A conserved GATA motif in a tissue-specific DNase I hypersensitive site of the cardiac alpha-myosin heavy chain gene

Unveiling the gene regulatory landscape in diseases through the identification of DNase I-hypersensitive sites

DNase I-hypersensitive sites (DHSs) serve key roles in the regulation of gene transcription as markers of cis-regulatory elements (CREs). Recent advances in next-generation sequencing have enabled the genome-wide location and annotation of DHSs in a variety of cells. Numerous studies have confirmed that DHSs are involved in several processes in cell fate decision and development. DHSs have also been indicated in cancer and inherited diseases as driver distal regulatory elements. Here, the definition of DHSs is reviewed, in addition to high-throughput methods of DHS identification. Furthermore, the function of DHSs in gene expression is probed. The roles of DHSs in disease occurrence are also reviewed and discussed. Concomitant advances in the identification of essential roles of DHSs will assist in disclosing the underlying molecular mechanisms, supplementing gene transcription and enlarging the molecular basis of DHS-related bioprocesses, phenotypes, distinct traits and diseases.

Chromatin modifications remodel cardiac gene expression

Signalling and transcriptional control involve precise programmes of gene activation and suppression necessary for cardiovascular physiology. Deep sequencing of DNA-bound transcription factors reveals a remarkable complexity of co-activators or co-repressors that serve to alter chromatin modification and regulate gene expression. The regulated complexes characterized by genome-wide mapping implicate the recruitment and exchange of proteins with specific enzymatic activities that include roles for histone acetylation and methylation in key developmental programmes of the heart. As for transcriptional changes in response to pathological stress, co-regulatory complexes are also differentially utilized to regulate genes in cardiac disease. Members of the histone deacetylase (HDAC) family catalyse the removal of acetyl groups from proteins whose pharmacological inhibition has profound effects preventing heart failure. HDACs interact with a complex co-regulatory network of transcription factors, chromatin-remodelling complexes, and specific histone modifiers to regulate gene expression in the heart. For example, the histone methyltransferase (HMT), enhancer of zeste homolog 2 (Ezh2), is regulated by HDAC inhibition and associated with pathological cardiac hypertrophy. The challenge now is to target the activity of enzymes involved in protein modification to prevent or reverse the expression of genes implicated with cardiac hypertrophy. In this review, we discuss the role of HDACs and HMTs with a focus on chromatin modification and gene function as well as the clinical treatment of heart failure.

Interplay of chromatin modifications and non-coding RNAs in the heart

Precisely regulated patterns of gene expression are dependent on the binding of transcription factors and chromatin-associated determinants referred to as co-activators and co-repressors. These regulatory components function with the core transcriptional machinery to serve in critical activities to alter chromatin modification and regulate gene expression. While we are beginning to understand that cell-type specific patterns of gene expression are necessary to achieve selective cardiovascular developmental programs, we still do not know the molecular machineries that localize these determinants in the heart. With clear implications for the epigenetic control of gene expression signatures, the ENCODE (Encyclopedia of DNA Elements) Project Consortium determined that about 90% of the human genome is transcribed while only 1-2% of transcripts encode proteins. Emerging evidence suggests that non-coding RNA (ncRNA) serves as a signal for decoding chromatin modifications and provides a potential molecular basis for cell type-specific and promoter-specific patterns of gene expression. The discovery of the histone methyltransferase enzyme EZH2 in the regulation of gene expression patterns implicated in cardiac hypertrophy suggests a novel role for chromatin-associated ncRNAs and is the focus of this article.

