Similar Datasets
Project description:RNA polymerase (RNAP) is essential for the transcription of genetic information encoded in genomes in all three domains of life. To determine the precise organization of bacterial transcription initiation complexes (TIC) in vivo, we exploited high-throughput sequencing to the DNA obtained from exonuclease-treated immunoprecipitates of the TIC. It reveals that sigma (σ) factor is mostly engaged in RNAP holoenzyme up to 13-14 nucleotides from transcription start site during abortive initiation.
2021-01-13 | GSE54406 | GEO
Project description:RNA polymerase (RNAP) is essential for the transcription of genetic information encoded in genomes in all three domains of life. To determine the precise organization of bacterial transcription initiation complexes (TIC) in vivo, we exploited high-throughput sequencing to the DNA obtained from exonuclease-treated immunoprecipitates of the TIC. It reveals that sigma (σ) factor is mostly engaged in RNAP holoenzyme up to 13-14 nucleotides from transcription start site during abortive initiation.
2021-01-13 | GSE54405 | GEO
Project description:RNA polymerase (RNAP) is essential for the transcription of genetic information encoded in genomes in all three domains of life. To determine the precise organization of bacterial transcription initiation complexes (TIC) in vivo, we exploited high-throughput sequencing to the DNA obtained from exonuclease-treated immunoprecipitates of the TIC. It reveals that sigma (σ) factor is mostly engaged in RNAP holoenzyme up to 13-14 nucleotides from transcription start site during abortive initiation.
2021-01-13 | GSE54403 | GEO
Project description:RNA polymerase (RNAP) is essential for the transcription of genetic information encoded in genomes in all three domains of life. To determine the precise organization of bacterial transcription initiation complexes (TIC) in vivo, we exploited high-throughput sequencing to the DNA obtained from exonuclease-treated immunoprecipitates of the TIC. It reveals that sigma (σ) factor is mostly engaged in RNAP holoenzyme up to 13-14 nucleotides from transcription start site during abortive initiation.
2021-01-13 | GSE54404 | GEO
Project description:In vivo organization of bacterial transcription initiation complexes at a genome-scale
| PRJNA236452 | ENA
Project description:A repertoire of transcription initiation factors engage the core promoter of mRNA genes to recruit RNA polymerase (Pol) II to initiate transcription, yet their precise spatial organization remains unclear. Using ChIP-exo, here we detail the interactions and genomic organization of initiation factors TBP, TFIIB, and Pol II at mRNA genes and within CpG islands. We find that when Pol II moves into a transcriptionally paused state, TBP/TFIIB remain at the promoter. We show that TBP and TFIIB bound to the core promoter at two separate, resolvable locations that coincided with sites of divergent transcription initiation. We also examine the precise binding of TBP at Pol III transcribed tRNA genes. We find that TBP crosslinked to tRNA genes in a similar manner as at Pol II transcribed genes. This comprehensive and high resolution genome-wide detection of the initiation machinery produces a consolidated view of transcription initiation events humans at Pol II coding and Pol III transcribed tRNA genes.
| S-EPMC4750860 | biostudies-literature
Project description:The human genome is pervasively transcribed, yet only a small fraction is coding. Here we address whether this non-coding transcription arises at promoters, and detail the interactions of initiation factors TATA box binding protein (TBP), transcription factor IIB (TFIIB) and RNA polymerase (Pol) II. Using ChIP-exo (chromatin immunoprecipitation with lambda exonuclease digestion followed by high-throughput sequencing), we identify approximately 160,000 transcription initiation complexes across the human K562 genome, and more in other cancer genomes. Only about 5% associate with messenger RNA genes. The remainder associates with non-polyadenylated non-coding transcription. Regardless, Pol II moves into a transcriptionally paused state, and TBP and TFIIB remain at the promoter. Remarkably, the vast majority of locations contain the four core promoter elements- upstream TFIIB recognition element (BREu), TATA, downstream TFIIB recognition element (BREd), and initiator element (INR)-in constrained positions. All but the INR also reside at Pol III promoters, where TBP makes similar contacts. This comprehensive and high-resolution genome-wide detection of the initiation machinery produces a consolidated view of transcription initiation events from yeast to humans at Pol II/III TATA-containing/TATA-less coding and non-coding genes.
