scholarly journals Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

Science ◽  
2008 ◽  
Vol 322 (5909) ◽  
pp. 1845-1848 ◽  
Author(s):  
Leighton J. Core ◽  
Joshua J. Waterfall ◽  
John T. Lis
Keyword(s):  
Messenger Rna ◽  
Large Scale ◽  
Molecular Machines ◽  
Antisense Transcription ◽  
Rna Polymerases ◽  
Promoter Regions ◽  
Rna Molecules ◽  
Genome Wide ◽  
Human Genes ◽  
Active Genes

RNA polymerases are highly regulated molecular machines. We present a method (global run-on sequencing, GRO-seq) that maps the position, amount, and orientation of transcriptionally engaged RNA polymerases genome-wide. In this method, nuclear run-on RNA molecules are subjected to large-scale parallel sequencing and mapped to the genome. We show that peaks of promoter-proximal polymerase reside on ∼30% of human genes, transcription extends beyond pre-messenger RNA 3′ cleavage, and antisense transcription is prevalent. Additionally, most promoters have an engaged polymerase upstream and in an orientation opposite to the annotated gene. This divergent polymerase is associated with active genes but does not elongate effectively beyond the promoter. These results imply that the interplay between polymerases and regulators over broad promoter regions dictates the orientation and efficiency of productive transcription.

scholarly journals Genome-wide Analysis of Alternative Pre-mRNA Splicing

2007 ◽  
Vol 283 (3) ◽  
pp. 1229-1233 ◽  
Author(s):  
Claudia Ben-Dov ◽  
Britta Hartmann ◽  
Josefin Lundgren ◽  
Juan Valcárcel
Keyword(s):  
Alternative Splicing ◽  
Large Scale ◽  
Mrna Splicing ◽  
Diagnostic Tools ◽  
Primary Transcript ◽  
Genome Wide ◽  
Human Genes ◽  
Multicellular Organisms ◽  
Eukaryotic Genomes ◽  
Key Questions

Alternative splicing of mRNA precursors allows the synthesis of multiple mRNAs from a single primary transcript, significantly expanding the information content and regulatory possibilities of higher eukaryotic genomes. High-throughput enabling technologies, particularly large-scale sequencing and splicing-sensitive microarrays, are providing unprecedented opportunities to address key questions in this field. The picture emerging from these pioneering studies is that alternative splicing affects most human genes and a significant fraction of the genes in other multicellular organisms, with the potential to greatly influence the evolution of complex genomes. A combinatorial code of regulatory signals and factors can deploy physiologically coherent programs of alternative splicing that are distinct from those regulated at other steps of gene expression. Pre-mRNA splicing and its regulation play important roles in human pathologies, and genome-wide analyses in this area are paving the way for improved diagnostic tools and for the identification of novel and more specific pharmaceutical targets.

scholarly journals Alternative Splicing: Expanding the Landscape of Cancer Biomarkers and Therapeutics

2020 ◽  
Vol 21 (23) ◽  
pp. 9032
Author(s):  
Cláudia Bessa ◽  
Paulo Matos ◽  
Peter Jordan ◽  
Vânia Gonçalves
Keyword(s):  
Alternative Splicing ◽  
Messenger Rna ◽  
Human Cancer ◽  
Genetic Alterations ◽  
Altered Expression ◽  
Genome Wide ◽  
Human Genes ◽  
Transcriptional Regulatory Mechanism ◽  
A Genome ◽  
Wide Scale

Alternative splicing (AS) is a critical post-transcriptional regulatory mechanism used by more than 95% of transcribed human genes and responsible for structural transcript variation and proteome diversity. In the past decade, genome-wide transcriptome sequencing has revealed that AS is tightly regulated in a tissue- and developmental stage-specific manner, and also frequently dysregulated in multiple human cancer types. It is currently recognized that splicing defects, including genetic alterations in the spliced gene, altered expression of both core components or regulators of the precursor messenger RNA (pre-mRNA) splicing machinery, or both, are major drivers of tumorigenesis. Hence, in this review we provide an overview of our current understanding of splicing alterations in cancer, and emphasize the need to further explore the cancer-specific splicing programs in order to obtain new insights in oncology. Furthermore, we also discuss the recent advances in the identification of dysregulated splicing signatures on a genome-wide scale and their potential use as biomarkers. Finally, we highlight the therapeutic opportunities arising from dysregulated splicing and summarize the current approaches to therapeutically target AS in cancer.

scholarly journals Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with repressed chromatin compartment and reveals transcription dynamics

2019 ◽  
Author(s):  
Alexey A. Gavrilov ◽  
Anastasiya A. Zharikova ◽  
Aleksandra A. Galitsyna ◽  
Artem V. Luzhin ◽  
Natalia M. Rubanova ◽  
...  
Keyword(s):  
Messenger Rna ◽  
K562 Cells ◽  
Biological Processes ◽  
Rna Molecules ◽  
Proximity Ligation ◽  
Genome Wide ◽  
Non Coding Rnas ◽  
Genomic Regions ◽  
Kinetics Of ◽  
Inactive Chromatin