A myocyte enhancer factor 2 (MEF2) site located in a hypersensitive region of the FGF16 gene locus is required for preferential promoter activity in neonatal cardiac myocytes

Fibroblast growth factor 16 (FGF16) is preferentially expressed in the heart after birth, suggesting its regulation is associated with tissue-specific chromatin remodeling and DNA-protein interactions. Here we have mapped the transcription initiation site of murine FGF16 to approximately 1.1 kilobases (kb) upstream of the translation start codon (ATG). Hybrid reporter genes directed by about 4.7 kb of upstream FGF16 DNA were expressed specifically in transfected neonatal rat cardiac myocytes, as well as in the heart of transgenic mice. A DNaseI hypersensitive site was mapped to a region about 1.2 kb upstream of the transcription initiation site in heart but not kidney tissue, and a nuclease protection assay gave evidence of a cardiac-specific protein-DNA interaction in this region. Deletion analysis indicated that a hybrid gene with 1205 bp but not 1054 bp of upstream DNA directed FGF16 promoter activity in transfected neonatal rat cardiac myocytes. We identified a putative myocyte enhancer factor 2 (MEF2)-binding site at nucleotides -1159/-1148, confirmed by electrophoretic mobility shift assay and MEF2 antibody binding. Mutation of the MEF2 site resulted in a blunting of FGF16 promoter activity in transfected neonatal rat cardiac myocytes. These data suggest that chromatin remodeling and MEF2 binding in the FGF16 promoter contribute to expression in the postnatal heart.

Intergenic transcription and developmental regulation of cardiac myosin heavy chain genes

Cardiac myosin heavy chain (MHC) gene expression undergoes a rapid transition from beta- to alpha-MHC during early rodent neonatal development (0-21 days of age). Thyroid hormone (3,5,3'-triiodothyronine, T(3)) is a major player in this developmental shift; however, the exact mechanism underlying this transition is poorly understood. The goal of this study was to conduct a more thorough analysis of transcriptional activity of the cardiac MHC gene locus during the early postnatal period in the rodent, in order to gain further insight on the regulation of cardiac MHC genes. We analyzed the expression of alpha- and beta-MHC at protein, mRNA, and pre-mRNA levels at birth and 7, 10, 15, and 21 days after birth in euthyroid and hypothyroid rodents. Using novel technology, we also analyzed RNA expression across the cardiac gene locus, and we discovered that the intergenic (IG) region between the two cardiac genes possesses bidirectional transcriptional activity. This IG transcription results in an antisense RNA product as described previously, which is thought to exert an inhibitory effect on beta-MHC gene transcription. On the second half of the IG region, sense transcription occurs, resulting in expression of a sense IG RNA that merges with the alpha-MHC pre-mRNA. This sense IG RNA transcription was detected in the alpha-MHC gene promoter, approximately -1.8 kb relative to the alpha-MHC transcription start site. Both sense and antisense IG RNAs were developmentally regulated and responsive to a hypothyroid state (11, 14). This novel observation provides more complexity to the cooperative regulation of the two genes, suggesting the involvement of epigenetic processes in the regulation of cardiac MHC gene locus.

Activity of the β-myosin heavy chain antisense promoter responds to diabetes and hypothyroidism

Two genes encoding cardiac myosin heavy chain (MHC) isoforms, β and α, are arranged in tandem 4.5 kb apart. We examined pre-mRNA and mature mRNA levels of β and α genes in control, diabetic (streptozotocin), hypothyroid (propylthiouracil), and hyperthyroid rat hearts and analyzed the naturally occurring antisense (AS) β RNA species that starts in the middle of the 4.5-kb intergenic region and extends upstream to the β-gene promoter. The β and α genes are expressed antithetically in control, diabetic, hypothyroid, and hyperthyroid hearts. Expression of AS β-RNA was positively correlated with α-mRNA and negatively correlated with sense β mRNA. These results support the novel idea of common promoter-regulatory elements situated in the intergenic region that likely control transcription of both sense α and AS β genes and that AS β transcription negatively regulates β-MHC gene expression. To test whether an intergenic promoter drives transcription of AS β RNA, a 1340-bp sequence of the intergenic region was inserted into a luciferase plasmid in the 3′-to-5′ AS direction and was injected into rat ventricle. This promoter was activated in control heart and decreased greatly in response to propylthiouracil and streptozotocin and increased in hyperthyroid rats, similar in pattern to the endogenous AS β RNA. When a putative retinoic acid receptor (RAR) site (a known thyroid hormone receptor cofactor) in this promoter was mutated, the reporter activity was almost abolished in control, propylthiouracil, and streptozotocin hearts. We conclude that there is an intergenic promoter that is active in the AS direction and that the putative RAR element is a vital regulatory site.

