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Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

ABSTRACT: Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

PROVIDER: PRJNA214036 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR946996_1.fastq.gz	Fastqsanger.gz
	SRR946996_2.fastq.gz	Fastqsanger.gz
	SRR946997_1.fastq.gz	Fastqsanger.gz
	SRR946997_2.fastq.gz	Fastqsanger.gz
	SRR946998_1.fastq.gz	Fastqsanger.gz

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Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs.

Project description:BACKGROUND:Mammalian transcriptomes contain thousands of long noncoding RNAs (lncRNAs). 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. We have followed up this observation by analyzing intergenic lncRNAs to determine the extent to which they might also originate from intergenic enhancers. RESULTS:We integrated high-resolution maps of transcriptional initiation and transcription to annotate a conservative set of intergenic lncRNAs expressed in mouse erythroblasts. We subclassified intergenic lncRNAs according to chromatin status at transcriptional initiation regions, defined by relative levels of histone H3K4 mono- and trimethylation. These transcripts are almost evenly divided between those arising from enhancer-associated (elncRNA) or promoter-associated (plncRNA) elements. 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. Nevertheless, elncRNAs are more tissue-restricted, less highly expressed and less well conserved during evolution. Of considerable interest, we found that expression of elncRNAs, but not plncRNAs, is associated with enhanced expression of neighboring protein-coding genes during erythropoiesis. CONCLUSIONS:We have determined globally the sites of initiation of intergenic lncRNAs in erythroid cells, allowing us to distinguish two similarly abundant classes of transcripts. 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.

| S-EPMC4054604 | biostudies-literature

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

Project description:This SuperSeries is composed of the SubSeries listed below.

2013-11-11 | GSE49460 | GEO

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-11-11 | E-GEOD-49460 | biostudies-arrayexpress

Single Nucleus Transcriptomics Identifies Separate Classes of UCP1 and Futile Cycle Adipocytes

Project description:Single Nucleus Transcriptomics Identifies Separate Classes of UCP1 and Futile Cycle Adipocytes

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Single Nucleus Transcriptomics Identifies Separate Classes of UCP1 and Futile Cycle Adipocytes [mouse snRNA-seq]

Project description:Single Nucleus Transcriptomics Identifies Separate Classes of UCP1 and Futile Cycle Adipocytes [mouse snRNA-seq]

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Single Nucleus Transcriptomics Identifies Separate Classes of UCP1 and Futile Cycle Adipocytes [human snRNA-seq]

Project description:Single Nucleus Transcriptomics Identifies Separate Classes of UCP1 and Futile Cycle Adipocytes [human snRNA-seq]

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Single Nucleus Transcriptomics Identifies Separate Classes of UCP1 and Futile Cycle Adipocytes [mouse snRNA-Seq Ucp1KO]

Project description:Single Nucleus Transcriptomics Identifies Separate Classes of UCP1 and Futile Cycle Adipocytes [mouse snRNA-Seq Ucp1KO]

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Genome Wide Analysis of Immune Activation in Human T and B Cells Reveals Distinct Classes of Alternatively Spliced Genes

Project description:Alternative splicing of pre-mRNA is a mechanism that increases the protein diversity of a single gene by differential exon inclusion during post-transcriptional processing. While alternative splicing is established to occur during lymphocyte activation, little is known about the role it plays during the immune response. Our study is among the first reports of a systematic genome-wide analysis using whole exon DNA microarrays integrating alternative splicing and differential gene expression. Purified human CD2+ T or CD19+ B cells were activated using protocols to model the early events in post-transplant allograft immunity and sampled as a function of time during the process of immune activation. Here we show that 3 distinct classes of alternatively spliced and/or differentially expressed genes change in an ordered manner as a function of immune activation. We mapped our results to function-based canonical pathways and demonstrated that some are populated by only one class of genes, like integrin signaling, while other pathways, such as purine metabolism and T cell receptor signaling, are populated by all three classes of genes. Our studies augment the current view of T and B cell activation in immunity that has been based exclusively upon differential gene expression by providing evidence for a large number of molecular networks populated as a function of time and activation by alternatively spliced genes, many of which are constitutively expressed. Keywords: T cells, B cells, alternative splicing, exon

2010-01-08 | GSE14352 | GEO

Expression in Intergenic Regions

Project description:Contains a row for each intergenic region in each sample, indicating whether our analysis called a window within the region "present" or "absent" in the sample. Intergenic regions are regions containing neither annotated genes nor intergenic clusters. Region coordinates refer to version 3 of the TIGR annotation as submitted to GenBank (GI numbers 22330780, 22326553, 22331929, 22329272, 22328163). Keywords: other

2003-10-30 | GSE639 | GEO

Expression in Intergenic Regions

2010-06-05 | E-GEOD-639 | biostudies-arrayexpress