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Unknown,Transcriptomics,Genomics,Proteomics

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Two-step RNA sequencing identifies a tissue-specific landscape of sense/antisense transcription

ABSTRACT: We report the complexity of the polyadenylated transcriptome of the mouse intestinal tract assessed by two step RNA sequencing. Screening and verification of non-annotated transcriptional units by different RNA-Seq protocols.

ORGANISM(S): Mus musculus

SUBMITTER: Robert Haesler

PROVIDER: E-GEOD-28207 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A tissue-specific landscape of sense/antisense transcription in the mouse intestine.

Klostermeier Ulrich C UC Barann Matthias M Wittig Michael M Häsler Robert R Franke Andre A Gavrilova Olga O Kreck Benjamin B Sina Christian C Schilhabel Markus B MB Schreiber Stefan S Rosenstiel Philip P

BMC genomics 20110610

<h4>Background</h4>The intestinal mucosa is characterized by complex metabolic and immunological processes driven highly dynamic gene expression programs. With the advent of next generation sequencing and its utilization for the analysis of the RNA sequence space, the level of detail on the global architecture of the transcriptome reached a new order of magnitude compared to microarrays.<h4>Results</h4>We report the ultra-deep characterization of the polyadenylated transcriptome in two closely r ...[more]

PMID: 21663663

Similar Datasets

Architectural complexity of the polyadenylated intestinal transcriptome revealed by hybrid RNA sequencing

Project description:We report the complexity of the polyadenylated transcriptome of the mouse intestinal tract assessed by a hybrid RNA-sequencing. We show that 90.72% of the polyA-derived unique reads map to known genes, but 9.28% of reads matched to nonannotated genomic regions. Screening and verification of non-annotated transcriptional units by different RNA-Seq protocols.

2011-01-06 | E-GEOD-21699 | biostudies-arrayexpress

Two-step RNA sequencing identifies a tissue-specific landscape of sense/antisense transcription

Project description:We report the complexity of the polyadenylated transcriptome of the mouse intestinal tract assessed by two step RNA sequencing.

2011-03-29 | GSE28207 | GEO

Characterization of Basal and Estrogen-Regulated Antisense Transcription in Breast Cancer Cells: Role in Regulating Sense Transcription

Project description:We have mined genomic data to define three classes of antisense transcription in MCF-7 cells based on where their antisense transcription termination sites reside relative to their cognate sense mRNA and lncRNA genes. These three classes differ in their response to estrogen treatment, the enrichment of a number of genomic features associated with active promoters (H3K4me3, RNA polymerase II, open chromatin architecture), and the biological functions of their cognate sense genes as analyzed by DAVID gene ontology. We further characterized two estrogen-regulated antisense transcripts arising from the MYC gene in MCF-7 cells, showing that these antisense transcripts are five-prime capped, three-prime polyadenylated, and localized to different compartments of the cell.

2022-08-02 | GSE140210 | GEO

Altered antisense-to-sense transcript ratios in breast cancer: Sage-Seq

Project description:Transcriptome profiling studies suggest that a large fraction of the genome is transcribed and many transcripts function independent of their protein coding potential. The relevance of noncoding RNAs (ncRNAs) in normal physiological processes and in tumorigenesis is increasingly recognized. Here, we describe consistent and significant differences in the distribution of sense and antisense transcripts between normal and neoplastic breast tissues. Many of the differentially expressed antisense transcripts likely represent long ncRNAs. A subset of genes that mainly generate antisense transcripts in normal but not cancer cells is involved in essential metabolic processes. These findings suggest fundamental differences in global RNA regulation between normal and cancer cells that might play a role in tumorigenesis. Global transcriptome profilings of 12 samples in normal and 9 samples in cancer from clinical breast tissue using Sage-Seq.

2010-12-10 | E-GEOD-25291 | biostudies-arrayexpress

Altered antisense-to-sense transcript ratios in breast cancer: ASSAGE

Project description:Transcriptome profiling studies suggest that a large fraction of the genome is transcribed and many transcripts function independent of their protein coding potential. The relevance of noncoding RNAs (ncRNAs) in normal physiological processes and in tumorigenesis is increasingly recognized. Here, we describe consistent and significant differences in the distribution of sense and antisense transcripts between normal and neoplastic breast tissues. Many of the differentially expressed antisense transcripts likely represent long ncRNAs. A subset of genes that mainly generate antisense transcripts in normal but not cancer cells is involved in essential metabolic processes. These findings suggest fundamental differences in global RNA regulation between normal and cancer cells that might play a role in tumorigenesis. Global strand-specific transcriptome profilings of 2 samples in cancer and 1 sample in normal from clinical breast tissue using asymmetrical strand-specific analysis of gene expression (ASSAGE).

2010-12-10 | E-GEOD-25932 | biostudies-arrayexpress

Antisense Drugs Make Sense for Neurological Diseases.