Reengineering inducible cardiac-specific transgenesis with an attenuated myosin heavy chain promoter

Despite the advantages of reversibly altering cardiac transgene expression, the number of successful studies with inducible cardiac-specific transgene expression remains limited. The utility of the current system is hampered by the large number of lines needed before a nonleaky inducible line is isolated and by the use of a heterologous virus-based minimal promoter in the responder line. We developed an efficient, experimentally flexible system that enables us to reversibly affect both abundant and nonabundant cardiomyocyte proteins. The use of bacterial-codon-based transactivators led to aberrant splicing, whereas other more efficient transactivators, by themselves, caused disease when expressed in the heart. The redesign of the system focused on developing stable transactivator-expressing lines in which expression was driven by the mouse alpha-myosin heavy chain promoter. A minimal responder locus was derived from the same promoter, in which the GATA sites and thyroid responsive elements responsible for robust cardiac specific expression were ablated, leading to an attenuated promoter that could be inducibly controlled. In all cases, whether activated or not, expression mimicked that of the parental promoter. By use of this system, an inducible expression of an abundant contractile protein, the atrial isoform of essential myosin light chain 1, and a powerful biological effector, glycogen synthase kinase-3beta (GSK-3beta), were obtained. Subsequently, we tested the hypothesis that GSK-3beta expression could reverse a preexisting hypertrophy. Inducible expression of GSK-3beta could both attenuate a hypertrophic response and partially reverse a pressure-overload-induced hypertrophy. The system appears to be robust and can be used to temporally control high levels of cardiac-specific transgene expression.

Control of cardiac myosin heavy chain gene expression

The alpha- and beta-myosin genes extend over 51 kb on chromosome 14 in human and 11 in mouse separated by about 4.5 kb of intergenic sequence. They are located in tandem in the order of their expression during development. Transcription of each gene is independently controlled but coordinately regulated. During each embryogenesis, the beta-MHC gene is expressed as part of the cardiac myogenic program under the control of NKX-2.5, MEF-2C, and GATA-4/5/6. After birth, thyroid hormone induces expression of alpha-MHC mRNA and inhibits expression of the beta-MHC gene. While a large number of physiological stimuli are capable of modifying this basic paradigm, thyroid hormone is required for expression of alpha-MHC in ventricular muscle. The positive TRE for T(3)-stimulation of alpha-MHC is an imperfect direct repeat located in the proximal promoter of the gene. The negative TRE for the beta-MHC gene is probably a binding half-site that is located adjacent to the TATA box. Binding of TEF-1 to a strong positive element in the proximal promoter is important in basal expression of beta-MHC gene and in the response to alpha(1)-adrenergic stimulation. The beta-MHC gene also is induced together with several other "fetal" genes during cardiac hypertrophy by a mechanism involving Ca(2+)-mediated activation of calcineurin and NF-AT3. Upon activation, NF-AT3 translocates to the nucleus and interacts with GATA-4 to stimulate beta-MHC expression. Changes in chromatin structure mediated by the association of histone acetylases and deacetylases with transcription factors are essential in regulating cell-specific expression of MHC genes.

