scholarly journals YeasTSS: An Integrative Web Database of Yeast Transcription Start Sites

2019 ◽  
Author(s):  
Jonathan McMillan ◽  
Zhaolian Lu ◽  
Judith S. Rodriguez ◽  
Tae-Hyuk Ahn ◽  
Zhenguo Lin
Keyword(s):  
Genome Annotation ◽  
Transcription Initiation ◽  
Yeast Species ◽  
Genomic Data ◽  
Human Society ◽  
Functional Genomic ◽  
Functional Genomic Data ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Core Promoters

AbstractThe transcription initiation landscape of eukaryotic genes is complex and highly dynamic. In eukaryotes, genes can generate multiple transcript variants that differ in 5’ boundaries due to usages of alternative transcription start sites (TSSs), and the abundance of transcript isoforms are highly variable. Due to a large number and complexity of the TSSs, it is not feasible to depict details of transcript initiation landscape of all genes using text-format genome annotation files. Therefore, it is necessary to provide data visualization of TSSs to represent quantitative TSS maps and the core promoters. In addition, the selection and activity of TSSs are influenced by various factors, such as transcription factors, chromatin remodeling, and histone modifications. Thus, integration and visualization of functional genomic data related to these features could provide a better understanding of the gene promoter architecture and regulatory mechanism of transcription initiation. Yeast species play important roles for the research and human society, yet no database provides visualization and integration of functional genomic data in yeast. Here, we generated quantitative TSS maps for twelve important yeast species, inferred their core promoters, and built a public database, YeasTSS (www.yeastss.org). YeasTSS was designed as a central portal for visualization and integration of the TSS maps, core promoters and functional genomic data related to transcription initiation in yeast. YeasTSS is expected to benefit the research community and public education for improving genome annotation, studies of promoter structure, regulated control of transcription initiation and inferring gene regulatory network.

scholarly journals YeasTSS: an integrative web database of yeast transcription start sites

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Jonathan McMillan ◽  
Zhaolian Lu ◽  
Judith S Rodriguez ◽  
Tae-Hyuk Ahn ◽  
Zhenguo Lin
Keyword(s):  
Genome Annotation ◽  
Transcription Initiation ◽  
Yeast Species ◽  
Genomic Data ◽  
Human Society ◽  
Functional Genomic ◽  
Functional Genomic Data ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Eukaryotic Genes

Abstract The transcription initiation landscape of eukaryotic genes is complex and highly dynamic. In eukaryotes, genes can generate multiple transcript variants that differ in 5′ boundaries due to usages of alternative transcription start sites (TSSs), and the abundance of transcript isoforms are highly variable. Due to a large number and complexity of the TSSs, it is not feasible to depict details of transcript initiation landscape of all genes using text-format genome annotation files. Therefore, it is necessary to provide data visualization of TSSs to represent quantitative TSS maps and the core promoters (CPs). In addition, the selection and activity of TSSs are influenced by various factors, such as transcription factors, chromatin remodeling and histone modifications. Thus, integration and visualization of functional genomic data related to these features could provide a better understanding of the gene promoter architecture and regulatory mechanism of transcription initiation. Yeast species play important roles for the research and human society, yet no database provides visualization and integration of functional genomic data in yeast. Here, we generated quantitative TSS maps for 12 important yeast species, inferred their CPs and built a public database, YeasTSS (www.yeastss.org). YeasTSS was designed as a central portal for visualization and integration of the TSS maps, CPs and functional genomic data related to transcription initiation in yeast. YeasTSS is expected to benefit the research community and public education for improving genome annotation, studies of promoter structure, regulated control of transcription initiation and inferring gene regulatory network.

scholarly journals Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

2008 ◽  
Vol 40 (7) ◽  
pp. 854-861 ◽  
Author(s):  
Jun Zhu ◽  
Bin Zhang ◽  
Erin N Smith ◽  
Becky Drees ◽  
Rachel B Brem ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Large Scale ◽  
Genomic Data ◽  
Functional Genomic ◽  
Functional Genomic Data

scholarly journals The histone variant H2A.Z in yeast is almost exclusively incorporated into the +1 nucleosome in the direction of transcription

2019 ◽  
Author(s):  
Dia N Bagchi ◽  
Anna M Battenhouse ◽  
Daechan Park ◽  
Vishwanath R Iyer
Keyword(s):  
Transcriptional Activation ◽  
Transcription Initiation ◽  
General Feature ◽  
Antisense Transcription ◽  
Histone Variant ◽  
Expression Data ◽  
Transcription Start ◽  
Chromatin Remodelers ◽  
Transcription Start Sites ◽  
Bidirectional Transcription

