Defining Candidate Imprinted loci in Bos taurus

Abstract

Using a whole-genome assembly of Bos taurus, I applied my bioinformatics strategy to locate candidate imprinting control regions (ICRs) genome-wide. In mammals, genomic imprinting plays essential roles in embryogenesis. In my strategy, peaks in plots mark the locations of known, inferred, and candidate ICRs. Genes in the vicinity of candidate ICRs correspond to potential imprinted genes. By displaying my datasets on the UCSC genome browser, one could view peak positions with respect to genomic landmarks. I give two examples of candidate ICRs in loci that influence spermatogenesis in bulls: CNNM1 and CNR1. I also give examples of candidate ICRs in loci that influence muscle development: SIX1 and BCL6. By examining the ENCODE data reported for mice, I deduced regulatory clues about cattle. I focused on DNase I hypersensitive sites (DHSs). Such sites reveal accessibility of chromatin to regulators of gene expression. For inspection, I chose DHSs in chromatin from mouse embryonic stem cells (ESCs) ES-E14, mesoderm, brain, heart, and skeletal muscle. The ENCODE data revealed that the SIX1 promoter was accessible to the transcription initiation apparatus in mouse ESCs, mesoderm, and skeletal muscles. The data also revealed accessibility of BCL6 locus to regulatory proteins in mouse ESCs and examined tissues.

Keywords: BCL6; CNNM1; CNR1; SIX1; ZFBS-morph overlaps; ZFP57; bull spermatogenesis; cattle genomics; cattle muscle; cattle spermatogenesis; farm animals; genome wide; genomic imprinting.

Figure 1

A snapshot of the density plot created for studies of chromosome 9. In this plot, a robust peak located the known ICR of ZAC1 in nearly 106 Mb long chromosomal DNA. Additional robust peaks point to candidate ICRs near potential imprinted genes including SMAP1, TENT5A, HACE1, CNR1, CITED2, and AFDN.

Figure 2

A candidate ICR at the 5′ end of CNNM1. In mice, Cnnm1 triggered differentiation of spermatogenic cells.

Figure 3

A candidate ICR at the 5′ end of CNR1. In mice, CNR1 was expressed in elongating spermatids and spermatozoa, impacting male germ cell progression and sperm maturation mediated by the endocannabinoids.

Figure 4

A candidate ICR at the 5′ end of SIX1. In adult muscle progenitor cells, SIX1 controls the expression of MYOD.

Figure 5

A candidate ICR at the 5′ end of BCL6 with respect to Non-Cow RefSeq Genes. In mice, at gestational day 17, BCL6 was primarily expressed in skeletal muscle.

Figure 6

A candidate ICR at the 5′ end of Six1 in mouse. Vertical bars reveal the positions of DHSs in chromatin prepared from mouse ESCs ES-E14, mesoderm, brain, heart, and skeletal muscle. Note cell-type and tissue-specific patterns of chromatin accessibility to regulatory proteins.

Figure 7

A candidate at the 5′ end of Bcl6in mouse. Several tracks display the positions of DHSs in chromatin prepared from mouse ESCs ES-E14, mesoderm, and skeletal muscle. Vertical bars mark the positions of DHSs in chromatin prepared from mouse ESCs ES-E14, mesoderm, brain, heart, and skeletal muscle. Note cell-type and tissue-specific patterns of chromatin accessibility to regulatory proteins.