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 Genome-wide CRISPR screen identifies ELP5 as a determinant of gemcitabine sensitivity in gallbladder cancer

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Sunwang Xu ◽  
Ming Zhan ◽  
Cen Jiang ◽  
Min He ◽  
Linhua Yang ◽  
...  
Keyword(s):  
Gallbladder Cancer ◽  
Locally Advanced ◽  
Internal Ribosomal Entry Site ◽  
Dependent Manner ◽  
Entry Site ◽  
P53 Expression ◽  
Elongator Complex ◽  
Genome Wide ◽  
A Genome ◽  
Crispr Screen

AbstractGemcitabine is the first-line treatment for locally advanced and metastatic gallbladder cancer (GBC), but poor gemcitabine response is universal. Here, we utilize a genome-wide CRISPR screen to identify that loss of ELP5 reduces the gemcitabine-induced apoptosis in GBC cells in a P53-dependent manner through the Elongator complex and other uridine 34 (U34) tRNA-modifying enzymes. Mechanistically, loss of ELP5 impairs the integrity and stability of the Elongator complex to abrogate wobble U34 tRNA modification, and directly impedes the wobble U34 modification-dependent translation of hnRNPQ mRNA, a validated P53 internal ribosomal entry site (IRES) trans-acting factor. Downregulated hnRNPQ is unable to drive P53 IRES-dependent translation, but rescuing a U34 modification-independent hnRNPQ mutant could restore P53 translation and gemcitabine sensitivity in ELP5-depleted GBC cells. GBC patients with lower ELP5, hnRNPQ, or P53 expression have poor survival outcomes after gemcitabine chemotherapy. These results indicate that the Elongator/hnRNPQ/P53 axis controls gemcitabine sensitivity in GBC cells.

scholarly journals The Antisense Transcriptomes of Human Cells

Science ◽  
2008 ◽  
Vol 322 (5909) ◽  
pp. 1855-1857 ◽  
Author(s):  
Yiping He ◽  
Bert Vogelstein ◽  
Victor E. Velculescu ◽  
Nickolas Papadopoulos ◽  
Kenneth W. Kinzler
Keyword(s):  
Mammalian Cells ◽  
Cell Types ◽  
Human Cells ◽  
Antisense Transcripts ◽  
Genome Wide ◽  
Human Genes ◽  
A Genome ◽  
Dna Strand ◽  
The Relationship ◽  
Rna Transcript

Transcription in mammalian cells can be assessed at a genome-wide level, but it has been difficult to reliably determine whether individual transcripts are derived from the plus or minus strands of chromosomes. This distinction can be critical for understanding the relationship between known transcripts (sense) and the complementary antisense transcripts that may regulate them. Here, we describe a technique that can be used to (i) identify the DNA strand of origin for any particular RNA transcript, and (ii) quantify the number of sense and antisense transcripts from expressed genes at a global level. We examined five different human cell types and in each case found evidence for antisense transcripts in 2900 to 6400 human genes. The distribution of antisense transcripts was distinct from that of sense transcripts, was nonrandom across the genome, and differed among cell types. Antisense transcripts thus appear to be a pervasive feature of human cells, which suggests that they are a fundamental component of gene regulation.

scholarly journals Comparative analysis reveals genomic features of stress-induced transcriptional readthrough

2017 ◽  
Vol 114 (40) ◽  
pp. E8362-E8371 ◽  
Author(s):  
Anna Vilborg ◽  
Niv Sabath ◽  
Yuval Wiesel ◽  
Jenny Nathans ◽  
Flonia Levy-Adam ◽  
...  
Keyword(s):  
Heat Shock ◽  
Osmotic Stress ◽  
Stress Responses ◽  
Failure Process ◽  
Mouse Fibroblast ◽  
Open Chromatin ◽  
Chromatin Signature ◽  
Genomic Features ◽  
Genome Wide ◽  
A Genome

Transcription is a highly regulated process, and stress-induced changes in gene transcription have been shown to play a major role in stress responses and adaptation. Genome-wide studies reveal prevalent transcription beyond known protein-coding gene loci, generating a variety of RNA classes, most of unknown function. One such class, termed downstream of gene-containing transcripts (DoGs), was reported to result from transcriptional readthrough upon osmotic stress in human cells. However, how widespread the readthrough phenomenon is, and what its causes and consequences are, remain elusive. Here we present a genome-wide mapping of transcriptional readthrough, using nuclear RNA-Seq, comparing heat shock, osmotic stress, and oxidative stress in NIH 3T3 mouse fibroblast cells. We observe massive induction of transcriptional readthrough, both in levels and length, under all stress conditions, with significant, yet not complete, overlap of readthrough-induced loci between different conditions. Importantly, our analyses suggest that stress-induced transcriptional readthrough is not a random failure process, but is rather differentially induced across different conditions. We explore potential regulators and find a role for HSF1 in the induction of a subset of heat shock-induced readthrough transcripts. Analysis of public datasets detected increases in polymerase II occupancy in DoG regions after heat shock, supporting our findings. Interestingly, DoGs tend to be produced in the vicinity of neighboring genes, leading to a marked increase in their antisense-generating potential. Finally, we examine genomic features of readthrough transcription and observe a unique chromatin signature typical of DoG-producing regions, suggesting that readthrough transcription is associated with the maintenance of an open chromatin state.

