scholarly journals An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation

2010 ◽  
Vol 11 (10) ◽  
Author(s):  
Gregory P Harhay ◽  
Timothy PL Smith ◽  
Leeson J Alexander ◽  
Christian D Haudenschild ◽  
John W Keele ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Annotation ◽  
Bovine Gene ◽  
Tissue Characteristics

scholarly journals Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis

2021 ◽  
Author(s):  
Dennis A Sun ◽  
Nipam H Patel
Keyword(s):  
Gene Expression ◽  
Genome Annotation ◽  
Time Course ◽  
Regulatory Elements ◽  
Rna Seq ◽  
Genome Wide ◽  
Long Read ◽  
Amphipod Crustacean ◽  
Accessible Chromatin

AbstractEmerging research organisms enable the study of biology that cannot be addressed using classical “model” organisms. The development of novel data resources can accelerate research in such animals. Here, we present new functional genomic resources for the amphipod crustacean Parhyale hawaiensis, facilitating the exploration of gene regulatory evolution using this emerging research organism. We use Omni-ATAC-Seq, an improved form of the Assay for Transposase-Accessible Chromatin coupled with next-generation sequencing (ATAC-Seq), to identify accessible chromatin genome-wide across a broad time course of Parhyale embryonic development. This time course encompasses many major morphological events, including segmentation, body regionalization, gut morphogenesis, and limb development. In addition, we use short- and long-read RNA-Seq to generate an improved Parhyale genome annotation, enabling deeper classification of identified regulatory elements. We leverage a variety of bioinformatic tools to discover differential accessibility, predict nucleosome positioning, infer transcription factor binding, cluster peaks based on accessibility dynamics, classify biological functions, and correlate gene expression with accessibility. Using a Minos transposase reporter system, we demonstrate the potential to identify novel regulatory elements using this approach, including distal regulatory elements. This work provides a platform for the identification of novel developmental regulatory elements in Parhyale, and offers a framework for performing such experiments in other emerging research organisms.Primary Findings-Omni-ATAC-Seq identifies cis-regulatory elements genome-wide during crustacean embryogenesis-Combined short- and long-read RNA-Seq improves the Parhyale genome annotation-ImpulseDE2 analysis identifies dynamically regulated candidate regulatory elements-NucleoATAC and HINT-ATAC enable inference of nucleosome occupancy and transcription factor binding-Fuzzy clustering reveals peaks with distinct accessibility and chromatin dynamics-Integration of accessibility and gene expression reveals possible enhancers and repressors-Omni-ATAC can identify known and novel regulatory elements

scholarly journals 5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation

2004 ◽  
Vol 101 (32) ◽  
pp. 11701-11706 ◽  
Author(s):  
C.-L. Wei ◽  
P. Ng ◽  
K. P. Chiu ◽  
C. H. Wong ◽  
C. C. Ang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Annotation

scholarly journals Evidence for Nitrogen Fixation by “Dehalococcoides ethenogenes” Strain 195

2009 ◽  
Vol 75 (23) ◽  
pp. 7551-7555 ◽  
Author(s):  
Patrick K. H. Lee ◽  
Jianzhong He ◽  
Stephen H. Zinder ◽  
Lisa Alvarez-Cohen
Keyword(s):  
Gene Expression ◽  
Nitrogen Fixation ◽  
Nitrogen Source ◽  
Genome Annotation ◽  
Fixed Nitrogen ◽  
Chlorinated Ethene ◽  
Dehalococcoides Ethenogenes ◽  
Growth Experiments ◽  
Isotope Measurements

ABSTRACT Genome annotation of the chlorinated ethene-respiring “Dehalococcoides ethenogenes” strain 195 indicated the presence of a complete nitrogenase operon. Here, results from long-term growth experiments, gene expression, and 15N2-isotope measurements confirm that strain 195 is capable of fixing atmospheric dinitrogen when a defined fixed-nitrogen source such as ammonium is unavailable.

scholarly journals Annotation depth confounds direct comparison of gene expression across species

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Elias Oziolor ◽  
Seda Arat ◽  
Matthew Martin
Keyword(s):  
Gene Expression ◽  
Genome Annotation ◽  
Genetic Background ◽  
Species Selection ◽  
Evolutionary Divergence ◽  
Top Down ◽  
Transcriptional Responses ◽  
Direct Gene ◽  
Basic Biology ◽  
Molecular Framework