Abstract Transcription start sites (TSS) in eukaryotes are characterized by a nucleosome-depleted region (NDR), which appears to be flanked upstream and downstream by strongly positioned nucleosomes incorporating the histone variant H2A.Z. H2A.Z associates with both active and repressed TSS and is important for priming genes for rapid transcriptional activation. However, the determinants of H2A.Z occupancy at specific nucleosomes and its relationship to transcription initiation remain unclear. To further elucidate the specificity of H2A.Z, we determined its genomic localization at single nucleosome resolution, as well as the localization of its chromatin remodelers Swr1 and Ino80. By analyzing H2A.Z occupancy in conjunction with RNA expression data that captures promoter-derived antisense initiation, we find that H2A.Z’s bimodal incorporation on either side of the NDR is not a general feature of TSS, but is specifically a marker for bidirectional transcription, such that the upstream flanking −1 H2A.Z-containing nucleosome is more appropriately considered as a +1 H2A.Z nucleosome for antisense transcription. The localization of H2A.Z almost exclusively at the +1 nucleosome suggests that a transcription-initiation dependent process could contribute to its specific incorporation.

scholarly journals A selector of transcription initiation in the protozoan parasite Toxoplasma gondii.

1995 ◽  
Vol 15 (1) ◽  
pp. 87-93 ◽  
Author(s):  
D Soldati ◽  
J C Boothroyd
Keyword(s):  
Toxoplasma Gondii ◽  
Gene Transcription ◽  
Transcription Initiation ◽  
Protozoan Parasite ◽  
Intracellular Parasite ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Obligate Intracellular ◽  
Obligate Intracellular Parasite ◽  
Sag1 Gene

The recent development of an efficient transfection system for the apicomplexan Toxoplasma gondii allows a comprehensive dissection of the elements involved in gene transcription in this obligate intracellular parasite. We demonstrate here that for the SAG1 gene, a stretch of six repeated sequences in the region 35 to 190 bp upstream of the first of two transcription start sites is essential for efficient and accurate transcription initiation. This repeat element shows characteristics of a selector in determining the position of the transcription start sites.

scholarly journals Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals

2011 ◽  
Vol 7 (6) ◽  
pp. e1002073 ◽  
Author(s):  
Nathan L. Nehrt ◽  
Wyatt T. Clark ◽  
Predrag Radivojac ◽  
Matthew W. Hahn
Keyword(s):  
Genomic Data ◽  
Functional Genomic ◽  
Functional Genomic Data

scholarly journals Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage

2020 ◽  
Author(s):  
D.E. Goszczynski ◽  
M.M. Halstead ◽  
A.D. Islas-Trejo ◽  
H. Zhou ◽  
P.J. Ross
Keyword(s):  
Transcription Initiation ◽  
Promoter Activity ◽  
Bovine Genome ◽  
Transcription Start ◽  
Protein Coding ◽  
Tissue Specific ◽  
Transcription Start Sites ◽  
Expression Control ◽  
Tissue Specific Promoter ◽  
Genome Annotations

ABSTRACTCharacterizing transcription start sites is essential for understanding the regulatory mechanisms that control gene expression. Recently, a new bovine genome assembly (ARS-UCD1.2) with high continuity, accuracy, and completeness was released; however, the functional annotation of the bovine genome lacks precise transcription start sites and includes a low number of transcripts in comparison to human and mouse. Using the RAMPAGE approach, this study identified transcription start sites at high resolution in a large collection of bovine tissues. We found several known and novel transcription start sites attributed to promoters of protein coding and lncRNA genes that were validated through experimental and in silico evidence. With these findings, the annotation of transcription start sites in cattle reached a level comparable to the mouse and human genome annotations. In addition, we identified and characterized transcription start sites for antisense transcripts derived from bidirectional promoters, potential lncRNAs, mRNAs, and pre-miRNAs. We also analyzed the quantitative aspects of RAMPAGE data for producing a promoter activity atlas, reaching highly reproducible results comparable to traditional RNA-Seq. Lastly, gene co-expression networks revealed an impressive use of tissue-specific promoters, especially between brain and testicle, which expressed several genes in common from alternate transcription start sites. Regions surrounding co-expressed modules were enriched in binding factor motifs representative of their tissues. This annotation will be highly useful for future studies on expression control in cattle and other species. Furthermore, these data provide significant insight into transcriptional activity for a comprehensive set of tissues.

scholarly journals The NSL complex mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise

