scholarly journals Argonaute High-Throughput Sequencing of RNAs Isolated by Cross-Linking Immunoprecipitation Reveals a Snapshot of miRNA Gene Regulation in the Mammalian Retina

Biochemistry ◽  
2014 ◽  
Vol 53 (37) ◽  
pp. 5831-5833 ◽  
Author(s):  
Thomas R. Sundermeier ◽  
Hui Jin ◽  
Matthew L. Kleinjan ◽  
Debarshi Mustafi ◽  
Donny D. Licatalosi ◽  
...  
Keyword(s):  
Gene Regulation ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Mirna Gene ◽  
Cross Linking ◽  
Mammalian Retina

High-throughput sequencing methods to study neuronal RNA–protein interactions

2009 ◽  
Vol 37 (6) ◽  
pp. 1278-1280 ◽  
Author(s):  
Jernej Ule
Keyword(s):  
Transcriptional Regulation ◽  
High Throughput ◽  
Protein Interactions ◽  
Translational Control ◽  
High Throughput Sequencing ◽  
Ribosome Profiling ◽  
Cross Linking ◽  
Rnase Protection ◽  
Temporal Precision ◽  
Post Transcriptional Regulation

UV-cross-linking and RNase protection, combined with high-throughput sequencing, have provided global maps of RNA sites bound by individual proteins or ribosomes. Using a stringent purification protocol, UV-CLIP (UV-cross-linking and immunoprecipitation) was able to identify intronic and exonic sites bound by splicing regulators in mouse brain tissue. Ribosome profiling has been used to quantify ribosome density on budding yeast mRNAs under different environmental conditions. Post-transcriptional regulation in neurons requires high spatial and temporal precision, as is evident from the role of localized translational control in synaptic plasticity. It remains to be seen if the high-throughput methods can be applied quantitatively to study the dynamics of RNP (ribonucleoprotein) remodelling in specific neuronal populations during the neurodegenerative process. It is certain, however, that applications of new biochemical techniques followed by high-throughput sequencing will continue to provide important insights into the mechanisms of neuronal post-transcriptional regulation.

scholarly journals High-throughput small RNA and transcriptome sequencing reveal reproduction-related microRNAs and mRNA in ovary of Geese in Counter-Season Production

2019 ◽  
Author(s):  
Jin-Shan Ran ◽  
Ling-Qian Yin ◽  
Jing-Jing Li ◽  
Yan-Qiang Tang ◽  
Jian Huang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Mirna Gene ◽  
Egg Laying ◽  
Differentially Expressed ◽  
Ovary Development ◽  
Regulation Mechanism ◽  
Pathway Network ◽  
Apoptosis Pathways

Abstract Background Broodiness is a phenomenon that occurs in most avian species and significantly reduces productivity. Several genes are known to play an important role in regulating the progress of reproduction, but the molecular regulation mechanism of broodiness remains unclear. In the current study, via high throughput sequencing, we identified and explored the differentially expressed miRNAs and mRNAs involved in ovarian atrophy. Results We identified a total of 901 mRNAs and 50 miRNAs that were differentially expressed in egg-laying and atrophic ovaries. Among them, numerous DEGs transcripts and target genes for miRNAs were significantly enriched in reproductive processes, cell proliferation, and apoptosis pathways. In addition, a miRNA- gene-pathway network was constructed by considering target relationships and correlation of the expression levels between ovary development-related genes and miRNAs. Conclusions We discovered mRNA and miRNAs transcripts that are candidate regulators of ovary development in broody geese. Our findings expanded our understanding of the functional of miRNAs in ovarian atrophy and demonstrated that RNA-Seq is a powerful tool for examining the molecular mechanism in regulating broodiness.

scholarly journals Identification of Transposable Elements in Conifer and Their Potential Application in Breeding

2020 ◽  
Vol 16 ◽  
pp. 117693432093026 ◽  
Author(s):  
Junhui Wang ◽  
Nan Lu ◽  
Fei Yi ◽  
Yao Xiao
Keyword(s):  
Gene Regulation ◽  
Picea Abies ◽  
Transposable Elements ◽  
Pinus Taeda ◽  
High Throughput ◽  
Genetic Study ◽  
High Throughput Sequencing ◽  
Genetics Research ◽  
Potential Applications ◽  
Functional Biology

Transposable elements (TEs) are known to play a role in genome evolution, gene regulation, and epigenetics, representing potential tools for genetics research in and breeding of conifers. Recently, thanks to the development of high-throughput sequencing, more conifer genomes have been reported. Using bioinformatics tools, the TEs of 3 important conifers ( Picea abies, Picea glauce, and Pinus taeda) were identified in our previous study, which provided a foundation for accelerating the use of TEs in conifer breeding and genetic study. Here, we review recent studies on the functional biology of TEs and discuss the potential applications for TEs in conifers.

scholarly journals Characterization of genomic regulation profiles in human mitral valve whole tissue to annotate genetic risk loci for mitral valve prolapse

2020 ◽  
Author(s):  
Sergiy Kyryachenko ◽  
Adrien Georges ◽  
Mengyao Yu ◽  
Takiy E. Berrandou ◽  
Patrick Bruneval ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Mitral Valve ◽  
High Throughput ◽  
Mitral Valve Prolapse ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Valve Disease ◽  
Open Chromatin ◽  
Mitral Valves ◽  
Causal Variants

Rationale: Mitral valve prolapse (MVP) is a common valve disease that leads to mitral insufficiency, heart failure and sudden death. The identification of risk loci provided insight into its genetic architecture, although the causal variants and target genes need to be fully characterized. Objective: To establish the chromatin accessibility profiles and gene regulation specificities of human mitral valve and identify functional variants and target genes at MVP loci. Methods and Results: We mapped the open chromatin accessible regions in nuclei from 11 human mitral valves by an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq). Compared to the heart tissue and cardiac fibroblasts, we found that mitral valve-specific ATAC-Seq peaks were enriched near genes involved in extracellular matrix organization, chondrocyte differentiation, and connective tissue development. The most enriched motif in mitral valve-specific open chromatin peaks was for the nuclear factor of activated T cells (NFATC) family of transcription factors, involved in valve endocardial and interstitial cells formation. We also found that MVP-associated variants (p < 10-5) observed in the current MVP GWAS were significantly enriched (p<0.05) in mitral valve open chromatin peaks. Integration of the ATAC-Seq data with GWAS loci, extensive functional annotation, and gene reporter assay revealed plausible causal variants at two risk loci: rs6723013 at the IGFBP5/TNS1 locus and rs2641440 at the SMG6/SRR locus. Circular chromosome conformation capture followed by high-throughput sequencing provided evidence for several target genes, including SRR, HIC1, and DPH1 at the SMG6/SRR locus and further supported TNS1 as the most likely target gene on Chr2. Conclusions: Here we describe unprecedented genome-wide open chromatin profiles from human mitral valves that indicates specific gene regulation profiles, compared to the heart. We also report in vitro functional evidence for potential causal variants and target genes at MVP risk loci involving established and new biological mechanisms relevant to mitral valve disease.

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