Polyadenylation sites and their characteristics in the genome of channel catfish (Ictalurus punctatus) as revealed by using RNA-Seq data

Suxu Tan, Wenwen Wang, Tao Zhou, Yujia Yang, Dongya Gao, Rex Dunham, Zhanjian "John" Liu

Research output: Contribution to journalArticle

Abstract

Polyadenylation plays important roles in gene expression regulation in eukaryotes, which typically involves cleavage and poly(A) tail addition at the polyadenylation site (PAS) of the pre-mature mRNA. Many eukaryotic genes contain more than one PASs, termed as alternative polyadenylation (APA). As a crucial post-transcriptional regulation, polyadenylation affects various aspects of RNA metabolism such as mRNA stability, translocation, and translation. However, polyadenylation has been rarely studied in teleosts. Here we conducted polyadenylation analysis in channel catfish, a commercially important aquaculture species around the world. Using RNA-Seq data, we identified 20,320 PASs which were classified into 14,500 clusters by merging adjacent PASs. Most of the PASs were found in 3′ UTRs, followed by intron regions based on the annotation of channel catfish reference genome. No apparent difference in PAS distribution was observed between the sense and antisense strand of the channel catfish genome. The sequence analysis of nucleotide composition and motif around PASs yielded a highly similar profile among various organisms, suggesting the conservation and importance of polyadenylation in evolution. Using APA genes with more than two PASs, gene ontology enrichment revealed genes particularly involved in RNA binding. Reactome pathway analysis showed the enrichment of the innate immune system, especially neutrophil degranulation.

Original languageEnglish (US)
Pages (from-to)248-255
Number of pages8
JournalComparative Biochemistry and Physiology - Part D: Genomics and Proteomics
Volume30
DOIs
StatePublished - Jun 1 2019

Fingerprint

Ictaluridae
Polyadenylation
Genes
Genome
RNA
Messenger RNA
Gene expression regulation
Aquaculture
Immune system
3' Untranslated Regions
Merging
Metabolism
Introns
Ontology
Conservation
Nucleotide Motifs
Gene Ontology
Nucleotides
RNA Precursors
RNA Stability

Keywords

  • Alternative polyadenylation
  • Genome
  • Poly(a) site
  • RNA-Seq
  • Transcriptome

ASJC Scopus subject areas

  • Biochemistry
  • Physiology
  • Molecular Biology
  • Genetics

Cite this

Polyadenylation sites and their characteristics in the genome of channel catfish (Ictalurus punctatus) as revealed by using RNA-Seq data. / Tan, Suxu; Wang, Wenwen; Zhou, Tao; Yang, Yujia; Gao, Dongya; Dunham, Rex; Liu, Zhanjian "John".

In: Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics, Vol. 30, 01.06.2019, p. 248-255.

Research output: Contribution to journalArticle

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