RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi.
Ontology highlight
ABSTRACT:
ORGANISM(S): Pyrococcus abyssi
PROVIDER: GSE58131 | GEO | 2014/05/31
SECONDARY ACCESSION(S): PRJNA249078
REPOSITORIES: GEO
Similar Datasets
Project description:The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi is investigated using the RNA-seq technology. A dedicated computational pipeline analyzes RNA-seq reads and prior genome annotation to identify small RNAs, untranslated regions of mRNAs, and cis-encoded antisense transcripts. Unlike other archaea, such as Sulfolobus and Halobacteriales, P. abyssi produces few leaderless mRNA transcripts. Antisense transcription is widespread (215 transcripts) and targets protein-coding genes that are less conserved than average genes. We identify at least three novel H/ACA-like guide RNAs among the newly characterized non-coding RNAs. Long 5' UTRs in mRNAs of ribosomal proteins and amino-acid biosynthesis genes strongly suggest the presence of cis-regulatory leaders in these mRNAs. We selected a high-interest subset of non-coding RNAs based on their strong promoters, high GC-content, phylogenetic conservation, or abundance. Some of the novel small RNAs and long 5' UTRs display high GC contents, suggesting unknown structural RNA functions. However, we were surprised to observe that most of the high-interest RNAs are AU-rich, which suggests an absence of stable secondary structure in the high-temperature environment of P. abyssi. Yet, these transcripts display other hallmarks of functionality, such as high expression or high conservation, which leads us to consider possible RNA functions that do not require extensive secondary structure. directional RNA-seq, Illumina GA-IIx
2014-05-31 | E-GEOD-58131 | biostudies-arrayexpress
Project description:There is abundant transcription from eukaryotic genomes unaccounted for by protein coding genes. A high-resolution genome-wide survey of transcription in a well annotated genome will help relate transcriptional complexity to function. By quantifying RNA expression on both strands of the complete genome of Saccharomyces cerevisiae using a high-density oligonucleotide tiling array, this study identifies the boundary, structure, and level of coding and noncoding transcripts. A total of 85% of the genome is expressed in rich media. Apart from expected transcripts, we found operon-like transcripts, transcripts from neighboring genes not separated by intergenic regions, and genes with complex transcriptional architecture where different parts of the same gene are expressed at different levels. We mapped the positions of 3' and 5' UTRs of coding genes and identified hundreds of RNA transcripts distinct from annotated genes. These nonannotated transcripts, on average, have lower sequence conservation and lower rates of deletion phenotype than protein coding genes. Many other transcripts overlap known genes in antisense orientation, and for these pairs global correlations were discovered: UTR lengths correlated with gene function, localization, and requirements for regulation; antisense transcripts overlapped 3' UTRs more than 5' UTRs; UTRs with overlapping antisense tended to be longer; and the presence of antisense associated with gene function. These findings may suggest a regulatory role of antisense transcription in S. cerevisiae. Moreover, the data show that even this well studied genome has transcriptional complexity far beyond current annotation.
2006-03-10 | E-TABM-14 | biostudies-arrayexpress
Project description:Three biological replicates of H. volcanii grown under optimal conditions to mid-exponential growth phase were used to determine the primary transcriptome and map 5â-ends of transcripts. In total, 4,749 potential transcriptional start sites (TSS) were detected. A position weight matrix was derived for promoter prediction, showing that 64% of the TSS were preceded by stringent or relaxed basal promoters. 1,851 TSS belonged to protein-coding genes, showing that less than half (46%) of the 4040 protein-coding genes are expressed under optimal growth conditions. 72% of all protein-coding transcripts were leaderless, underscoring that this is the default pathway for translation initiation in haloarchaea. The 5â-UTRs of transcripts with leaders had a widely varying length distribution without any optimum. 2,898 of the TSS belong to potential non-coding RNAs, representing an unexpectedly high fraction (61%) among all transcripts. 2792 of the non-coding TSS had not been described before and were thus novel (59% of all TSS). A large fraction of the potential novel non-coding transcripts are cis-antisense RNAs (1,244 aTSS). There was a strong negative correlation between the levels of antisense transcripts and cognate sense mRNAs, suggesting that negative regulation of gene expression via antisense RNAs may play an important role in haloarchaea. The other types of novel non-coding transcripts correspond to internal transcripts overlapping with mRNAs (1,153 iTSS) and intergenic small RNA (sRNA) candidates (395 TSS). Three biological replicates were performed with slight differences in library preparation. In each case, part of the sample was treated with terminator 5'-phosphate-dependent exonuclease (+TEX), while part of the sample remained untreated (-TEX). Therefore, in total, six samples were analysed by high-throughput sequencing.
