Search Results for: long noncoding rna expression
Chromosome conformation capture-on-chip analysis of long-range cis-interactions of the SOX9 promoter
Evolutionarily conserved transcription factor SOX9 is essential for the differentiation of chondrocytes and the development of testes. Heterozygous point mutations and genomic deletions involving SOX9 lead to campomelic dysplasia (CD), a skeletal malformation syndrome often associated with sex reversal. Chromosomal rearrangements with breakpoints mapping up to 1.6 Mb up- and downstream to SOX9, and likely disrupting its distant cis-regulatory elements, have been described in patients with milder forms of CD. Based on the location of these aberration breakpoints, four clusters upstream of SOX9 have been defined.
Researchers at the Institute of Mother and Child, Poland have found that each of these intervals overlaps a gene encoding long noncoding RNA (lncRNA), suggesting that lncRNAs may contribute to long-range regulation of SOX9 expression. One of the four upstream regions, RevSex (517-595 kb 5′ to SOX9), is associated with sex reversal, and was suggested to harbor a testis-specific and sex-determining enhancer. Another sex-determining interval was mapped to a gene desert >1.3 Mb downstream of SOX9.
They have performed chromosome conformation capture-on-chip (4C) analysis in Sertoli cells and lymphoblasts to verify the proposed long-range interactions of the SOX9 promoter and to identify potential novel regulatory elements that might be responsible for sex reversal in patients with CD. They identified several novel potentially cis-interacting regions both up- and downstream to SOX9, with some of them overlapping lncRNA genes. This data point to lncRNAs as likely mediators of some of these regulatory interactions.
- Smyk M, Szafranski P, Startek M, Gambin A, Stankiewicz P. (2013) Chromosome conformation capture-on-chip analysis of long-range cis-interactions of the SOX9 promoter. Chromosome Res [Epub ahead of print]. [abstract]
Incoming search terms:
- lincrna promotoer
Long noncoding RNAs (lncRNAs) are a recently identified class of molecules that regulate the expression of protein-coding genes through a number of mechanisms, some of them poorly characterized. The GAL gene cluster of the yeast Saccharomyces cerevisiae encodes a series of three inducible genes that are turned on or off by the presence or absence of specific carbon sources in the environment. Previous studies have documented the presence of two lncRNAs—GAL10 and GAL10s—encoded by genes that overlap the GAL cluster.
Researchers at Purdue University have now uncovered a role for both these lncRNAs in promoting the activation of the GAL genes when they are released from repressive conditions. This activation occurs at the kinetic level, through more rapid recruitment of RNA polymerase II and decreased association of the co-repressor, Cyc8. Under normal conditions, but also especially when they are stabilized and their levels are up-regulated, these GAL lncRNAs promote faster GAL gene activation. The researchers suggest that these lncRNA molecules poise inducible genes for quick response to extracellular cues, triggering a faster switch in transcriptional programs.
- Cloutier SC, Wang S, Ma WK, Petell CJ, Tran EJ (2013) Long Noncoding RNAs Promote Transcriptional Poising of Inducible Genes. PLoS Biol 11(11), e1001715. [article]
We present here long-range epigenetic silencing (LRES) as a means for downregulation of stretches of the genome as well as long-range epigenetic activation (LREA). These two opposing effects appear to be mediated by an interplay between DNA methylation and chromatin modification. We’ve focused this analysis on an interrogation of prostate cancer.
Also presented herein are potential associations of long noncoding RNAs (lncRNAs) with distinct cancer classes. The potential utility of lncRNAs in finely modulating the expression of distinct regions of the genome makes this class of molecules attractive potential biomarkers and perhaps even therapeutic targets in the future.
Incoming search terms:
- lncRNA epigenetic
- epigenetic lncRNA
- genome with coding non-coding image
Deep RNA sequencing (RNA-Seq) has opened a new horizon for understanding global gene expression. The functional annotation of non-model mammalian genomes including bovines is still poor compared to that of human and mouse. This particularly applies to tissues without direct significance for milk and meat production, like skin, in spite of its multifunctional relevance for the individual.
