Proximal Regulatory Region Research Articles

5-hydroxymethylcytosine represses the activity of enhancers in embryonic stem cells: a new epigenetic signature for gene regulation.

BackgroundRecent mapping of 5-hydroxymethylcytosine (5hmC) provides a genome-wide view of the distribution of this important chromatin mark. However, the role of 5hmC in specific regulatory regions is not clear, especially at enhancers.ResultsWe found a group of distal transcription factor binding sites highly enriched for 5-hdroxymethylcytosine (5hmC), but lacking any known activating histone marks and being depleted for nascent transcripts, suggesting a repressive role for 5hmC in mouse embryonic stem cells (mESCs). 5-formylcytosine (5fC), which is known to mark poised enhancers where H3K4me1 is enriched, is also observed at these sites. Furthermore, the 5hmC levels were inversely correlated with RNA polymerase II (PolII) occupancy in mESCs as well as in fully differentiated adipocytes. Interestingly, activating H3K4me1/2 histone marks were enriched at these sites when the associated genes become activated following lineage specification. These putative enhancers were shown to be functional in embryonic stem cells when unmethylated. Together, these data suggest that 5hmC suppresses the activity of this group of enhancers, which we termed “silenced enhancers”.ConclusionsOur findings indicate that 5hmC has a repressive role at specific proximal and distal regulatory regions in mESCs, and suggest that 5hmC is a new epigenetic mark for silenced enhancers.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-670) contains supplementary material, which is available to authorized users.

92 : STAT5 activates the C-Myc proximal promoter: Elevated STAT5 or C-Myc expression relative to STAT1 is linked with reduced survival of melanoma patients given IFNγ therapy

Recently, a role for IFN γ in the genesis of melanoma was reported. Here, we define the mechanism whereby IFN γ becomes a growth stimulator of melanoma cells. In this study, IFN γ stimulated STAT5 to activate the expression of c- myc , an oncogene linked with reduced melanoma patient survival. In a preliminary retrospective study of 27 stage III melanoma patients who received IFN α 2 therapy, STAT5A and c- myc expression levels in metastatic lymph node biopsies were highly correlated (Pearson’s r = 0.914; P myc or STAT5 relative to STAT1 were prognostic markers indicating reduced patient survival. In vitro studies showed that STAT5 activated the c- myc proximal promoter via a functional STAT5A binding site, conferring significant inducibility by IFN γ or EGF (but not IFN α ) in luciferase reporter assays of melanoma cells overexpressing STAT5A. IFN γ caused markedly different responses in wild-type A375 cells compared with A375-STAT5A cells, supporting a key role for STAT5A in IFN γ -mediated regulation of c- myc expression in melanoma. ChIP assays confirmed direct STAT5A binding during IFN γ -mediated activation of the c- myc proximal SBE regulatory region. 5′ RACE and Q-PCR showed that increased levels of c- myc in A375-STAT5A cells induced by IFN γ were associated with a shift in the initiation of transcription near to or at the proximal STAT5 binding element. These results indicate that overexpression of STAT5 in cancer cells is responsible for growth-stimulation by IFN γ .

Genome-Wide Variation of Cytosine Modifications Between European and African Populations and the Implications for Complex Traits

Elucidating cytosine modification differences between human populations can enhance our understanding of ethnic specificity in complex traits. In this study, cytosine modification levels in 133 HapMap lymphoblastoid cell lines derived from individuals of European or African ancestry were profiled using the Illumina HumanMethylation450 BeadChip. Approximately 13% of the analyzed CpG sites showed differential modification between the two populations at a false discovery rate of 1%. The CpG sites with greater modification levels in European descent were enriched in the proximal regulatory regions, while those greater in African descent were biased toward gene bodies. More than half of the detected population-specific cytosine modifications could be explained primarily by local genetic variation. In addition, a substantial proportion of local modification quantitative trait loci exhibited population-specific effects, suggesting that genetic epistasis and/or genotype × environment interactions could be common. Distinct correlations were observed between gene expression levels and cytosine modifications in proximal regions and gene bodies, suggesting epigenetic regulation of interindividual expression variation. Furthermore, quantitative trait loci associated with population-specific modifications can be colocalized with expression quantitative trait loci and single nucleotide polymorphisms previously identified for complex traits with known racial disparities. Our findings revealed abundant population-specific cytosine modifications and the underlying genetic basis, as well as the relatively independent contribution of genetic and epigenetic variations to population differences in gene expression.

