Inter-3' ends CpG islands are enriched in human chromosome 19p13.3 region: A genomic signature of metabolism-associated genes :Ze Zheng, Kezhong Zhang, Environmental Disease

ORIGINAL ARTICLE
Year : 2021 | Volume : 6 | Issue : 1 | Page : 24--29

Inter-3' ends CpG islands are enriched in human chromosome 19p13.3 region: A genomic signature of metabolism-associated genes

Ze Zheng¹, Kezhong Zhang²,
¹ Department of Medicine, Division of Endocrinology and Molecular Medicine; Cardiovascular Center, Medical College of Wisconsin; Versiti Blood Center of Wisconsin, Blood Research Institute, Milwaukee, WI, USA
² Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University; Department of Biochemistry, Microbiology and Immunology, School of Medicine, Wayne State University, Detroit, MI, USA

Correspondence Address:
Kezhong Zhang
Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201; Department of Biochemistry, Microbiology and Immunology, School of Medicine, Wayne State University, Detroit, MI 48201
USA
Ze Zheng
Division of Endocrinology and Molecular Medicine, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226; Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA. Blood Research Institute, Versiti Blood Center of Wisconsin, Milwaukee, WI 53226
USA

Abstract

Metabolic disease is a pandemic in modern times. However, understanding of the genomic basis associated with metabolism remains to be further elucidated. CpG islands are the genomic regions enriched in cytosine nucleotide (C) and guanine nucleotide (G), mostly located at promoters and contain the 5' end of the gene transcript. In this study, we utilize the UCSC Genome Browser to map the genomic locations and extract the CpG island tracks that are associated with the genes encoding functions in cell metabolism or metabolic disease. We identified a new genomic signature, namely inter-3' end CpG island (ITCI), associated with the genes encoding major metabolic regulators or enzymes in the human chromosome 19p13.3 region. In this region, the gene encoding a major metabolic regulator, CREB3L3, possesses a conserved CpG island in its 3' end. This unique ITCI genomic signature has been found in nine pairs of genes in the human chromosome 19p13.3 region. Many of these genes are associated with metabolism. In conclusion, we discovered a new type of genomic signature, ITCI, which is featured by a dozen of metabolic genes possessing conserved CpG islands in their 3' ends, in a specific human chromosome. Identification of ITCI signature and decoding of the ITCI-associated associated metabolic genes provide important insights into the genomic basis of metabolism or metabolic disease.

How to cite this article:
Zheng Z, Zhang K. Inter-3' ends CpG islands are enriched in human chromosome 19p13.3 region: A genomic signature of metabolism-associated genes.Environ Dis 2021;6:24-29

How to cite this URL:
Zheng Z, Zhang K. Inter-3' ends CpG islands are enriched in human chromosome 19p13.3 region: A genomic signature of metabolism-associated genes. Environ Dis [serial online] 2021 [cited 2023 Jun 4 ];6:24-29
Available from: http://www.environmentmed.org/text.asp?2021/6/1/24/312682

Full Text

Introduction

The CpG islands are evolutionarily important for DNA methylation, transcriptional regulation, and transposing genomic elements.[1],[2],[3] Although most of CpG islands are located at the 5' ends of genes,[1] the distribution of CpG island could be variable from intergenic, terminal, exonic, and intragenic regions, and it is related to the transcriptional regulation and function of the gene.[4],[5] Non-CpG island promoter has been found related to the tissue-specific expression.[6] Although less frequent, the 3' end CpG islands do exist, while CpG islands between two genes' 3' ends are extremely rare, namely inter-3' end CpG island (ITCI). However, the function of ITCI has not been identified.

