pubmed.ncbi.nlm.nih.gov

The MicroRNAs and their targets in the channel catfish (Ictalurus punctatus) - PubMed

. 2012 Sep;39(9):8867-72.

doi: 10.1007/s11033-012-1753-2. Epub 2012 Jun 24.

Affiliations

PMID: 22729904
DOI: 10.1007/s11033-012-1753-2

The MicroRNAs and their targets in the channel catfish (Ictalurus punctatus)

Muhammad Younas Khan Barozai. Mol Biol Rep. 2012 Sep.

Abstract

MicroRNAs (miRNAs) are small, non-coding and negative regulatory RNAs about 22 nucleotides. They are mostly conserved among the organisms and this conservation makes them a good source for the identification of novel miRNAs by computational genomic homology. The miRNA repertoire of the major aquaculture species, channel catfish (Ictalurus punctatus), is unknown. This study is focused on computational search for novel miRNA homologs and their targets along with their characterization in channel catfish. Total 60 novel precursor miRNAs having 73 mature sequences belong to 45 families in channel catfish were identified and characterized. They belong to the miRNA families; ipu-let-7, miR-7, 10, 16, 24, 29, 32, 93, 99, 101, 105, 126, 127, 133, 135, 141, 142, 143, 144 145, 148, 150, 152, 153, 203, 210, 214, 221, 223, 293, 429, 430, 466, 682, 731, 737, 1388, 1594, 1642, 1701, 1782, 1814, 2145, 2182 and 3074 are reported for the first time in channel catfish. All the 73 mature miRNAs are observed in the stem portion of the stable minimum free energy stem-loop structures. Total 341 proteins targeted by the novel channel catfish miRNAs were also identified. They are involved in immune-related (32 %), signaling (15 %), transcription factors (15 %), metabolism (12 %), transportation (8 %), growth & development (5 %), structural (5 %) and others (8 %) proteins.

PubMed Disclaimer

Cited by

Identification and Characterization of Osmoregulation Related MicroRNAs in Gills of Hybrid Tilapia Under Three Types of Osmotic Stress.
Su H, Fan J, Ma D, Zhu H. Su H, et al. Front Genet. 2021 Apr 6;12:526277. doi: 10.3389/fgene.2021.526277. eCollection 2021. Front Genet. 2021. PMID: 33889171 Free PMC article.
Profiling and characterization of eggplant (Solanum melongena L.) microRNAs and their targets.
Din M, Barozai MY. Din M, et al. Mol Biol Rep. 2014 Feb;41(2):889-94. doi: 10.1007/s11033-013-2932-5. Epub 2014 Jan 4. Mol Biol Rep. 2014. PMID: 24390233
In-silico based identification and functional analyses of miRNAs and their targets in Cowpea (Vigna unguiculata L.).
Gul Z, Barozai MYK, Din M. Gul Z, et al. AIMS Genet. 2017 Jun 29;4(2):138-165. doi: 10.3934/genet.2017.2.138. eCollection 2017. AIMS Genet. 2017. PMID: 31435506 Free PMC article.
Identification and characterization of microRNAs in channel catfish (Ictalurus punctatus) by using Solexa sequencing technology.
Xu Z, Chen J, Li X, Ge J, Pan J, Xu X. Xu Z, et al. PLoS One. 2013;8(1):e54174. doi: 10.1371/journal.pone.0054174. Epub 2013 Jan 16. PLoS One. 2013. PMID: 23342099 Free PMC article.
Structural and functional based identification of the bean (Phaseolus) microRNAs and their targets from expressed sequence tags.
Barozai MY, Din M, Baloch IA. Barozai MY, et al. J Struct Funct Genomics. 2013 Mar;14(1):11-8. doi: 10.1007/s10969-013-9152-z. Epub 2013 Apr 19. J Struct Funct Genomics. 2013. PMID: 23605779

References

1. Cell Cycle. 2008 Aug;7(15):2327-32 - PubMed
1. Curr Biol. 2008 Jul 8;18(13):943-50 - PubMed
1. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D109-11 - PubMed
1. Retrovirology. 2004 Dec 15;1:43 - PubMed
1. Mol Biol Rep. 2010 Oct;37(7):3171-6 - PubMed

MeSH terms

Substances

LinkOut - more resources

Full Text Sources
- Springer