Priming of regulatory DNA elements activates inflammatory cytokine genes synergistically with TLR signaling to increase transcription (P1230)

Abstract Synergistic activation of inflammatory cytokine genes by IFN-γ and Toll-like receptor signaling is important for innate immunity and inflammatory disease pathogenesis. Enhancement of Toll-like receptor signaling events, a previously proposed mechanism, is insufficient to explain massive activation of cytokine production in human macrophages. We found that IFN-γ induced sustained occupancy of STAT1 and IRF1 at proximal and distal regulatory regions of the TNF, IL6 and IL12B gene loci in human macrophages, which was associated with increased histone acetylation, an indicator of an active histone state. This opening of chromatin greatly facilitated further recruitment of other transcription factors and the assembly of the RNA polymerase II complex upon Toll-like receptor activation, which resulted in increased and prolonged transcription of these inflammatory cytokines. Genome-wide analysis revealed pervasive priming of regulatory elements by IFN-γ and linked coordinate priming of promoters and enhancers with synergistic induction of transcription. Furthermore, IFN-γ-mediated priming conferred sensitivity of cytokine gene transcription to inhibitors of Jak kinases or chromatin regulators of the bromo and extra terminal protein family. Our results provide a synergy mechanism whereby IFN-γ creates a primed chromatin environment to augment Toll-like receptor-induced gene transcription, and suggest therapeutic approaches that selectively target priming mechanisms.

Transcriptional Plasticity in the Brain following Metabolic Challenge

Assessment of gene expression is a good place to start a quest for mechanisms of neural plasticity (McClung and Nestler, 2008). Of course, these mRNA and subsequent protein-level changes must eventually lead to synaptic alterations in order to have a role in neural adaptation. Nonetheless, the efficiency of large-scale transcription studies makes it a powerful initial approach. Although this strategy has been used extensively within the field of drug addiction (Robison and Nestler, 2011), few studies have systematically evaluated brain transcriptional adaptation in response to metabolic challenge. We recently completed a microarray analysis to identify changes in gene expression in response to a brief (5 days) and moderate (<10% weight loss) reduction in food intake (Guarnieri et al, 2012). Analysis was conducted on RNA from four brain regions: ventral tegmental area, prefrontal cortex, hypothalamus and nucleus accumbens. Stress responsive genes were prominent in the list of genes that change after restriction, and corticosterone was shown to be necessary and sufficient for many of these changes. There were some surprises in these results that deserve emphasis: (1) the gene changes occurred rapidly (within the first 24 h of restriction) before any weight loss was apparent and (2) the expression changes detected were not restricted to one region, and usually were seen in 2–4 of the regions surveyed. This fast and universal response was not something that was anticipated, but is reasonable if a systemic factor such as corticosterone is the key signal. Finally, the changes seen were implicated in increased food motivation that occurred after restriction. Previously published work supports the role of stress response in mediating effects of caloric restriction. Work from the Bale lab has shown that a longer (21 days) caloric restriction leads to stress pathway activation, including corticosterone as well as corticotropin-releasing factor (CRF) in the bed nucleus of the stria terminalis (Pankevich et al, 2010). Restriction increased stress responses as well as binge eating. Interestingly, the changes in CRF did not reverse upon re-feeding, and subsequent analysis showed that the CRF regulatory sequences also maintained altered methylation patterns. Moreover, withdrawal from high-fat food produced similar adaptions in gene expression and chromatin state. Other work with animals exposed to high-fat diet also supports a role for chromatin changes and transcriptional adaptation within dopamine circuits. Reyes and colleagues (Vucetic et al, 2011) have shown specific gene changes in the nucleus accumbens following long-term high-fat-diet exposure. Specifically, decreases in mu-opioid receptor expression correlated with increased methylation and MECP2 binding in the proximal regulatory regions. Moreover, H3K9 methylation was increased and acetylation was reduced, which is consistent with an inactive chromatin state. In sum, changes in metabolic state can have specific and significant effects on the transcription profile of the brain. These changes are mediated by alterations in chromatin and, most importantly, are likely to have a role in behavioral adaptation to different food environments. Defining these molecular responses will help us to understand how intake and weight control is influenced by previous metabolic experience. These pathways are targets for potential therapeutics that can reverse or otherwise modulate this plasticity and help with weight loss. Moreover, as with drugs of abuse, stress is a common cause for loss of control over eating. The above work suggests that the brain might interpret stress hormones as a state of hunger, and should inspire stress response attenuation as a potential therapeutic strategy for obesity.

Multiple Histone Methyl and Acetyltransferase Complex Components Bind the HLA-DRA Gene

Major histocompatibility complex class II (MHC-II) genes are fundamental components that contribute to adaptive immune responses. While characterization of the chromatin features at the core promoter region of these genes has been studied, the scope of histone modifications and the modifying factors responsible for activation of these genes are less well defined. Using the MHC-II gene HLA-DRA as a model, the extent and distribution of major histone modifications associated with active expression were defined in interferon-γ induced epithelial cells, B cells, and B-cell mutants for MHC-II expression. With active transcription, nucleosome density around the proximal regulatory region was diminished and histone acetylation and methylation modifications were distributed throughout the gene in distinct patterns that were dependent on the modification examined. Irrespective of the location, the majority of these modifications were dependent on the binding of either the X-box binding factor RFX or the class II transactivator (CIITA) to the proximal regulatory region. Importantly, once established, the modifications were stable through multiple cell divisions after the activating stimulus was removed, suggesting that activation of this system resulted in an epigenetic state. A dual crosslinking chromatin immunoprecipitation method was used to detect histone modifying protein components that interacted across the gene. Components of the MLL methyltransferase and GCN5 acetyltransferase complexes were identified. Some MLL complex components were found to be CIITA independent, including MLL1, ASH2L and RbBP5. Likewise, GCN5 containing acetyltransferase complex components belonging to the ATAC and STAGA complexes were also identified. These results suggest that multiple complexes are either used or are assembled as the gene is activated for expression. Together the results define and illustrate a complex network of histone modifying proteins and multisubunit complexes participating in MHC-II transcription.