CREB3L3 (cAMP-responsive element-binding protein 3 like 3) is an endoplasmic reticulum (ER)-resident transcription factor of CREB/ATF family.[7],[8] Activated CREB3L3 functions as a potent transcription factor to drive expression of genes encoding functions in hepatic acute phase response as well as lipid and glucose metabolism.[7],[9],[10],[11],[12],[13],[14] Specifically, CREB3L3 regulates (1) expression of genes involved in hepatic lipolysis, fatty acid oxidation, and lipogenesis;[9] (2) activates fibroblast growth factor 21 through interaction with peroxisome proliferator–activated receptor α;[10],[15] (3) functions as a circadian metabolic regulator;[11] and (4) promotes gluconeogenesis and glycogenolysis by activating expression of the genes encoding phosphoenolpyruvate arboxykinase 1, glucose 6-phosphatase, and glycogen phosphorylase, liver form.[12],[13],[14] CREB3L3 deficiencies or gene mutations are associated with profound nonalcoholic steatohepatitis and hyperlipidemia phenotypes in both animal models and human patients.[9],[16],[17] In this study, we revealed that human CREB3L3 gene possesses a conserved CpG island in its 3' end in chromosome 19p13.3 region where additional nine pairs of metabolic genes display the same genomic signature. This finding provides important novel insights into the genomic basis of metabolism and metabolic disease.

Methods

Annotated genomic data were retrieved from the human and mouse genomes (hg19 and mm9). CpG islands located between the 3' ends of two adjacent genes were included in the dataset. CpG islands proximately located to 5' ends of genes were removed from the dataset. We used the University of California Santa Cruz (UCSC) Genome Browser to map the genomic locations and extract the CpG island track (http://genome.ucsc/edu/). The CpG islands were defined as GC content was >50%, the length was >200 bps, and CG: GC ratio was >60%.[5] The ENCODE transcription factor-binding ChIP-seq tracks were annotated at the UCSC Genome Browser. Gene Ontology (GO) was analyzed using Panther Classification System (http://www.pantherdb.org/).

Results

As the non-CpG island promoter has been found related to the tissue-specific expression,[6] we first hypothesized that the ITCI signature might be related to tissue-specific expression and functions as an enhancer at the 3' ends of genes. We, therefore, explored the liver-specific genes such as human CREB3L3 (CAMP-responsive element-binding Protein, hepatic-specific, also called CREBH), which has an ITCI signature and a tissue-enriched expression pattern in the liver. However, the liver-specific genes, such as CRP, C4BPA, Albumin, ADH1A, ADH1B, ADH1C, ADH4, ADH5, ALDOB, and FGA, do not have CpG island in the inter-3' end regions between themselves and their neighbor genes. Interestingly, most of them do not contain CpG islands in their promoter, exonic, and intronic regions, consistent with the previous observation that promoter non-CpG islands might be involved in tissue-specific expression.[6]

The human chromosome 19p13.3 region has a higher-than-average genetic recombination rate and is a gene-rich telomeric region. The mouse homologous region of human 19p13.3 has a much lower recombination rate that suggests the human 19p13.3 could be a hot spot of recombination lost in the mouse genome but present in the human genome.[18] Human chromosome 19 has the highest repeat density and gene density, associated with Alu elements, among all human chromosomes.[19] We then hypothesized that the ITCI signature might be involved in evolutionary chromosome recombination or genomic element transposition, by screening the entire region of human 19p13.3 region. Surprisingly, there are 9 inter-3' end CpG islands between nine pairs of the genes located in the human 19p13.3 region [Table 1] and [Figure 1]. However, only a few additional ITCIs exist outside of the 19p13.3 region in the entire human genome [Table 2].{Figure 1}{Table 1}{Table 2}

CREB3L3 is located in chromosome 19p13.3 of the human genome and chromosome 10qC1 of the mouse genome. The mouse Crebh is about 500 kb upstream of Sirt6, and both the genes are on the minus strand. The human CREB3L3 is about 1 kb upstream of SIRT6. The human CREB3L3 is on the plus strand, and SIRT6 is on the minus strand. While there is no CpG island flanking the mouse Creb3l3 genomic region, a CpG island locates between 3' ends of human CREB3L3 and SIRT6.