2016-08-10 | E-GEOD-82206 | biostudies-arrayexpress
Project description:Three biological replicates of H. volcanii grown under optimal conditions to mid-exponential growth phase were used to determine the primary transcriptome and map 5’-ends of transcripts. In total, 4,749 potential transcriptional start sites (TSS) were detected. A position weight matrix was derived for promoter prediction, showing that 64% of the TSS were preceded by stringent or relaxed basal promoters. 1,851 TSS belonged to protein-coding genes, showing that less than half (46%) of the 4040 protein-coding genes are expressed under optimal growth conditions. 72% of all protein-coding transcripts were leaderless, underscoring that this is the default pathway for translation initiation in haloarchaea. The 5’-UTRs of transcripts with leaders had a widely varying length distribution without any optimum. 2,898 of the TSS belong to potential non-coding RNAs, representing an unexpectedly high fraction (61%) among all transcripts. 2792 of the non-coding TSS had not been described before and were thus novel (59% of all TSS). A large fraction of the potential novel non-coding transcripts are cis-antisense RNAs (1,244 aTSS). There was a strong negative correlation between the levels of antisense transcripts and cognate sense mRNAs, suggesting that negative regulation of gene expression via antisense RNAs may play an important role in haloarchaea. The other types of novel non-coding transcripts correspond to internal transcripts overlapping with mRNAs (1,153 iTSS) and intergenic small RNA (sRNA) candidates (395 TSS).
2016-08-10 | GSE82206 | GEO
Project description:Recent studies have revealed a myriad of non-coding transcripts in different organisms. For instances, the presence of short bidirectional transcripts is a hallmark of active promoters in mammals, while upstream non-coding transcripts can be detected at most expressed genes in conditions where the RNA degradation machinery is inhibited. Here, we used RNA-seq with very high sequencing depth to characterize strand specific transcripts from primary mouse tissues. We found that a substantial fraction of gene promoters sustain expression of long non-coding antisense transcripts. These transcripts have an average size of 6 kb, have features of mature transcripts, but remain associated with the chromatin. We named this new class of non-coding RNAs Long Upstream Antisense Transcripts (LUAT). Strikingly, the LUAT and coding gene pairs are usually co-regulated, with the associated genes often/generally coding for transcriptional regulators functioning during development and cell differentiation. Indeed, these bidirectional promoters share several characteristic of developmental gene promoters, including large CpG islands and high degree of conservation, and display symetrical GC skews. Finally, we found that bidirectional promoters have enlarged platforms of Pol II initiation, associated with an intensified rate of early transcriptional elongation. We concluded that promoters of developmental regulators are characterized by a specialized mechanism of Pol II transcription, whereby Pol II poising is directly coupled to relaxed bidirectional transcription. H3K79me2 ChIP in CD4+,CD8+ double positive thymocytes from C57BL/6 mice was studied, using Illumina sequencer
2014-01-01 | E-GEOD-44577 | biostudies-arrayexpress
Project description:Recent studies have revealed a myriad of non-coding transcripts in different organisms. For instances, the presence of short bidirectional transcripts is a hallmark of active promoters in mammals, while upstream non-coding transcripts can be detected at most expressed genes in conditions where the RNA degradation machinery is inhibited. Here, we used RNA-seq with very high sequencing depth to characterize strand-specific transcripts from primary mouse tissues. We found that a substantial fraction of gene promoters sustain expression of long non-coding antisense transcripts. These transcripts have an average size of 6 kb, have features of mature transcripts, but remain associated with the chromatin. We named this new class of non-coding RNAs Long Upstream Antisense Transcripts (LUAT). Strikingly, the LUAT and coding gene pairs are usually co-regulated, with the associated genes often/generally coding for transcriptional regulators functioning during development and cell differentiation. Indeed, these bidirectional promoters share several characteristics of developmental gene promoters, including large CpG islands and high degree of conservation, and display symetrical GC skews. Finally, we found that bidirectional promoters have enlarged platforms of Pol II initiation, associated with an intensified rate of early transcriptional elongation. We concluded that promoters of developmental regulators are characterized by a specialized mechanism of Pol II transcription, whereby Pol II poising is directly coupled to relaxed bidirectional transcription. Runx1 ChIP-seq in CD4+,CD8+ double-positive (DP) mice thymocytes using single-end sequencing on AB SOLiD Systems.
