
LINK . SPRINGER . COM {
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Title:
Genome-wide profiling and functional characterization of circular RNAs in neural development and injury: insights from a rat model research | Cellular and Molecular Life Sciences
Description:
Circular RNAs (circRNAs) have re-emerged as promising gene regulators in various physiological and pathological conditions. However, the expression patterns of circRNAs in the developing spinal cord of mammals and the comprehensive distribution of circRNAs across different tissues remain poorly understood. In this study, rats were used as the model organism. We conducted a comprehensive analysis of 15 RNA-Seq datasets comprising 217 rat samples and developed a web-based resource, CiRNat, to facilitate access to these data. We identified 15,251 credible circRNAs and validated them through experimental approaches. Notably, we observed two significant time points for circRNA increase during spinal cord development, approximately at embryonic day 14 (E14d) and postnatal week 4 (P4w). Analysis of circRNA expression in various rat tissues revealed higher expression levels in central nervous system tissues compared to peripheral nervous system tissues and other tissues. Furthermore, some highly abundant circRNAs exhibited tissue- and species-specific expression patterns and differed from their cognate linear RNAs, such as those derived from Gigyf2. Integrating polysome profiling and bioinformatic predictions suggested potential functions of certain circRNAs as miRNA sponges and translational templates. Collectively, this study provides the first comprehensive landscape of circRNAs in the developing spinal cord, offering an important resource and new insights for future exploration of functional circRNAs in central nervous system development and related diseases.
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Keywords {๐}
circrnas, pubmed, expression, fig, spinal, article, cord, rat, circular, google, scholar, tissues, rnas, circrna, central, rna, development, cas, loci, datasets, mouse, linear, supplementary, file, showed, developing, analysis, sequencing, number, abundant, injury, abundance, including, yang, cns, total, zhang, bsj, host, cell, wang, chen, brain, rnaseq, system, top, generated, higher, functional, potential,
Topics {โ๏ธ}
org/pub/release-109/fasta/rattus_norvegicus/ long-term time-series dataset abnormal lncrna-mirna-mrna network article download pdf ciri-deep enables single-cell gtf-formatted annotation files long-term time-series synapse-related protein-coding genes framed k-mer features quantitative real-time pcr central nervous system analyzing rna-seq datasets cerebral ischemia-reperfusion injury rrna-depleted rna-seq full size image total rna-seq dataset user-friendly web application rnase r-treated transcriptomes fast gapped-read alignment ribosome-depleted rna sequencing targeting circular rna-zranb1 bbs9-dervied circrna ranked included rna-seq datasets mir-125a/b-5p sided unpaired t-test liftover command-line tool paired-end sequencing strategy zpbp-derived circrna ranked hspa1a-regulated gene expression molecular network features back-splicing junction sequences including mir-125b-2-3p high-throughput sequencing data relevant public datasets multiple rere-dervied circrnas rnase r-treated rna single-exon derived circrnas remove low-quality reads coding rna locus species-specific expression patterns injured-regulated circrna analysis raw sequencing data small sample size uncropped electrophoresis image results genome-wide characterization 15 rna-seq datasets 7 rna-seq datasets 22 rna-seq datasets rna-seq datasets dorsal root ganglion
Questions {โ}
- Whether this characteristic also present using the dataset of injured spinal cord?