To investigate the ITCI signature's potential function, we first screened the transcription factor ChIP-seq signals (ENCODE on UCSC Genome Browser) in these ITCI regions. However, no common transfer function (TF)-binding signals have been found in all 9 ITCI regions [Table 1]. Interestingly, although the ITCI between ZBTB7A and PIAS4 does not contain any TF signals, four out of the other eight ITCIs have strong ZBTB7A-binding signals. The other two transcription regulators, Egr-1 and CTCF, also presented in four out of nine of these ITCI regions. One important consideration is that the ENCODE TF ChIP-seq data were based on multiple cell lines, which could have different transcriptional regulations in human tissues and primary cells.

Alu sequence is the most common short interspersed element (SINE) associated with gene density in the genome. We next screened repeat elements in the UCSC genome browser, and as we predicted, all nine ITCIs have SINEs in their adjacent regions [Table 1].

We next analyzed those 18 ITCI-associated genes by their GO terms using Panther Classification System [Table 3]. Since CIRBP-AS1 is a noncoding RNA, only 17 genes have been analyzed by GO terms. All 17 genes are enriched in binding and catalytic activity terms by GO molecular function, and all are enriched in the metabolic process by GO biological process. Text mining indicates that these ITCI genes are closely related to gastrointestinal system functions and diseases. However, the protein class and pathway analysis showed an evenly distribution of many other GO terms.{Table 3}

Discussion

Our finding of this unique ITCI genomic signature provides speculation of potential roles of CpG island in DNA transposable elements for clustering of functionally related genes during evolution, such as metabolism-associated genes described in the current study. One example is that in the adjacent ± 500 kb region of human CREB3L3, MAP2K2 is next to 5' of CREB3L3 in both mouse and human genomes, while Thop1 is only next to mouse Crebh's 3' end. In the human genome, THOP1 is ~1,000 kb upstream of CREB3L3. Interestingly, TLE6 gene is close to THOP1 in the human genome and is close to Sirt6 in the mouse genome. One hypothesis is that the regions of Sirt6 and Thop1 are flipped by a transposon, while the other genes, including Crebh, Map2k2, Aes, Gna11, Gna15, Ncln, Tle2, and Tle6, remained in more stable locations of the region.

Importantly, the human chromosome 19 is enriched in genes encoding for zinc finger transcription factor proteins,[20] so the high density of transcription factors could explain the enriched GO terms of binding, catalytic activity, and metabolic process. However, the specific CpG island located in the inter-3' end regions of two adjacent genes might be associated with the high recombination rate. The 19p13.3 region is close to telomere in the human genome, but not in the mouse genome, an interesting point that is potentially related to the development and aging from the evolutionary perspective for transcription regulation. Since none of these CpG islands are conserved in the mouse genome, a potential ITCI-mediated human-specific mechanism distinguishes the transcription of the nearby two genes, especially those in between the two genes within 2 kb. The high presence rates of SINEs in the adjacent region of these ITCIs in the human chromosome 19p13.3 region might be evidence for the recombination from the evolutionary perspective. The CpG islands between the two genes with longer distances could be explained by sharing one or multiple common CpG islands in their enhancer regions. However, all of these hypotheses require further functional analysis to validate. (Perspective) Identification of the ITCI genomic signature with the genes encoding major metabolic regulators in specific human chromosome 19p13.3 region shed new light into the genomic basis of cell metabolism. For the future research, it is important to perform genome-wide studies on potential ITCI signatures across all the chromosome regions. Correlation of functional gene groups with potential ITCI signatures will have important implications in understanding the connection between genome and function or phenotype.

Acknowledgment

Portions of this work were supported by a startup fund to ZZ from the Medical College of Wisconsin and Blood Research Institute through the Advancing a Healthier Wisconsin Endowment, a Fellow Scholar Award to ZZ from the American Society of Hematology, and a Career Development Award (19CDA34660043) to ZZ from the American Heart Association, and by National Institutes of Health grants DK090313 and ES017829 (to KZ), and AHA Grants 0635423Z (to KZ).

Financial support and sponsorship

Nil.

Conflicts of interest

Prof. Kezhong Zhang is Editor-in-Chief of Environmental Disease.

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