Transactivation of the parathyroid hormone promoter by specificity proteins and the nuclear factor Y complex

Molecular mechanism for transcriptional regulation of the parathyroid hormone gene by Epiprofin

Epiprofin (Epfn), an Sp/KLF family transcription factor that regulates cell proliferation and determines cell fates, is essential for normal skin, hair follicle, and tooth development. We found that Epfn was expressed in parathyroid glands, and Epfn-knockout mice displayed elevated serum parathyroid hormone (PTH) concentrations, decreased bone volume, and intracranial ectopic calcification. To investigate the role of Epfn in the regulation of PTH expression, parathyroid gland explant and parathyroid cell line culture methods were used. Epfn expression was found to be upregulated in response to an increase in extracellular calcium concentration, whereas PTH expression was downregulated, thus demonstrating an inverse correlation. Forced expression of Epfn inhibited PTH gene expression and PTH promoter reporter activity in parathyroid cells. In addition, with a high extracellular calcium concentration, Epfn silencing in cultured parathyroid glands failed to block PTH gene expression. ChIP-qPCR analysis also revealed Epfn binding in the proximal region of the PTH promoter, which was accelerated in the presence of a high concentration of calcium ions. The results from our in vitro and ex vivo analyses suggest that Epfn is a newly identified negative regulator of PTH transcription by regulating the proximal PTH promoter. Furthermore, the expression of Epfn was significantly reduced in parathyroid adenomas of primary hyperparathyroidism patients. The identification of Epfn as a potential therapeutic target for the control of PTH production in hyperparathyroidism patients opens new avenues for targeted treatment approaches.

Identification of Age-Specific and Common Key Regulatory Mechanisms Governing Eggshell Strength in Chicken Using Random Forests

In today's chicken egg industry, maintaining the strength of eggshells in longer laying cycles is pivotal for improving the persistency of egg laying. Eggshell development and mineralization underlie a complex regulatory interplay of various proteins and signaling cascades involving multiple organ systems. Understanding the regulatory mechanisms influencing this dynamic trait over time is imperative, yet scarce. To investigate the temporal changes in the signaling cascades, we considered eggshell strength at two different time points during the egg production cycle and studied the genotype-phenotype associations by employing the Random Forests algorithm on chicken genotypic data. For the analysis of corresponding genes, we adopted a well established systems biology approach to delineate gene regulatory pathways and master regulators underlying this important trait. Our results indicate that, while some of the master regulators (Slc22a1 and Sox11) and pathways are common at different laying stages of chicken, others (e.g., Scn11a, St8sia2, or the TGF- β pathway) represent age-specific functions. Overall, our results provide: (i) significant insights into age-specific and common molecular mechanisms underlying the regulation of eggshell strength; and (ii) new breeding targets to improve the eggshell quality during the later stages of the chicken production cycle.

An Excess of CYP24A1, Lack of CaSR, and a Novel lncRNA Near the PTH Gene Characterize an Ectopic PTH-Producing Tumor

Thus far, only 23 cases of the ectopic production of parathyroid hormone (PTH) have been reported. We have characterized the genome-wide transcription profile of an ectopic PTH-producing tumor originating from a retroperitoneal histiocytoma. We found that the calcium-sensing receptor (CaSR) was barely expressed in the tumor. Lack of CaSR, a crucial braking apparatus in the presence of both intraparathyroid and, probably, serendipitous PTH expression, might contribute strongly to the establishment and maintenance of the ectopic transcriptional activation of the PTH gene in nonparathyroid cells. Along with candidate drivers with a crucial frameshift mutation or copy number variation at specific chromosomal areas obtained from whole exome sequencing, we identified robust tumor-specific cytochrome P450 family 24 subfamily A member 1 (CYP24A1) overproduction, which was not observed in other non–PTH-expressing retroperitoneal histiocytoma and parathyroid adenoma samples. We then found a 2.5-kb noncoding RNA in the PTH 3′-downstream region that was exclusively present in the parathyroid adenoma and our tumor. Such a co-occurrence might act as another driver of ectopic PTH-producing tumorigenesis; both might release the control of PTH gene expression by shutting down the other branches of the safety system (e.g., CaSR and the vitamin D3–vitamin D receptor axis).

Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding

Background

The combinatorial binding of trans-acting factors (TFs) to the DNA is critical to the spatial and temporal specificity of gene regulation. For certain regulatory regions, more than one regulatory module (set of TFs that bind together) are combined to achieve context-specific gene regulation. However, previous approaches are limited to either pairwise TF co-association analysis or assuming that only one module is used in each regulatory region.

Results

We present a new computational approach that models the modular organization of TF combinatorial binding. Our method learns compact and coherent regulatory modules from in vivo binding data using a topic model. We found that the binding of 115 TFs in K562 cells can be organized into 49 interpretable modules. Furthermore, we found that tens of thousands of regulatory regions use multiple modules, a structure that cannot be observed with previous hard clustering based methods. The modules discovered recapitulate many published protein-protein physical interactions, have consistent functional annotations of chromatin states, and uncover context specific co-binding such as gene proximal binding of NFY + FOS + SP and distal binding of NFY + FOS + USF. For certain TFs, the co-binding partners of direct binding (motif present) differs from those of indirect binding (motif absent); the distinct set of co-binding partners can predict whether the TF binds directly or indirectly with up to 95% accuracy. Joint analysis across two cell types reveals both cell-type-specific and shared regulatory modules.

Conclusions

Our results provide comprehensive cell-type-specific combinatorial binding maps and suggest a modular organization of combinatorial binding.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3434-3) contains supplementary material, which is available to authorized users.

Tissue-specific regulatory regions of the PTH gene localized by novel chromosome 11 rearrangement breakpoints in a parathyroid adenoma

Parathyroid adenomas can contain clonal rearrangements of chromosome 11 that activate the cyclin D1 oncogene through juxtaposition with the PTH gene. Here we describe such a chromosomal rearrangement whose novel features provide clues to locating elusive cis-regulatory elements in the PTH gene and also expand the physical spectrum of pathogenetic breakpoints in the cyclin D1 gene region. Southern blot analyses of the parathyroid adenoma revealed rearrangement in the PTH gene locus. Analysis of rearranged DNA clones that contained the breakpoint, obtained by screening a tumor genomic library, pinpointed the breakpoint in the PTH locus 3.3 kb upstream of the first exon. Accordingly, highly conserved distal elements of the PTH 5' regulatory region were rearranged at the breakpoint approximately 450 kb upstream of the cyclin D1 oncogene, resulting in overexpression of cyclin D1 mRNA. Thus, PTH-cyclin D1 gene rearrangement breakpoints in parathyroid tumors can be located far from those previously recognized. In addition to expanding the molecular spectrum of pathogenetic chromosomal lesions in this disease, features of this specific rearrangement reinforce the existence of one or more novel cis-enhancer/regulatory elements for PTH gene expression and narrow their location to a 1.7-kb DNA segment in the distal PTH promoter.

Involvement of GCMB in the transcriptional regulation of the human parathyroid hormone gene in a parathyroid-derived cell line PT-r: effects of calcium and 1,25(OH)2D3

Expression of the PTH gene is known to be under strict tissue-specific control and is also regulated by extracellular calcium and 1,25(OH)(2)D. However, the precise mode of transcriptional regulation remains to be elucidated, because of the unavailability of appropriate cell lines derived from the parathyroid gland. We tried to identify the transcription factor(s) regulating the human PTH gene transcription using the PT-r cell line. We found that PT-r cells endogenously express PTH and several parathyroid-related genes. Using the cells, we investigated the transcriptional regulation of human PTH gene. We found that GCMB binds to the PTH gene 5'-promoter (-390/-383 bp) and positively regulates its transcription. On the other hand, 1,25(OH)(2)D(3), and, in the presence of the calcium sensing receptor, high extracellular calcium, exerted inhibitory effects on PTH gene expression. These results indicate that GCMB and vitamin D receptor are involved in the positive and negative regulation of PTH gene expression, respectively. Our data also suggest that PT-r cells retain some of the characteristics of parathyroid cells.