2018 ◽  
Author(s):  
Kin Chung Lam ◽  
Ho-Ryun Chung ◽  
Giuseppe Semplicio ◽  
Vivek Bhardwaj ◽  
Shantanu S. Iyer ◽  
...  
Keyword(s):  
Transcription Initiation ◽  
Dependent Manner ◽  
Gene Promoters ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Chromatin Remodeling Complex ◽  
Selection For ◽  
Necessary And Sufficient ◽  
Target Promoters ◽  
Active Genes

AbstractNucleosomal organization at gene promoters is critical for transcription, with a nucleosome-depleted region (NDR) at transcription start sites (TSSs) being required for transcription initiation. How NDR and the precise positioning of the +1 nucleosome is maintained on active genes remains unclear. Here, we report that the Drosophila Non-Specific Lethal (NSL) complex is necessary to maintain this stereotypical nucleosomal organization at promoters. Upon NSL1 depletion, nucleosomes invade the NDRs at TSSs of NSL-bound genes. NSL complex member NSL3 binds to TATA-less promoters in a sequence-dependent manner. The NSL complex interacts with the NURF chromatin remodeling complex and is necessary and sufficient to recruit NURF to target promoters. The NSL complex is not only essential for transcription but is required for accurate TSS selection for genes with multiple TSSs. Further, loss of NSL complex leads to an increase in transcriptional noise. Thus, the NSL complex establishes a canonical nucleosomal organization that enables transcription and determines TSS fidelity.

scholarly journals Semi-supervised segmentation and genome annotation

2020 ◽  
Author(s):  
Rachel C.W. Chan ◽  
Matthew McNeil ◽  
Eric G. Roberts ◽  
Mickaël Mendez ◽  
Maxwell W. Libbrecht ◽  
...  
Keyword(s):  
Supervised Learning ◽  
Prior Knowledge ◽  
Genome Annotation ◽  
Whole Genome ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Annotation Method ◽  
Supervised Segmentation ◽  
Unseen Data ◽  
Genome Annotations

AbstractSegmentation and genome annotation methods automatically discover joint signal patterns in whole genome datasets. Previously, researchers trained these algorithms in a fully unsupervised way, with no prior knowledge of the functions of particular regions. Adding information provided by expert-created annotations to supervise training could improve the annotations created by these methods. We implemented semi-supervised learning using virtual evidence in the annotation method Segway. Additionally, we defined a positionally tolerant precision and recall metric for scoring genome annotations based on the proximity of each annotation feature to the truth set. We demonstrate semi-supervised Segway’s ability to learn patterns corresponding to provided transcription start sites on a specified supervision label, and subsequently recover other transcription start sites in unseen data on the same supervision label.

scholarly journals Chinese Glioma Genome Atlas (CGGA): A Comprehensive Resource with Functional Genomic Data for Chinese Glioma Patients

2020 ◽  
Author(s):  
Zheng Zhao ◽  
Ke’nan Zhang ◽  
Qiangwei Wang ◽  
Guanzhang Li ◽  
Fan Zeng ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Survival Data ◽  
Messenger Rna ◽  
Genomic Data ◽  
Biological Research ◽  
Analysis Tool ◽  
Functional Genomic ◽  
Functional Genomic Data ◽  
Who Grade ◽  
Genome Atlas

AbstractGliomas are the most common and malignant intracranial tumours in adults. Recent studies have shown that functional genomics greatly aids in the understanding of the pathophysiology and therapy of glioma. However, comprehensive genomic data and analysis platforms are relatively limited. In this study, we developed the Chinese Glioma Genome Atlas (CGGA, http://www.cgga.org.cn), a user-friendly data portal for storage and interactive exploration of multi-dimensional functional genomic data that includes nearly 2,000 primary and recurrent glioma samples from Chinese cohorts. CGGA currently provides access to whole-exome sequencing (286 samples), messenger RNA sequencing (1,018 samples) and microarray (301 samples), DNA methylation microarray (159 samples), and microRNA microarray (198 samples) data, as well as detailed clinical data (e.g., WHO grade, histological type, critical molecular genetic information, age, sex, chemoradiotherapy status and survival data). In addition, we developed an analysis tool to allow users to browse mutational, mRNA/microRNA expression, and DNA methylation profiles and perform survival and correlation analyses of specific glioma subtypes. CGGA greatly reduces the barriers between complex functional genomic data and glioma researchers who seek rapid, intuitive, and high-quality access to data resources and enables researchers to use these immeasurable data sources for biological research and clinical application. Importantly, the free provision of data will allow researchers to quickly generate and provide data to the research community.

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