Application of sequence semantic and integrated cellular geography approach to study biogenesis of exonic circular RNA
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Abstract
Background
Concurrent existence of lncRNA and circular RNA at both nucleus and cytosol within a cell at different proportion is well reported. Secondly, information on genes transcribing both circular and lncRNAs along with total number of RBP binding sites for both of these RNA types is extractable from databases. This study showed how these apparently unconnected pieces of reports could be put together to build a model leading to biogenesis of circular RNA.
Results
As a result of this study, a model was built under the premises that, sequences with special semantics were molecular precursors in biogenesis of circular RNA which occurred through catalytic role of some specific RBPs. The model outcome was further strengthened by fulfillment of three logical lemmas which were extracted and assimilated in this work using a novel data analytic approach, Integrated Cellular Geography. Result of the study was found to be in well agreement with proposed model. Furthermore this study also indicated that biogenesis of circular RNA was a post-transcriptional event.
Conclusions
Overall, this study provides a novel systems biology based model under the paradigm of Integrated Cellular Geography which can assimilate independently performed experimental results and data published by global researchers on RNA biology to provide important information on biogenesis of exonic circular RNAs considering lncRNAs as precursor molecule.
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SciScore rigor report
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Not required = Field is not applicable to this study
Not detected = Field is applicable to this study, but not included.
Ethics
Field Sample Permit: Collection of data for detecting cellular spatiotemporal condition supporting circularization For this purpose, online database and web server were used by taking specific queries like , RBP-types or lncRNAs to search out their special location inside cellular spaces
Inclusion and Exclusion Criteria
not required.
Attrition
not required.
Sex as a biological variable
not required.
Subject Demographics
Age: not required.
Weight: not required.
Randomization
To…
SciScore rigor report
Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.
Not required = Field is not applicable to this study
Not detected = Field is applicable to this study, but not included.
Ethics
Field Sample Permit: Collection of data for detecting cellular spatiotemporal condition supporting circularization For this purpose, online database and web server were used by taking specific queries like , RBP-types or lncRNAs to search out their special location inside cellular spaces
Inclusion and Exclusion Criteria
not required.
Attrition
not required.
Sex as a biological variable
not required.
Subject Demographics
Age: not required.
Weight: not required.
Randomization
To reduce computational complexity in dealing with very large database where number of data is greater than 1000 , sample datasets were used through random selection of data from the original database .
Blinding
not detected.
Power Analysis
not detected.
Replication
not required.
Data Information
Identifiers: We analyzed the spread of this biomolecular entity outside and inside the sub- cellular space along with assimilating other reported pieces of information (e.g., about RBP molecules involved in circularization of such bioRxiv preprint doi: https:// doi.org/10.1101/2021.10.26.465935; this version posted October 26, 2021. https://doi.org/10.1101/2021.10.26.465935
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