Abstract Background Comparisons of the molecular framework among organisms can be done on both structural and functional levels. One of the most common top-down approaches for functional comparisons is RNA sequencing. This estimation of organismal transcriptional responses is of interest for understanding evolution of molecular activity, which is used for answering a diversity of questions ranging from basic biology to pre-clinical species selection and translation. However, direct comparison between species is often hindered by evolutionary divergence in structure of molecular framework, as well as large difference in the depth of our understanding of the genetic background between humans and other species. Here, we focus on the latter. We attempt to understand how differences in transcriptome annotation affect direct gene abundance comparisons between species. Results We examine and suggest some straightforward approaches for direct comparison given the current available tools and using a sample dataset from human, cynomolgus monkey, dog, rat and mouse with a common quantitation and normalization approach. In addition, we examine how variation in genome annotation depth and quality across species may affect these direct comparisons. Conclusions Our findings suggest that further efforts for better genome annotation or computational normalization tools may be of strong interest.

scholarly journals Transcriptomic profiling of PBDE-exposed HepaRG cells unveils critical lncRNA-PCG pairs involved in intermediary metabolism

2019 ◽  
Author(s):  
Angela Zhang ◽  
Cindy Yanfei Li ◽  
Edward J. Kelly ◽  
Lianne Sheppard ◽  
Julia Yue Cui
Keyword(s):  
Gene Expression ◽  
Polybrominated Diphenyl Ethers ◽  
Genome Annotation ◽  
Flame Retardants ◽  
Expression Profiles ◽  
Intermediary Metabolism ◽  
Differentially Expressed ◽  
Human Liver Tissue ◽  
Heparg Cells ◽  
Canonical Pathways

ABSTRACTPolybrominated diphenyl ethers (PBDEs) were formally used as flame-retardants and are chemically stable, lipophlic persistent organic pollutants which are known to bioaccumulate in humans. Although its toxicities are well characterized, little is known about the changes in transcriptional regulation caused by PBDE exposure. Long non-coding RNAs (lncRNAs) are increasingly recognized as key regulators of transcriptional and translational processes. It is hypothesized that lncRNAs can regulate nearby protein-coding genes (PCGs) and changes in the transcription of lncRNAs may act in cis to perturb gene expression of its neighboring PCGs. The goals of this study were to 1) characterize PCGs and lncRNAs that are differentially regulated from exposure to PBDEs; 2) identify PCG-lncRNA pairs through genome annotation and predictive binding tools; and 3) determine enriched canonical pathways caused by differentially expressed lncRNA-PCGs pairs. HepaRG cells, which are human-derived hepatic cells that accurately represent gene expression profiles of human liver tissue, were exposed to BDE-47 and BDE-99 at a dose of 25 μM for 24 hours. Differentially expressed lncRNA-PCG pairs were identified through DESeq2 and HOMER; significant canonical pathways were determined through Ingenuity Pathway Analysis (IPA). LncTar was used to predict the binding of 19 lncRNA-PCG pairs with known roles in drug-processing pathways. Genome annotation revealed that the majority of the differentially expressed lncRNAs map to PCG introns. PBDEs regulated overlapping pathways with PXR and CAR such as protein ubiqutination pathway and PPARα-RXRα activation but also regulate distinctive pathways involved in intermediary metabolism. BDE-47 uniquely regulated signaling by Rho Family GTPases and PBDE-99 uniquely regulates JAK/Stat signaling, bile acid biosynthesis, sirtuin signaling pathway, and autophagy. In conclusion, lncRNAs play essential roles in modifying important pathways involved in intermediary metabolism such as carbohydrate and lipid metabolism.

scholarly journals SQuIRE: Software for Quantifying Interspersed Repeat Elements

2018 ◽  
Author(s):  
Wan R. Yang ◽  
Daniel Ardeljan ◽  
Clarissa N. Pacyna ◽  
Lindsay M. Payer ◽  
Kathleen H. Burns
Keyword(s):  
Gene Expression ◽  
Repetitive Sequence ◽  
Genome Annotation ◽  
Rna Expression ◽  
Rna Seq ◽  
Analysis Pipeline ◽  
Repeat Elements ◽  
Consensus Sequences ◽  
Repeat Sequences ◽  
Star Gene

