Genes long intergenic rna gene. Medical search. Frequent questions

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)
and a plethora of 'intergenic', overlapping, antisense and intronic transcripts. (blogspot.com)
Some lncRNAs originate from intragenic enhancers which, when active, behave as alternative promoters producing transcripts that are processed using the canonical signals of their host gene. (biomedcentral.com)
These two classes of 5′ capped and polyadenylated RNA transcripts are indistinguishable with regard to their length, number of exons or transcriptional orientation relative to their closest neighboring gene. (biomedcentral.com)
We have determined globally the sites of initiation of intergenic lncRNAs in erythroid cells, allowing us to distinguish two similarly abundant classes of transcripts. (biomedcentral.com)
First, what is the relative prevalence of promoter- and enhancer-associated transcripts within sets of transcripts that are annotated simply as being intergenic lncRNAs? (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)
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)
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)

Mammalian transcriptomes contain thousands of long noncoding RNAs (lncRNAs). (biomedcentral.com)
We have followed up this observation by analyzing intergenic lncRNAs to determine the extent to which they might also originate from intergenic enhancers. (biomedcentral.com)
We integrated high-resolution maps of transcriptional initiation and transcription to annotate a conservative set of intergenic lncRNAs expressed in mouse erythroblasts. (biomedcentral.com)
We subclassified intergenic lncRNAs according to chromatin status at transcriptional initiation regions, defined by relative levels of histone H3K4 mono- and trimethylation. (biomedcentral.com)
Different correlations between the levels of elncRNAs, plncRNAs and expression of neighboring genes suggest that functional lncRNAs from the two classes may play contrasting roles in regulating the transcript abundance of local or distal loci. (biomedcentral.com)
At least 50,000 lncRNAs are expressed from intergenic regions of the human genome, more than twice the number of protein-coding genes [ 5 ]. (biomedcentral.com)
In this study, for simplicity, we refer to intergenic lncRNAs as those that are transcribed by RNA-polymerase II, 5′ end capped and polyadenylated. (biomedcentral.com)
Here we address two important, and incompletely answered, questions concerning the origins (transcriptional initiation regions (TIRs)) and classification of intergenic lncRNAs. (biomedcentral.com)
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)
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)

Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. (genomicglossaries.com)
Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes. (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)
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)
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 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)
The list of non-coding RNA genes (antisense or long intergenic) was downloaded from HGNC and the transcription start sites from Ensembl Genes 95. (expasy.org)
CTBP1 antisense RNA [Source:HGN. (gsea-msigdb.org)

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)
This section includes genomic Reference Sequences (RefSeqs) from all assemblies on which this gene is annotated, such as RefSeqs for chromosomes and scaffolds (contigs) from both reference and alternate assemblies. (nih.gov)
RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. (genomicglossaries.com)
Various combinations of coding sequences and signals operate dynamically to produce multiple RNA and protein molecules from a single stretch of DNA. (huffpost.com)
Finally, C) hundreds of thousands of intergenic smORFs appear in the genome as DNA sequences neither conserved nor transcribed, but resembling dwarf smORFs in the other aspects. (cabd.es)
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)

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)

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)
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)
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)
Many intergenic long noncoding RNA (lncRNA) loci regulate the expression of adjacent protein coding genes. (ox.ac.uk)
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)

Long intergenic non-protein coding RNA 483 is a protein that in humans is encoded by the LINC00483 gene. (wikipedia.org)
The mammalian genome harbors only ∼20 000 protein-coding genes, similar in number and with largely orthologous functions as those in other animals, including simple nematodes. (blogspot.com)
Moreover, high throughput analyses have shown that the majority of the mammalian genome is differentially and dynamically transcribed during development to produce tens if not hundreds of thousands of short and long non-protein-coding RNAs that show highly specific expression patterns and subcellular locations. (blogspot.com)
What does this gene/protein do? (cancerindex.org)
What pathways are this gene/protein implicaed in? (cancerindex.org)
Of considerable interest, we found that expression of elncRNAs, but not plncRNAs, is associated with enhanced expression of neighboring protein-coding genes during erythropoiesis. (biomedcentral.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)
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)
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)
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)
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)
long intergenic non-protein cod. (gsea-msigdb.org)
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)

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)
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)
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)

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)
Programmable DNA binding proteins have emerged as an exciting platform for engineering synthetic transcription factors for modulating endogenous gene expression 5 - 11 . (cdc.gov)
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)

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)

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)

Second, do differences in the chromatin status at intergenic lncRNA TIRs reflect their potential function? (biomedcentral.com)
By integrating these two datasets, 16 overlapped genes were detected, including downregulated lncRNA‑NEAT1 and upregulated TF‑ETV5. (spandidos-publications.com)
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)
Finally, a lncRNA prognostic signature-related competing endogenous RNA (ceRNA) network was constructed. (biomedcentral.com)

Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.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)

The Kim lab is particularly interested in the role of micro-RNAs (miRNA) and long intergenic non-coding RNAs (lincRNAs). (umaine.edu)
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)

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)

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)
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)

These dCas9-activator fusions targeted to the promoter region of endogenous genes can then modulate gene expression 7 - 11 . (cdc.gov)