AbstractNon-coding RNAs (ncRNAs) participate in various biological processes, including regulating transcription and sustaining genome 3D organization. Here, we present a method termed Red-C that exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncovered the RNA–DNA interactome of human K562 cells and identified hundreds of ncRNAs enriched in active or repressed chromatin, including previously undescribed RNAs. We found two microRNAs—MIR3648 and MIR3687 transcribed from the rRNA locus—that are associated with inactive chromatin genome wide. These miRNAs favor bulk heterochromatin over Polycomb-repressed chromatin and interact preferentially with late-replicating genomic regions. Analysis of the RNA–DNA interactome also allowed us to trace the kinetics of messenger RNA production. Our data support the model of co-transcriptional intron splicing, but not the hypothesis of the circularization of actively transcribed genes.

scholarly journals RSC primes the quiescent genome for hypertranscription upon cell cycle re-entry

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Christine E Cucinotta ◽  
Rachel H Dell ◽  
Keean CA Braceros ◽  
Toshio Tsukiyama
Keyword(s):  
Cell Cycle ◽  
Rna Polymerase Ii ◽  
Large Scale ◽  
Cell Activation ◽  
Immune Cell ◽  
Antisense Transcription ◽  
Cell Renewal ◽  
Promoter Regions ◽  
Term Survival ◽  
Pol Ii

Quiescence is a reversible G0 state essential for differentiation, regeneration, stem cell renewal, and immune cell activation. Necessary for long-term survival, quiescent chromatin is compact, hypoacetylated, and transcriptionally inactive. How transcription activates upon cell-cycle re-entry is undefined. Here we report robust, widespread transcription within the first minutes of quiescence exit. During quiescence, the chromatin-remodeling enzyme RSC was already bound to the genes induced upon quiescence exit. RSC depletion caused severe quiescence exit defects: a global decrease in RNA polymerase II (Pol II) loading, Pol II accumulation at transcription start sites, initiation from ectopic upstream loci, and aberrant antisense transcription. These phenomena were due to a combination of highly robust Pol II transcription and severe chromatin defects in the promoter regions and gene bodies. Together, these results uncovered multiple mechanisms by which RSC facilitates initiation and maintenance of large-scale, rapid gene expression despite a globally repressive chromatin state.

scholarly journals Antisense transcription-dependent chromatin signature modulates sense transcription and transcript dynamics

2017 ◽  
Author(s):  
Thomas Brown ◽  
Francoise S. Howe ◽  
Struan C. Murray ◽  
Emily Seward ◽  
Scott Rata ◽  
...  
Keyword(s):  
Antisense Transcript ◽  
Antisense Transcription ◽  
Mathematical Framework ◽  
Dependent Manner ◽  
Chromatin Signature ◽  
Transcript Stability ◽  
Rna Fish ◽  
Genome Wide ◽  
Human Genes ◽  
A Genome

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 alters sense transcription dynamics, reducing rates of transcript production and processing, while increasing transcript stability, which is also 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.

scholarly journals Demonstration of Balbiani ring RNA sequences in polysomes.

1977 ◽  
Vol 73 (1) ◽  
pp. 260-264 ◽  
Author(s):  
L Wieslander ◽  
B Daneholt
Keyword(s):  
In Situ Hybridization ◽  
Messenger Rna ◽  
Sucrose Gradient ◽  
Balbiani Ring ◽  
Rna Sequences ◽  
Rna Molecules ◽  
Labeled Rna ◽  
Active Genes

A polysome extract from salivary glands of C. tentans was sedimented in a 15-60% sucrose gradient. Fractions from the heavy polysome region (1,000-2,000S) and fractions from the light polysome region (200-1,000S) were pooled separately, and the long-term labeled RNA was released by Sarkosyl/pronase and analysed by in situ hybridization. The results showed that BR 1 and BR 2 sequences were present in the heavy and the light polysome regions of the sucrose gradient. From control experiments with EDTA-treated extracts, it was concluded that most of the recorded BR 1 and BR 2 sequences were in fact located in polysomes. The finding that BR products enter polysomes suggests that they act as messenger RNA molecules. This study therefore strongly supports the concept that chromosome puffs represent active genes.

scholarly journals RSC primes the quiescent genome for hypertranscription upon cell cycle re-entry

2021 ◽  
Author(s):  
Christine E. Cucinotta ◽  
Rachel H. Dell ◽  
Keean C.A. Braceros ◽  
Toshio Tsukiyama
Keyword(s):  
Cell Cycle ◽  
Rna Polymerase Ii ◽  
Large Scale ◽  
Cell Activation ◽  
Immune Cell ◽  
Antisense Transcription ◽  
Cell Renewal ◽  
Promoter Regions ◽  
Term Survival ◽  
Pol Ii

AbstractQuiescence is a reversible G0 state essential for differentiation, regeneration, stem cell renewal, and immune cell activation. Necessary for long-term survival, quiescent chromatin is compact, hypoacetylated, and transcriptionally inactive. How transcription activates upon cell-cycle re-entry is undefined. Here we report robust, widespread transcription within the first minutes of quiescence exit. During quiescence, the chromatin-remodeling enzyme RSC was already bound to the genes induced upon quiescence exit. RSC depletion caused severe quiescence exit defects: a global decrease in RNA polymerase II (Pol II) loading, Pol II accumulation at transcription start sites, initiation from ectopic upstream loci, and aberrant antisense transcription. These phenomena were due to a combination of highly robust Pol II transcription and severe chromatin defects in the promoter regions and gene bodies. Together, these results uncovered multiple mechanisms by which RSC facilitates initiation and maintenance of large-scale, rapid gene expression despite a globally repressive chromatin state.

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