causes of the many complex diseases that have thus far remained largely unexplained, despite hundreds of large GWAS and other experiments. (biomedcentral.com)
Most of the identified genetic variation was found in genes controlling the host response to microbes [ 14 ]. (biomedcentral.com)

Analyze stranded RNA-seq data with ease using the GeneGlobe-integrated RNA-seq Analysis Portal - an intuitive, web-based data analysis solution created for biologists and included with QIAseq Stranded RNA Library Kits. (qiagen.com)
Module analysis disclosed 17 genes associated to asthma at distinct level. (researchsquare.com)
The Kim lab recently completed RNA sequencing analysis to measure the dysregulation of genes in response to these factors in zebrafish embryos. (umaine.edu)
Gene set variation analysis was performed to assess potential differences in biological functions between the two groups. (biomedcentral.com)

Anatomy9

Organisms17

Chemicals and Drugs83

Analytical, Diagnostic and Therapeutic Techniques and Equipment21

Phenomena and Processes88

Disciplines and Occupations2

Anthropology, Education, Sociology and Social Phenomena1

Information Science5

Health Care1

LncRNAs15

Transcripts15

Molecules11

Protein24

Endogenous6

LincRNAs2

Noncoding RNAs4

Sequences4

NcRNAs4

Indicating that USF1 may indirectly1

NcRNA2

Transcription9

Loci1

Polymerase II promoter1

Sequencing RNA-Seq data1

MiRNAs2

Natural antisense1

Small RNAs8

MRNA8

Regulation2

Biogenesis1

Functional5

Datasets2

Pathway6

Whole transcriptome1

Enhancer3

Sequence9

Downstream1

LncRNA2

Chromosome3

Variants6

Molecular3

Expression20

Differentially1

Chromosomes1

Interference1

Cytosine methylation1

Arabidopsis3

Putative1

Regions4

Proteins2

Regulatory1

Methylation5

Transcriptome analysis1

Specific genes2

Epigenetic2

Mutations3

Khalil1

Repeats1

Genome Biology1

Binds3

Functionally1

Target genes2

Several genes1

Identify genes1

Genetic2

Analysis4