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 prediction and prioritization of human aging genes by data fusion: a machine learning approach

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Masoud Arabfard ◽  
Mina Ohadi ◽  
Vahid Rezaei Tabar ◽  
Ahmad Delbari ◽  
Kaveh Kavousi
Keyword(s):  
Machine Learning ◽  
Process Comparison ◽  
Age Related ◽  
Genome Wide ◽  
Human Genes ◽  
Disease Candidate Gene ◽  
A Genome ◽  
Machine Learning Approach ◽  
Wide Scale ◽  
Biological Aspects

Abstract Background Machine learning can effectively nominate novel genes for various research purposes in the laboratory. On a genome-wide scale, we implemented multiple databases and algorithms to predict and prioritize the human aging genes (PPHAGE). Results We fused data from 11 databases, and used Naïve Bayes classifier and positive unlabeled learning (PUL) methods, NB, Spy, and Rocchio-SVM, to rank human genes in respect with their implication in aging. The PUL methods enabled us to identify a list of negative (non-aging) genes to use alongside the seed (known age-related) genes in the ranking process. Comparison of the PUL algorithms revealed that none of the methods for identifying a negative sample were advantageous over other methods, and their simultaneous use in a form of fusion was critical for obtaining optimal results (PPHAGE is publicly available at https://cbb.ut.ac.ir/pphage). Conclusion We predict and prioritize over 3,000 candidate age-related genes in human, based on significant ranking scores. The identified candidate genes are associated with pathways, ontologies, and diseases that are linked to aging, such as cancer and diabetes. Our data offer a platform for future experimental research on the genetic and biological aspects of aging. Additionally, we demonstrate that fusion of PUL methods and data sources can be successfully used for aging and disease candidate gene prioritization.

Whole human exome capture for high-throughput sequencing

Genome ◽  
2010 ◽  
Vol 53 (7) ◽  
pp. 568-574 ◽  
Author(s):  
Dae-Won Kim ◽  
Seong-Hyeuk Nam ◽  
Ryong Nam Kim ◽  
Sang-Haeng Choi ◽  
Hong-Seog Park
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Exome Capture ◽  
Microarray Design ◽  
Genome Wide ◽  
Human Genes ◽  
Practical Usefulness ◽  
A Genome ◽  
Wide Scale ◽  
Total Base

We captured the whole human exome by hybridization using synthesized oligonucleotides, based on a high-density microarray design, and we sequenced those captured human exons using high-throughput sequencing on a Genome Sequencer FLX instrument. Of the uniquely mapped reads, 71% fell within target regions, and these corresponded to coverage of 94% of human genes, 87% of exons, and 70% of the total base-pair length of the CCDS set. Our study provides strong evidence for the practical usefulness of this method on a genome-wide scale, showing the resequenced whole human exome database with 501 microRNAs and 307 novel SNPs.

scholarly journals Analysis of Temporal Gene Expression during Bacillus subtilis Spore Germination and Outgrowth

2007 ◽  
Vol 189 (9) ◽  
pp. 3624-3634 ◽  
Author(s):  
Bart J. F. Keijser ◽  
Alex Ter Beek ◽  
Han Rauwerda ◽  
Frank Schuren ◽  
Roy Montijn ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Spore Germination ◽  
Dependent Manner ◽  
Temporal Gene Expression ◽  
Bacillus Subtilis Spore ◽  
Physiological Processes ◽  
Genome Wide ◽  
Extracellular Metabolites ◽  
A Genome ◽  
Spore Outgrowth

ABSTRACT Bacillus subtilis forms dormant spores upon nutrient depletion. Under favorable environmental conditions, the spore breaks its dormancy and resumes growth in a process called spore germination and outgrowth. To elucidate the physiological processes that occur during the transition of the dormant spore to an actively growing vegetative cell, we studied this process in a time-dependent manner by a combination of microscopy, analysis of extracellular metabolites, and a genome-wide analysis of transcription. The results indicate the presence of abundant levels of late sporulation transcripts in dormant spores. In addition, the results suggest the existence of a complex and well-regulated spore outgrowth program, involving the temporal expression of at least 30% of the B. subtilis genome.