Schema {๐บ๏ธ}
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headline:Genome-wide profiling and functional characterization of circular RNAs in neural development and injury: insights from a rat model research
description:Circular RNAs (circRNAs) have re-emerged as promising gene regulators in various physiological and pathological conditions. However, the expression patterns of circRNAs in the developing spinal cord of mammals and the comprehensive distribution of circRNAs across different tissues remain poorly understood. In this study, rats were used as the model organism. We conducted a comprehensive analysis of 15 RNA-Seq datasets comprising 217 rat samples and developed a web-based resource, CiRNat, to facilitate access to these data. We identified 15,251 credible circRNAs and validated them through experimental approaches. Notably, we observed two significant time points for circRNA increase during spinal cord development, approximately at embryonic day 14 (E14d) and postnatal week 4 (P4w). Analysis of circRNA expression in various rat tissues revealed higher expression levels in central nervous system tissues compared to peripheral nervous system tissues and other tissues. Furthermore, some highly abundant circRNAs exhibited tissue- and species-specific expression patterns and differed from their cognate linear RNAs, such as those derived from Gigyf2. Integrating polysome profiling and bioinformatic predictions suggested potential functions of certain circRNAs as miRNA sponges and translational templates. Collectively, this study provides the first comprehensive landscape of circRNAs in the developing spinal cord, offering an important resource and new insights for future exploration of functional circRNAs in central nervous system development and related diseases.
datePublished:2025-04-01T00:00:00Z
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CircRNA
Neurogenesis
Tissue-specific expression
Gene regulation
Nervous system
Translational potential
Cell Biology
Biomedicine
general
Life Sciences
Biochemistry
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headline:Genome-wide profiling and functional characterization of circular RNAs in neural development and injury: insights from a rat model research
description:Circular RNAs (circRNAs) have re-emerged as promising gene regulators in various physiological and pathological conditions. However, the expression patterns of circRNAs in the developing spinal cord of mammals and the comprehensive distribution of circRNAs across different tissues remain poorly understood. In this study, rats were used as the model organism. We conducted a comprehensive analysis of 15 RNA-Seq datasets comprising 217 rat samples and developed a web-based resource, CiRNat, to facilitate access to these data. We identified 15,251 credible circRNAs and validated them through experimental approaches. Notably, we observed two significant time points for circRNA increase during spinal cord development, approximately at embryonic day 14 (E14d) and postnatal week 4 (P4w). Analysis of circRNA expression in various rat tissues revealed higher expression levels in central nervous system tissues compared to peripheral nervous system tissues and other tissues. Furthermore, some highly abundant circRNAs exhibited tissue- and species-specific expression patterns and differed from their cognate linear RNAs, such as those derived from Gigyf2. Integrating polysome profiling and bioinformatic predictions suggested potential functions of certain circRNAs as miRNA sponges and translational templates. Collectively, this study provides the first comprehensive landscape of circRNAs in the developing spinal cord, offering an important resource and new insights for future exploration of functional circRNAs in central nervous system development and related diseases.
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Neurogenesis
Tissue-specific expression
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Translational potential
Cell Biology
Biomedicine
general
Life Sciences
Biochemistry
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affiliation:
name:The Second Affiliated Hospital of Nantong University, Nantong University
address:
name:Department of Spine Surgery, The Second Affiliated Hospital of Nantong University, Nantong University, Nantong, China
type:PostalAddress
type:Organization
email:[email protected]
name:Lian Xu
affiliation:
name:Nantong University
address:
name:Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
type:PostalAddress
type:Organization
name:The Second Affiliated Hospital of Nantong University, Nantong University
address:
name:Institute for Translational Neuroscience, The Second Affiliated Hospital of Nantong University, Nantong University, Nantong, China
type:PostalAddress
type:Organization
email:[email protected]
PostalAddress:
name:Department of Neurosurgery, Peopleโs Hospital of Deyang City, Sichuan Clinical Research Center for Neurological Diseases, Deyang, China
name:Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
name:Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
name:Institute for Translational Neuroscience, The Second Affiliated Hospital of Nantong University, Nantong University, Nantong, China
name:Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
name:Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
name:Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
name:Institute for Translational Neuroscience, The Second Affiliated Hospital of Nantong University, Nantong University, Nantong, China
name:Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
name:Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
name:Institute for Translational Neuroscience, The Second Affiliated Hospital of Nantong University, Nantong University, Nantong, China
name:Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
name:Department of Spine Surgery, The Second Affiliated Hospital of Nantong University, Nantong University, Nantong, China
name:Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
name:Institute for Translational Neuroscience, The Second Affiliated Hospital of Nantong University, Nantong University, Nantong, China
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