Project description:The genetic basis for most inherited neurodegenerative diseases has been identified, yet there are limited disease-modifying therapies for these patients. A new class of drugs-antisense oligonucleotides (ASOs)-show promise as a therapeutic platform for treating neurological diseases. ASOs are designed to bind to the RNAs either by promoting degradation of the targeted RNA or by elevating expression by RNA splicing. Intrathecal injection into the cerebral spinal fluid results in broad distribution of antisense drugs and long-term effects. Approval of nusinersen in 2016 demonstrated that effective treatments for neurodegenerative diseases can be identified and that treatments not only slow disease progression but also improve some symptoms. Antisense drugs are currently in development for amyotrophic lateral sclerosis, Huntington's disease, Alzheimer's disease, Parkinson's disease, and Angelman syndrome, and several drugs are in late-stage research for additional neurological diseases. This review highlights the advances in antisense technology as potential treatments for neurological diseases.

| S-EPMC8682074 | biostudies-literature

Spt6 regulates intragenic and antisense transcription, nucleosome positioning, and histone modifications genome-wide in fission yeast [ChIP-seq]

Project description:Spt6 is a highly conserved histone chaperone that interacts directly with both RNA polymerase II and histones to regulate gene expression. To gain a comprehensive understanding of the requirements for this critical factor, we have performed genome-wide analyses of transcription, chromatin structure, and histone modifications in an S. pombe spt6 mutant. Our results demonstrate several dramatic changes to transcription and chromatin structure in the spt6 mutant, including an elevation of antisense transcripts at over 70 percent of all genes and general loss of the +1 nucleosome. Furthermore, Spt6 is required for the trimethylation of histone H3 on lysines 4 and 36, marks associated with active transcription. Taken together, our results indicate that Spt6 is critical for the accuracy of transcription and the integrity of chromatin, likely via its direct interactions with RNA polymerase II and histones. ChIP-seq experiments were performed on wild type and spt6-1 strains on the following proteins: RNA polymerase II (Rpb1), Paf1 Complex (Ctr9), COMPASS (Swd1), Set2, Spt6, histones H2B and H3, histone modifications H3K4me3 and H3K36me3. Experiments were performed in replicates and matching inputs were also sequenced.

2013-10-09 | E-GEOD-49574 | biostudies-arrayexpress

Characterization of plastid psbT sense and antisense RNAs.

Project description:The plastid psbB operon is composed of the psbB, psbT, psbH, petB and petD genes. The psbN gene is located in the intergenic region between psbT and psbH on the opposite DNA strand. Transcription of psbN is under control of sigma factor 3 (SIG3) and psbN read-through transcription produces antisense RNA to psbT mRNA. To investigate on the question of whether psbT gene expression might be regulated by antisense RNA, we have characterized psbT sense and antisense RNAs. Mapping of 5' and 3'-ends by circular RT-PCR and /or 5'-RACE experiments reveal the existence of two different sense and antisense RNAs each, one limited to psbT RNA and a larger one that covers, in addition, part of the psbB coding region. Sense and antisense RNAs seem to form double-stranded RNA/RNA hybrids as indicated by nuclease digestion experiments followed by RT-PCR amplification to reveal nuclease resistant RNA. Western immunoblotting using antibodies made against PSBT protein and primer extension analysis of different plastid mRNA species and psbT antisense RNA suggest that sequestering of psbT mRNA by hybrid formation results in translational inactivation of the psbT mRNA and provides protection against nucleolytic degradation of mRNA during photooxydative stress conditions.

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Convergent Sense/Antisense Transcription At Intragenic Super-Enhancers Targets AID-initiated Genomic Instability

Project description:Activation-induced cytidine deaminase (AID) initiates both somatic hypermutation (SHM) for antibody affinity maturation and DNA breakage for antibody class switch recombination (CSR) via transcription-dependent cytidine deamination of single stranded DNA targets. While largely specific for immunglobulin genes, AID also acts on a limited set of off-targets, generating oncogenic translocations and mutations that contribute to B cell lymphoma. How AID is recruited to off-targets has been a long-standing mystery. Based on deep GRO-Seq studies of mouse and human B lineage cells activated for CSR or SHM, we report that most robust AID off-target translocations occur within highly focal regions of target genes in which sense and antisense transcription converge. Moreover, we found that such AID-targeting "convergent" transcription arises from antisense transcription that emanates from Super-Enhancers within sense transcribed gene bodies. Our findings provide a mechanistic explanation for AID off-targeting to a small subset of mostly lineage-specific genes in activated B cells. We performed GRO-Seq and H3K27Ac ChIP-Seq with different B lineage cell types and MEF cells to find the signatures associated with AID targeting.

2014-12-04 | E-GEOD-62296 | biostudies-arrayexpress

Antisense transcription-dependent chromatin signature modulates sense transcript dynamics.

Project description:Antisense transcription is widespread in genomes. Despite large differences in gene size and architecture, we find that yeast and human genes share a unique, antisense transcription-associated chromatin signature. We asked whether this signature is related to a biological function for antisense transcription. Using quantitative RNA-FISH, we observed changes in sense transcript distributions in nuclei and cytoplasm as antisense transcript levels were altered. To determine the mechanistic differences underlying these distributions, we developed a mathematical framework describing transcription from initiation to transcript degradation. At GAL1, high levels of antisense transcription alter sense transcription dynamics, reducing rates of transcript production and processing, while increasing transcript stability. This relationship with transcript stability is also observed as a genome-wide association. Establishing the antisense transcription-associated chromatin signature through disruption of the Set3C histone deacetylase activity is sufficient to similarly change these rates even in the absence of antisense transcription. Thus, antisense transcription alters sense transcription dynamics in a chromatin-dependent manner.

| S-EPMC5810148 | biostudies-literature

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