AbstractTransposable elements are interspersed repeat sequences that make up much of the human genome. Conventional approaches to RNA-seq analysis often exclude these sequences, fail to optimally adjudicate read alignments, or align reads to interspersed repeat consensus sequences without considering these transcripts in their genomic contexts. As a result, repetitive sequence contributions to transcriptomes are not well understood. Here, we present Software for Quantifying Interspersed Repeat Expression (SQuIRE), an RNA-seq analysis pipeline that integrates repeat and genome annotation (RepeatMasker), read alignment (STAR), gene expression (StringTie) and differential expression (DESeq2). SQuIRE uniquely provides a locus-specific picture of interspersed repeat-encoded RNA expression. SQuIRE can be downloaded at (github.com/wyang17/SQuIRE).

scholarly journals Characterisation of the horse transcriptome from immunologically active tissues

2014 ◽  
Author(s):  
Joanna Moreton ◽  
Sunir Malla ◽  
Aziz Aboobaker ◽  
Rachael Tarlinton ◽  
Richard D Emes
Keyword(s):  
Gene Expression ◽  
Immune System ◽  
Animal Models ◽  
Genome Annotation ◽  
Large Animal ◽  
Suitable Model ◽  
Rodent Models ◽  
Large Animal Models ◽  
Human Disorders ◽  
Novel Isoforms

The immune system of the horse has not been well studied, despite the fact that the horse displays several features such as sensitivity to bacterial lipopolysaccharide that make them in many ways a more suitable model of some human disorders than the current rodent models. The difficulty of working with large animal models has however limited characterisation of gene expression in the horse immune system with current annotations for the equine genome restricted to predictions from other mammals and the few described horse proteins. This paper outlines sequencing of 184 million transcriptome short reads from immunologically active tissues of three horses including the genome reference “Twilight”. In a comparison with the Ensembl horse genome annotation, we found 8,763 potentially novel isoforms.

scholarly journals Comparative analysis of gene expression between Babesia bovis blood stages and kinetes allowed by improved genome annotation

2020 ◽  
Author(s):  
Massaro W. Ueti ◽  
Wendell C. Johnson ◽  
Lowell S. Kappmeyer ◽  
David R. Herndon ◽  
Michelle R. Mousel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Comparative Analysis ◽  
Genome Annotation ◽  
Babesia Bovis

scholarly journals PSV-31 Mechanisms and biochemical pathways affecting the eating quality of Triceps brachii muscle

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 341-341
Author(s):  
Esther O Ijiwade ◽  
Heather L Bruce ◽  
Le Luo Guan ◽  
Yanhong Chen ◽  
Bimol Roy ◽  
...  
Keyword(s):  
Gene Expression ◽  
Candidate Gene ◽  
Eating Quality ◽  
Beef Steers ◽  
Triceps Brachii ◽  
Expression Levels ◽  
Breed Type ◽  
Expression Of Genes ◽  
Mean Differences ◽  
Tissue Characteristics

Abstract Twenty-four beef steers (Angus, Charolais and Angus crossbred) were used to test the hypothesis that phenotypic measurements of meat quality attributes and intramuscular connective tissue characteristics will be related to the differences in the expression level of genes involved in the synthesis and degradation of collagen. Triceps brachii muscles from steers with low and high intramuscular collagen solubility at 3 days post mortem (dpm) were selected within each breed type for candidate gene analysis. Expression levels of 27 candidate genes were evaluated using quantitative real-time polymerase chain reaction (RT-qPCR) and the mean differences in expression between candidate and control (18s RNA) genes were calculated. Analysis of variance indicated that breed type had significant effects (P < 0.05) on expression of genes related to collagen types I, V, and VI (COL1A1, COL5A1 and COL6A1), fibroblast growth factor (FGF), lysyl hydroxylase (LH), matrix metalloproteinases (MMP) 1, 8 and 13, prolyl 4-hydroxylase (P4HA1), SMAD (2, 3 and 7), and tissue inhibitor of MMPs (TIMP). Collagen heat solubility had no effect on gene expression (P > 0.05), although there was a significant interaction between breed type and collagen solubility (P < 0.05) for COL3A1, FGF2, MMP13, and SMAD 6 expressions. Candidate gene expression levels were correlated to intramuscular pH, 3 and 13 dpm Warner-Bratzler shear force (WBSF), total intramuscular collagen, and collagen heat solubility at 3 and 13 dpm. Negative correlations (P < 0.05) existed between FGF1 and 13 dpm soluble collagen (r = -0.44), MMP8 and total collagen (r = -0.55) and MMP13 and wet perimysium weight (r = -0.46). Positive correlations (P < 0.05) existed between FGF1 and 3dpm WBSF (r = 0.44) and, TIMP3 and 3 dpm WBSF (r = 0.33). Results indicated genes associated with increased collagen synthesis and inhibition of MMPs were related to increased beef toughness.

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