| Title |
RNA secondary structure profiling in zebrafish reveals unique regulatory features
|
|---|---|
| Published in |
BMC Genomics, February 2018
|
| DOI | 10.1186/s12864-018-4497-0 |
| Pubmed ID | |
| Authors |
Kriti Kaushik, Ambily Sivadas, Shamsudheen Karuthedath Vellarikkal, Ankit Verma, Rijith Jayarajan, Satyaprakash Pandey, Tavprithesh Sethi, Souvik Maiti, Vinod Scaria, Sridhar Sivasubbu |
| Abstract |
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. 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. 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. |
X Demographics
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Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Montenegro | 1 | 50% |
| United Kingdom | 1 | 50% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 1 | 50% |
| Members of the public | 1 | 50% |
Mendeley readers
The data shown below were compiled from readership statistics for 32 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 32 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 8 | 25% |
| Researcher | 6 | 19% |
| Student > Master | 5 | 16% |
| Other | 3 | 9% |
| Student > Bachelor | 2 | 6% |
| Other | 4 | 13% |
| Unknown | 4 | 13% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 15 | 47% |
| Agricultural and Biological Sciences | 4 | 13% |
| Engineering | 2 | 6% |
| Nursing and Health Professions | 1 | 3% |
| Unspecified | 1 | 3% |
| Other | 2 | 6% |
| Unknown | 7 | 22% |
Attention Score in Context
This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 28 February 2018.
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#15,492,327
of 23,023,224 outputs
Outputs from BMC Genomics
#6,724
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Outputs of similar age
#291,593
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Outputs of similar age from BMC Genomics
#128
of 202 outputs
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