After second- strand cDNA synthesis, T7 RNA polymerase was used to generate aRNA. (genomicglossaries.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)

Transcriptome analysis has been utilized extensively to identify non-coding RNAs such as miRNAs and long intergenic non-coding (LINC) RNAs. (intechopen.com)

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

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)

Moreover, like the major introns, we found that these AS events were more prevalent in long minor introns, while retention was favoured in shorter introns. (biomedcentral.com)
Splicing of introns is required for the expression of most eukaryotic genes. (biomedcentral.com)
In these minor intron-containing genes (MIGs), the majority of introns are usually spliced by the major spliceosome, with only one or two introns being spliced by the minor spliceosome. (biomedcentral.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)

Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (nih.gov)
B) Thousands of 'dwarf' smORFs appear in polycistronic arrangements in 80% of putative non-coding RNAs and in 60% of 5'UTRs of standard mRNAs (also called uORFs). (cabd.es)

The figure is supposed to show that by 2020 junk DNA had been eliminated and almost all of the mammalian genome is devoted to functional DNA-mostly in the form of noncoding genes. (blogspot.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)

He believes that he and his colleagues have discovered a vast world of noncoding genes responsible for intricate gene regulation in complex eukaryotes. (blogspot.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)
Given that the minor spliceosome is ubiquitously expressed, we hypothesized that these restricted phenotypes might be caused by the tissue-specific regulation of the minor spliceosome targets, i.e. minor intron-containing genes (MIGs). (biomedcentral.com)
Achieving systematic, genome-scale perturbations within intact biological systems is important for elucidating gene function and epigenetic regulation. (cdc.gov)

QIAseq Stranded RNA Library Kits are intended for molecular biology applications. (qiagen.com)
Mattick, J.S. (2023) A Kuhnian revolution in molecular biology: Most genes in complex organisms express regulatory RNAs. (blogspot.com)
The paradigm that has held sway since the inception of molecular biology is that genes (mainly) encode proteins. (blogspot.com)
Fig. 1: Molecular features that define enhancer RNAs. (nature.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)
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)

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)
Model RNAs and proteins are also reported here. (nih.gov)
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)

Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. (inra.fr)

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)

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)

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)

There's only one very tiny problem with this picture-it's not supported by any evidence that all those functional noncoding genes exist. (blogspot.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)

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)

That is, it had demonstrated only limited success as a way to activate specific genes. (genengnews.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)

These observations suggest that the original conception of genetic information was deficient and that most genes in complex organisms specify regulatory RNAs, some of which convey intergenerational information. (blogspot.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)
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)

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)
We analysed 8929 regions harboring genes for potential long non-coding RNA that were retrieved from data from the ENCODE project. (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)
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)

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)
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)

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)

To understand how the immune system is being modulated by these factors the role of non-coding RNAs (ncRNA) were investigated. (umaine.edu)

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)

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 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)

Sternberg seems to think that redefining the gene shows that evolutionary biology is out of touch with reality. (blogspot.com)
The identification of DNA as the key molecule of heredity and Crick's Central Dogma of Molecule Biology initially seemed to confirm Beadle and Tatum's "one gene -- one enzyme" hypothesis. (huffpost.com)

Schoenfelder, S. & Fraser, P. Long-range enhancer-promoter contacts in gene expression control. (nature.com)

Then he brings up the ENCODE results and claims that they challenged the concept of a gene (not true). (blogspot.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)
METHODS: Ten paired adenoma and adenocarcinoma colorectal samples were subjected to microarray gene expression analysis. (bvsalud.org)
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)

HGNC, TSS collection for non-coding RNAs. (expasy.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)
Dr. Roderic Guig�'s group from the Centre de Regulaci� Gen�mica (Barcelona, Spain), in collaboration with the group of Dr. Stylianos Antonarakis from the University of Geneva (Switzerland), and Dr. Rotem Sorek's team from Compugen (Tel Aviv, Israel) independently derived estimates that at least 2-5% of the genes in the human genome are involved in these events. (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)

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)

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)

RNA-Seq offers the potential for substantially improved gene annotations and for the identification of posttranscriptional RNA modifications, such as alternative splicing and RNA editing. (biomedcentral.com)

Genes up-regulated in monocytes (6h): muramyl dipeptide [PubChem=11620162] versus muramyl dipeptide [PubChem=11620162] and M. tuberculosis 19 kDa lipopeptide. (gsea-msigdb.org)
human blood monocytes were isolated, activated and harvested at several timepoints In this study, we identified genes that were differentially expressed in human monocytes activated with eiter NOD2L and/or TLR2/1L. (gsea-msigdb.org)

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

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Transcripts14

LncRNAs16

Antisense8

Noncoding RNAs4

Sequences7

Indicating that USF1 may indirectly1

Loci5

Protein21

Molecules7

Transcription7

NcRNAs4

Transcript1

LncRNA6

Datasets1

Small RNAs5

MiRNA2

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Sequence8

Endogenous1

Polymerase2

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Introns4

Putative2

Mammalian1

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Regulation4

Molecular7

Proteins3

Post-transcriptional1

Chromatin1

Pathway3

Interference1

Functional nonco1

Roles1

Transcriptome analysis1

Specific genes1

Regulate gene expression1

Organisms1

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Several genes2

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