Isolation and characterization of the murine cardiotrophin-1 gene: expression and norepinephrine-induced transcriptional activation

Cardiotrophin-1 (CT-1) is a novel cytokine capable of inducing hypertrophy in cardiac myocytes and belongs to the interleukin-6 family that exert their biological effects through gp130. To clarify the involvement and pathophysiological role of CT-1 in myocardial diseases, it is important to characterize the regulation of CT-1 gene expression. In this study, we isolated and characterized the mouse CT-1 gene and studied the expression of CT-1 mRNA under norepinephrine (NE) stimulation. The mouse CT-1 gene constitutes 5.4 kilobases (kb) in length and consists of three exons and two introns. When nucleotide sequences of the coding regions of exons were compared with those of human, exon 1, 2 and 3 share 96%, 84% and 81% homology, respectively. The 2.2 kb of 5; flanking lesion of the mouse CT-1 gene contains a variety of transcription factor binding motif (e.g. CREB, MyoD, NF-IL6, Nkx2.5, GATA). Fluorescent in situ hybridization (FISH) analysis demonstrated that the mouse CT-1 gene was located on chromosome 7F3. The expression of CT-1 mRNA in cardiac myocytes was markedly augmented by NE stimulation, both in vivo and in vitro. Promoter analysis using deletion constructs of the CT-1 gene indicated that the NE responsive element located between -2174/-1540 and this region contained the cAMP responsive element (CRE). Electrophoretic gel mobility shift assays showed enhanced binding activity to the CRE motif in the nuclear extracts from NE-stimulated cardiac myocytes. These studies indicate that CT-1 is abundantly expressed in the heart and that the CRE is a possible cis -acting element of the CT-1 gene under NE-stimulation. These data suggest that the CT-1 gene expression is regulated, at least partially, by transcriptional machinery.

Chromatin remodelling of the cardiac beta-myosin heavy chain gene

To investigate the role of chromatin structure in cardiac gene expression, we used the DNase I and micrococcal nuclease to probe the chromatin structure of the hamster cardiac beta-MyHC gene. Two cardiac-specific DNase I hypersensitive sites (DHS) were identified, one of which was mapped to the -2.3 kb (beta-2.3 kb) region and the other to the proximal promoter region of the beta-MyHC gene. The two sites were readily detectable using nuclei from neonatal hamster heart; however, the proximal promoter site disappeared when adult hamster heart nuclei were used, and the -2.3 kb site decreased in intensity. We were able to demonstrate the gradual disappearance of this proximal promoter DHS by comparing heart nuclei isolated from animals at late-gestation and 1-day-old stages. Furthermore, injecting thyroid hormone caused the disappearance of the proximal promoter DHS in late gestational fetal ventricular nuclei. Digestion of nuclei from various tissues by micrococcal nuclease revealed that the beta-MyHC gene proximal promoter exists in an array of three specifically-positioned nucleosomes only in fetal heart chromatin. The beta-MyHC gene proximal promoter is DNase I hypersensitive within one of the nucleosomal particles. Our data suggest that chromatin structure may participate actively in cardiac gene expression.

Multiple muscle-specific regulatory elements are associated with a DNase I hypersensitive site of the cardiac beta-myosin heavy-chain gene

Using nuclei isolated from neonatal cardiomyocytes, we have mapped the DNase I hypersensitive sites (DHSs) residing within the 5'-upstream regions of the hamster cardiac myosin heavy-chain (MyHC) gene. Two cardiac-specific DHSs within the 5 kb upstream region of the cardiac MyHC gene were identified. One of the DHSs was mapped to the -2.3 kb (beta-2.3 kb) region and the other to the proximal promoter region. We further localized the beta-2.3 kb site to a range of 250 bp. Multiple, conserved, muscle regulatory motifs were found within the beta-2.3 kb site, consisting of three E-boxes, one AP-2 site, one CArG motif, one CT/ACCC box and one myocyte-specific enhancer factor-2 site. This cluster of regulatory elements is strikingly similar to a cluster found in the enhancer of the mouse muscle creatine kinase gene (-1256 to -1050). The specific interaction of the motifs within the beta-2.3 kb site and the cardiac nuclear proteins was demonstrated using gel mobility-shift assays and footprinting analysis. In addition, transfection analysis revealed a significant increase in chloramphenicol acetyltransferase activity when the beta-2.3 kb site was linked to a heterologous promoter. These results suggest that previously undefined regulatory elements of the beta-MyHC gene may be associated with the beta-2.3 kb site.