Preliminary Results about Lamb Meat Tenderness Based on the Study of Novel Isoforms and Alternative Splicing Regulation Pathways Using Iso-seq, RNA-seq and CTCF ChIP-seq Data

Zehu Yuan; Ling Ge; Weibo Zhang; Xiaoyang Lv; Shanhe Wang; Xiukai Cao; Wei Sun

doi:10.3390/foods11081068

Preliminary Results about Lamb Meat Tenderness Based on the Study of Novel Isoforms and Alternative Splicing Regulation Pathways Using Iso-seq, RNA-seq and CTCF ChIP-seq Data

Foods. 2022 Apr 7;11(8):1068. doi: 10.3390/foods11081068.

Authors

Zehu Yuan¹, Ling Ge², Weibo Zhang², Xiaoyang Lv¹, Shanhe Wang², Xiukai Cao¹, Wei Sun^{1

2}

Affiliations

¹ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou 225000, China.
² College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China.

Abstract

Tenderness is an important indicator of meat quality. Novel isoforms associated with meat tenderness and the role of the CCCTC-binding factor (CTCF) in regulating alternative splicing to produce isoforms in sheep are largely unknown. The current project studied six sheep from two crossbred populations (Dorper × Hu × Hu, DHH and Dorper × Dorper × Hu, DDH) with divergent meat tenderness. Pooled Iso-seq data were used to annotate the sheep genomes. Then, the updated genome annotation and six RNA-seq data were combined to identify differentially expressed isoforms (DEIs) in muscles between DHH and DDH. These data were also combined with peaks detected from CTCF ChIP-seq data to investigate the regulatory role of CTCF for the alternative splicing. As a result, a total of 624 DEIs were identified between DDH and DHH. For example, isoform 7.524.18 transcribed from CAPN3 may be associated with meat tenderness. In addition, a total of 86 genes were overlapped between genes with transcribed DEIs and genes in differential peaks identified by CTCF ChIP-seq. Among these overlapped genes, ANKRD23 produces different isoforms which may be regulated by CTCF via methylation. As preliminary research, our results identified novel isoforms associated with meat tenderness and revealed the possible regulating mechanisms of alternative splicing to produce isoforms.

Keywords: CTCF; ChIP-seq; Iso-seq; alternative splicing; novel isoforms; sheep; tenderness.

Abstract

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