| S-EPMC4018585 | biostudies-literature
Project description:Transcription and regulation of genes originate from transcription pre-initiation complexes (PICs). Their structural and positional organization across eukaryotic genomes is unknown. Here we applied lambda exonuclease to chromatin immunoprecipitates (termed ChIP-exo) to examine the precise location of 6,045 PICs in Saccharomyces. PICs, including RNA polymerase II and protein complexes TFIIA, TFIIB, TFIID (or TBP), TFIIE, TFIIF, TFIIH and TFIIK were positioned within promoters and excluded from coding regions. Exonuclease patterns were in agreement with crystallographic models of the PIC, and were sufficiently precise to identify TATA-like elements at so-called TATA-less promoters. These PICs and their transcription start sites were positionally constrained at TFIID-engaged downstream +1 nucleosomes. At TATA-box-containing promoters, which are depleted of TFIID, a +1 nucleosome was positioned to be in competition with the PIC, which may allow greater latitude in start-site selection. Our genomic localization of messenger RNA and non-coding RNA PICs reveals that two PICs, in inverted orientation, may occupy the flanking borders of nucleosome-free regions. Their unambiguous detection may help distinguish bona fide genes from transcriptional noise.
| S-EPMC3306527 | biostudies-literature
Project description:Transcription initiation is a major step in gene regulation for all organisms. In bacteria, the promoter DNA is first recognized by RNA polymerase (RNAP) to yield an initial closed complex. This complex subsequently undergoes conformational changes resulting in DNA strand separation to form a transcription bubble and an RNAP-promoter open complex; however, the series and sequence of conformational changes, and the factors that influence them are unclear. To address the conformational landscape and transitions in transcription initiation, we applied single-molecule Förster resonance energy transfer (smFRET) on immobilized Escherichia coli transcription open complexes. Our results revealed the existence of two stable states within RNAP-DNA complexes in which the promoter DNA appears to adopt closed and partially open conformations, and we observed large-scale transitions in which the transcription bubble fluctuated between open and closed states; these transitions, which occur roughly on the 0.1 s timescale, are distinct from the millisecond-timescale dynamics previously observed within diffusing open complexes. Mutational studies indicated that the σ70 region 3.2 of the RNAP significantly affected the bubble dynamics. Our results have implications for many steps of transcription initiation, and support a bend-load-open model for the sequence of transitions leading to bubble opening during open complex formation.
| S-EPMC5778504 | biostudies-literature
Project description:The computational identification of gene transcription start sites (TSSs) can provide insights into the regulation and function of genes without performing expensive experiments, particularly in organisms with incomplete annotations. High-resolution general-purpose TSS prediction remains a challenging problem, with little recent progress on the identification and differentiation of TSSs which are arranged in different spatial patterns along the chromosome.In this work, we present the Transcription Initiation Pattern Recognizer (TIPR), a sequence-based machine learning model that identifies TSSs with high accuracy and resolution for multiple spatial distribution patterns along the genome, including broadly distributed TSS patterns that have previously been difficult to characterize. TIPR predicts not only the locations of TSSs but also the expected spatial initiation pattern each TSS will form along the chromosome-a novel capability for TSS prediction algorithms. As spatial initiation patterns are associated with spatiotemporal expression patterns and gene function, this capability has the potential to improve gene annotations and our understanding of the regulation of transcription initiation. The high nucleotide resolution of this model locates TSSs within 10 nucleotides or less on average.Model source code is made available online at http://megraw.cgrb.oregonstate.edu/software/TIPR/.megrawm@science.oregonstate.edu.Supplementary data are available at Bioinformatics online.
| S-EPMC4804766 | biostudies-literature