Here, researchers fromthe Leibniz Institute for Farm Animal Biology, Germany performed a whole transcriptome analysis of pigmented and nonpigmented bovine skin to describe the comprehensive transcript catalogue of this tissue. A total of 39,577 unique primary skin transcripts were mapped to the bovine reference genome assembly. The majority of the transcripts were mapped to known transcriptional units (65%). In addition to the reannotation of known genes, a substantial number (10,884) of unknown transcripts (UTs) were discovered, which had not previously been annotated. The classification of UTs was based on the prediction of their coding potential and comparative sequence analysis, subsequently followed by meticulous manual curation. The classification analysis and experimental validation of selected UTs confirmed that RNA-Seq data can be used to amend the annotation of known genes by providing evidence for additional exons, untranslated regions or splice variants, by approving genes predicted in silico and by identifying novel bovine loci. A large group of UTs (4,848) was predicted to potentially represent long noncoding RNA (lncRNA). Predominantly, potential lncRNAs mapped in intergenic chromosome regions (4,365) and therefore, were classified as potential intergenic lncRNA. This analysis revealed that only about 6% of all UTs displayed interspecies conservation and discovered a variety of unknown transcripts without interspecies homology but specific expression in bovine skin.
The results of this study demonstrate a complex transcript pattern for bovine skin and suggest a possible functional relevance of novel transcripts, including lncRNA, in the modulation of pigmentation processes. The results also indicate that the comprehensive identification and annotation of unknown transcripts from whole transcriptome analysis using RNA-Seq data remains a tremendous future challenge.
- Weikard R, Hadlich F, Kuehn C. (2013) Identification of novel transcripts and noncoding RNAs in bovine skin by deep next generation sequencing. BMC Genomics 14(1), 789. [abstract]
Incoming search terms:
- classification lncrna
- long non-coding RNA classification
- long noncoding rna next generation sequencing non coding
- rna chromosome
from Genetic Engineering News 2013 (Vol. 33, No. 19) by Jeanene Swanson
RNAi screens for functional genomics typically look for loss- or gain-of-function phenotypes. They currently have many applications, including target discovery and validation, lead identification and optimization, mechanism of action discovery, predictive toxicology, and biomarker identification.
While reagents are gaining ground, technical difficulties remain in how best to perform and analyze these assays.
“RNAi reagents are being used ubiquitously,” says David Root, Ph.D., director of the RNAi Platform and project leader of the RNAi Consortium (TRC) at the Broad Institute. Dr. Root was among a handful of scientists and corporate partners who created one of the early genome-wide libraries of shRNA constructs (called TRC1). As of 2011, TRC2 has expanded the library (to 300,000 shRNAs) and has measured the knockdown performance of 100,000 of those constructs.
To perform RNAi screens, researchers can choose among a growing variety of reagents, including siRNA, shRNA, miRNA, and lncRNA constructs, as well as pooled libraries and constructs coupled to inducers. Synthetic siRNA has a transient effect, and it is eventually degraded. shRNA can be introduced into a cell within a lentiviral backbone, which allows the construct to be incorporated into the host cell’s genome and then stably expressed. This means the gene is always expressing the shRNA.
“Our philosophy has always been ‘siRNA if you can, shRNA if you must,’” says Christophe Echeverri, Ph.D., CEO and CSO of Cenix BioScience USA. “If the chosen cell system allows for good target knockdown by siRNA transfection, and the timeline needed for the experiments and assays is compatible with the duration of the siRNA effects, then it’ll almost certainly be an siRNA-based study.”
Incoming search terms:
- single cell lncRNA
- lncrna santa fe
- problems with shrna knockdown of lncrna
- non coding rna drug disovery
- miRNA and lncRNA
- long non-coding RNA next generation sequencing
- lncRNA TALEN
- lncrna editing
- function of coding region on genes