RNA secondary structure profiling in zebrafish reveals unique regulatory features

Background RNA is known to play diverse roles in gene regulation. The clues for this regulatory function of RNA are embedded in its ability to fold into intricate secondary and tertiary structure. Results We report the transcriptome-wide RNA secondary structure in zebrafish at single nucleotide reso...

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Veröffentlicht in:BMC genomics Jg. 19; H. 1; S. 147 - 17
Hauptverfasser: Kaushik, Kriti, Sivadas, Ambily, Vellarikkal, Shamsudheen Karuthedath, Verma, Ankit, Jayarajan, Rijith, Pandey, Satyaprakash, Sethi, Tavprithesh, Maiti, Souvik, Scaria, Vinod, Sivasubbu, Sridhar
Format: Journal Article
Sprache:Englisch
Veröffentlicht: London BioMed Central 15.02.2018
BioMed Central Ltd
BMC
Schlagworte:
3' Untranslated Regions - genetics
5' Untranslated Regions - genetics
Animal Genetics and Genomics
Animals
Base Sequence
Biomedical and Life Sciences
Codon, Initiator - genetics
Codon, Terminator - genetics
Gene Expression Profiling - methods
Gene Expression Regulation
Gene regulation
Genetic aspects
Genetic regulation
Life Sciences
Microarrays
Microbial Genetics and Genomics
Non-human and non-rodent vertebrate genomics
Nucleic Acid Conformation
PARS
Plant Genetics and Genomics
Protein Biosynthesis
Proteomics
Research Article
RNA
RNA - chemistry
RNA - genetics
RNA secondary structure
RNA, Messenger - chemistry
RNA, Messenger - genetics
Sequence Homology, Nucleic Acid
Structure
Transcriptome
Zebrafish
Zebrafish - genetics
Zebrafish
Gene regulation
RNA secondary structure
PARS
Transcriptome
ISSN:1471-2164, 1471-2164
Online-Zugang:Volltext
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Zusammenfassung:Background RNA is known to play diverse roles in gene regulation. The clues for this regulatory function of RNA are embedded in its ability to fold into intricate secondary and tertiary structure. Results We report the transcriptome-wide RNA secondary structure in zebrafish at single nucleotide resolution using Parallel Analysis of RNA Structure (PARS). This study provides the secondary structure map of zebrafish coding and non-coding RNAs. The single nucleotide pairing probabilities of 54,083 distinct transcripts in the zebrafish genome were documented. We identified RNA secondary structural features embedded in functional units of zebrafish mRNAs. Translation start and stop sites were demarcated by weak structural signals. The coding regions were characterized by the three-nucleotide periodicity of secondary structure and display a codon base specific structural constrain. The splice sites of transcripts were also delineated by distinct signature signals. Relatively higher structural signals were observed at 3’ Untranslated Regions (UTRs) compared to Coding DNA Sequence (CDS) and 5’ UTRs. The 3′ ends of transcripts were also marked by unique structure signals. Secondary structural signals in long non-coding RNAs were also explored to better understand their molecular function. Conclusions Our study presents the first PARS-enabled transcriptome-wide secondary structure map of zebrafish, which documents pairing probability of RNA at single nucleotide precision. Our findings open avenues for exploring structural features in zebrafish RNAs and their influence on gene expression.
Bibliographie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1471-2164
1471-2164
DOI:10.1186/s12864-018-4497-0