2014-01-01 | E-GEOD-45014 | biostudies-arrayexpress
Project description:Recent studies have revealed a myriad of non-coding transcripts in different organisms. For instances, the presence of short bidirectional transcripts is a hallmark of active promoters in mammals, while upstream non-coding transcripts can be detected at most expressed genes in conditions where the RNA degradation machinery is inhibited. Here, we used RNA-seq with very high sequencing depth to characterize strand specific transcripts from primary mouse tissues. We found that a substantial fraction of gene promoters sustain expression of long non-coding antisense transcripts. These transcripts have an average size of 6 kb, have features of mature transcripts, but remain associated with the chromatin. We named this new class of non-coding RNAs Long Upstream Antisense Transcripts (LUAT). Strikingly, the LUAT and coding gene pairs are usually co-regulated, with the associated genes often/generally coding for transcriptional regulators functioning during development and cell differentiation. Indeed, these bidirectional promoters share several characteristic of developmental gene promoters, including large CpG islands and high degree of conservation, and display symetrical GC skews. Finally, we found that bidirectional promoters have enlarged platforms of Pol II initiation, associated with an intensified rate of early transcriptional elongation. We concluded that promoters of developmental regulators are characterized by a specialized mechanism of Pol II transcription, whereby Pol II poising is directly coupled to relaxed bidirectional transcription. Expression of noncoding RNA transcripts in CD4-,CD8- double negative thymocytes from Rag2-/- mice was studied by strand-specific, ribosomal-depleted RNA-seq experiment, using Illumina sequencer
2014-01-01 | E-GEOD-44575 | biostudies-arrayexpress
Project description:Recent studies have revealed a myriad of non-coding transcripts in different organisms. For instances, the presence of short bidirectional transcripts is a hallmark of active promoters in mammals, while upstream non-coding transcripts can be detected at most expressed genes in conditions where the RNA degradation machinery is inhibited. Here, we used RNA-seq with very high sequencing depth to characterize strand specific transcripts from primary mouse tissues. We found that a substantial fraction of gene promoters sustain expression of long non-coding antisense transcripts. These transcripts have an average size of 6 kb, have features of mature transcripts, but remain associated with the chromatin. We named this new class of non-coding RNAs Long Upstream Antisense Transcripts (LUAT). Strikingly, the LUAT and coding gene pairs are usually co-regulated, with the associated genes often/generally coding for transcriptional regulators functioning during development and cell differentiation. Indeed, these bidirectional promoters share several characteristic of developmental gene promoters, including large CpG islands and high degree of conservation, and display symetrical GC skews. Finally, we found that bidirectional promoters have enlarged platforms of Pol II initiation, associated with an intensified rate of early transcriptional elongation. We concluded that promoters of developmental regulators are characterized by a specialized mechanism of Pol II transcription, whereby Pol II poising is directly coupled to relaxed bidirectional transcription. Expression of noncoding RNA transcripts in CD4-,CD8- double negative thymocytes from Rag2-/- mice was studied by strand-specific, ribosomal-depleted RNA-seq experiment, using paired-end sequencing on AB SOLiD System 4.0
2014-01-01 | E-GEOD-44232 | biostudies-arrayexpress
Project description:Recent studies have revealed a myriad of non-coding transcripts in different organisms. For instances, the presence of short bidirectional transcripts is a hallmark of active promoters in mammals, while upstream non-coding transcripts can be detected at most expressed genes in conditions where the RNA degradation machinery is inhibited. Here, we used RNA-seq with very high sequencing depth to characterize strand specific transcripts from primary mouse tissues. We found that a substantial fraction of gene promoters sustain expression of long non-coding antisense transcripts. These transcripts have an average size of 6 kb, have features of mature transcripts, but remain associated with the chromatin. We named this new class of non-coding RNAs Long Upstream Antisense Transcripts (LUAT). Strikingly, the LUAT and coding gene pairs are usually co-regulated, with the associated genes often/generally coding for transcriptional regulators functioning during development and cell differentiation. Indeed, these bidirectional promoters share several characteristic of developmental gene promoters, including large CpG islands and high degree of conservation, and display symetrical GC skews. Finally, we found that bidirectional promoters have enlarged platforms of Pol II initiation, associated with an intensified rate of early transcriptional elongation. We concluded that promoters of developmental regulators are characterized by a specialized mechanism of Pol II transcription, whereby Pol II poising is directly coupled to relaxed bidirectional transcription.
2014-01-01 | GSE44577 | GEO
Project description:Recent studies have revealed a myriad of non-coding transcripts in different organisms. For instances, the presence of short bidirectional transcripts is a hallmark of active promoters in mammals, while upstream non-coding transcripts can be detected at most expressed genes in conditions where the RNA degradation machinery is inhibited. Here, we used RNA-seq with very high sequencing depth to characterize strand specific transcripts from primary mouse tissues. We found that a substantial fraction of gene promoters sustain expression of long non-coding antisense transcripts. These transcripts have an average size of 6 kb, have features of mature transcripts, but remain associated with the chromatin. We named this new class of non-coding RNAs Long Upstream Antisense Transcripts (LUAT). Strikingly, the LUAT and coding gene pairs are usually co-regulated, with the associated genes often/generally coding for transcriptional regulators functioning during development and cell differentiation. Indeed, these bidirectional promoters share several characteristic of developmental gene promoters, including large CpG islands and high degree of conservation, and display symetrical GC skews. Finally, we found that bidirectional promoters have enlarged platforms of Pol II initiation, associated with an intensified rate of early transcriptional elongation. We concluded that promoters of developmental regulators are characterized by a specialized mechanism of Pol II transcription, whereby Pol II poising is directly coupled to relaxed bidirectional transcription.
2014-01-01 | GSE44575 | GEO