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 Genome-wide analysis of Escherichia coli fitness determinants in a cross-feeding mutualism with Rhodopseudomonas palustris

2020 ◽  
Author(s):  
Breah LaSarre ◽  
Adam M. Deutschbauer ◽  
Crystal E. Love ◽  
James B. McKinlay
Keyword(s):  
Escherichia Coli ◽  
Microbial Communities ◽  
Rhodopseudomonas Palustris ◽  
Microbial Interactions ◽  
Dependent Manner ◽  
Fermentation Products ◽  
E Coli ◽  
Cellular Processes ◽  
Genome Wide ◽  
A Genome

ABSTRACTMicrobial interactions abound in natural ecosystems and shape community structure and function. Substantial attention has been given to cataloging mechanisms by which microbes interact, but there is a limited understanding of the genetic landscapes that promote or hinder microbial interactions. We previously developed a mutualistic coculture pairing Escherichia coli and Rhodopseudomonas palustris, wherein E. coli provides carbon to R. palustris in the form of glucose fermentation products and R. palustris fixes N2 gas and provides nitrogen to E. coli in the form of NH4+. The stable coexistence and reproducible trends exhibited by this coculture make it ideal for interrogating the genetic underpinnings of a cross-feeding mutualism. Here, we used random barcode transposon sequencing (RB-TnSeq) to conduct a genome-wide search for E. coli genes that influence fitness during cooperative growth with R. palustris. RB-TnSeq revealed hundreds of genes that increased or decreased E. coli fitness in a mutualism-dependent manner. Some identified genes were involved in nitrogen sensing and assimilation, as expected given the coculture design. The other identified genes were involved in diverse cellular processes, including energy production and cell wall and membrane biogenesis. Additionally, we discovered unexpected purine cross-feeding from R. palustris to E. coli, with coculture rescuing growth of an E. coli purine auxotroph. Our data provide insight into the genes and gene networks that can influence a cross-feeding mutualism and underscore that microbial interactions are not necessarily predictable a priori.IMPORTANCEMicrobial communities impact life on earth in profound ways, including driving global nutrient cycles and influencing human health and disease. These community functions depend on the interactions that resident microbes have with the environment and each other. Thus, identifying genes that influence these interactions will aid the management of natural communities and the use of microbial consortia as biotechnology. Here, we identified genes that influenced Escherichia coli fitness during cooperative growth with a mutualistic partner, Rhodospeudomonas palustris. Although this mutualism centers on the bidirectional exchange of essential carbon and nitrogen, E. coli fitness was positively and negatively affected by genes involved in diverse cellular processes. Furthermore, we discovered an unexpected purine cross-feeding interaction. These results contribute knowledge on the genetic foundation of a microbial cross-feeding interaction and highlight that unanticipated interactions can occur even within engineered microbial communities.

scholarly journals A Genome-Wide Association Study Reveals a Novel Regulator of Ovule Number and Fertility in Arabidopsis thaliana

2018 ◽  
Author(s):  
Jing Yuan ◽  
Sharon A. Kessler
Keyword(s):  
Arabidopsis Thaliana ◽  
Flower Development ◽  
Natural Variation ◽  
Pleiotropic Effects ◽  
Genome Wide Association ◽  
Egg Cell ◽  
Dependent Manner ◽  
Genome Wide ◽  
A Genome ◽  
Ovule Number

AbstractOvules contain the female gametophytes which are fertilized during pollination to initiate seed development. Thus, the number of ovules that are produced during flower development is an important determinant of seed crop yield and plant fitness. Mutants with pleiotropic effects on development often alter the number of ovules, but specific regulators of ovule number have been difficult to identify in traditional mutant screens. We used natural variation in Arabidopsis accessions to identify new genes involved in the regulation of ovule number. The ovule numbers per flower of 189 Arabidopsis accessions were determined and found to have broad phenotypic variation that ranged from 39 ovules to 84 ovules per pistil. Genome-Wide Association tests revealed several genomic regions that are associated with ovule number. T-DNA insertion lines in candidate genes from the most significantly associated loci were screened for ovule number phenotypes. The NEW ENHANCER of ROOT DWARFISM (NERD1) gene was found to have pleiotropic effects on plant fertility that include regulation of ovule number and both male and female gametophyte development. Overexpression of NERD1 increased ovule number per fruit in a background-dependent manner and more than doubled the total number of flowers produced in all backgrounds tested, indicating that manipulation of NERD1 levels can be used to increase plant productivity.Author SummaryOvules are the precursors of seeds in flowering plants. Each ovule contains an egg cell and a central cell that fuse with two sperm cells during double fertilization to generate seeds containing an embryo and endosperm. The number of ovules produced during flower development determines the maximum number of seeds that can be produced by a flower. In this paper, we used natural variation in Arabidopsis thaliana accessions to identify regions of the genome that are associated with ovule number. Polymorphisms in the plant-specific NERD1 gene on chromosome 3 were significantly associated with ovule number. Mutant and overexpression analyses revealed that NERD1 is a positive regulator of ovule number, lateral branching, and flower number in Arabidopsis. Manipulation of NERD1 expression levels could potentially be used to increase yield in crop plants.

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