Biphasic wnt8a expression is achieved through interactions of multiple regulatory inputs

Vertebrate axis development depends upon wnt8a transcription in a dynamic pool of mesoderm progenitors at the posterior pole of the gastrulating embryo. The transcriptional mechanisms controlling wnt8a expression are not understood, but previous studies identified two phases of wnt8a expression in zebrafish: Nodal-dependent activation during early gastrulation (phase I) and No tail (Ntl)-dependent regulation from mid gastrula stages (phase II). We identified two upstream cis-regulatory regions, proximal and distal, each of which possesses a promoter. The proximal regulatory region contains a margin-specific enhancer that is required for both the Nodal and Ntl responses. Phase I expression requires Nodal activation of the margin enhancer in combination with the transcription factor Zbtb4 and the distal regulatory region. Phase II expression requires Ntl regulation of the margin enhancer in the context of the proximal regulatory region. An additional mechanism is required to ensure the transition from phase I to phase II regulation. Analysis of stickleback wnt8a suggests this mechanism of regulation may be conserved. The seemingly simple wnt8a expression pattern reflects complex interactions of multiple regulatory inputs.

Effects of human papillomavirus (HPV) type 16 oncoproteins on the expression of involucrin in human keratinocytes

BackgroundThe human papillomavirus (HPV) life cycle is closely linked to keratinocyte differentiation. Oncogenic HPV infection has been shown to hamper the normal differentiation of keratinocytes; however, the underlying mechanisms responsible for this phenomenon are yet to be clarified. Here, we aimed to study the effects of HPV16 E6 and E7 oncogenes on the expression of involucrin (IVL), an established marker of keratinocyte differentiation, in human foreskin keratinocyte (HFK) cells.ResultsThe differentiation of HFK cells by serum and high calcium significantly increased both the mRNA and the protein levels of IVL. The E6 and E7 oncoproteins of HPV16 together caused strong down-regulation of IVL mRNA and protein both in proliferating and in differentiating HFK cells. To study the effects of HPV oncogenes on the IVL promoter, we made transient transfection assays and luciferase tests and found that HPV 16 E6 but not E7 repressed IVL promoter activity in proliferating HFK cells. The inhibitory effect of HPV 16 E6 on the human IVL promoter could be localised to the proximal regulatory region (PRR) of the gene.ConclusionsThese results suggest that the down-regulation of IVL promoter activity by HPV 16 E6 significantly contribute to the inhibition of endogenous IVL expression by the HPV 16 oncoproteins. In contrast, the down-regulation of endogenous IVL expression by HPV16 E7 is probably not caused by a direct and specific effect of E7 on the IVL promoter.

ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites

Motivation: The prediction and annotation of the genomic regions involved in gene expression has been largely explored. Most of the energy has been devoted to the development of approaches that detect transcription start sites, leaving the identification of regulatory regions and their functional transcription factor binding sites (TFBSs) largely unexplored and with important quantitative and qualitative methodological gaps.Results: We have developed ReLA (for REgulatory region Local Alignment tool), a unique tool optimized with the Smith–Waterman algorithm that allows local searches of conserved TFBS clusters and the detection of regulatory regions proximal to genes and enhancer regions. ReLA's performance shows specificities of 81 and 50% when tested on experimentally validated proximal regulatory regions and enhancers, respectively.Availability: The source code of ReLA's is freely available and can be remotely used through our web server under http://www.bsc.es/cg/rela.Contact: david.torrents@bsc.esSupplementary information: Supplementary data are available at Bioinformatics online.

Cohesin Regulates MHC Class II Genes through Interactions with MHC Class II Insulators

Cohesin is a multiprotein, ringed complex that is most well-known for its role in stabilizing the association of sister chromatids between S phase and M. More recently, cohesin was found to be associated with transcriptional insulators, elements that are associated with the organization of chromatin into regulatory domains. The human MHC class II (MHC-II) locus contains 10 intergenic elements, termed MHC-II insulators, which bind the transcriptional insulator protein CCCTC-binding factor. MHC-II insulators interact with each other, forming a base architecture of discrete loops and potential regulatory domains. When MHC-II genes are expressed, their proximal promoter regulatory regions reorganize to the foci established by the interacting MHC-II insulators. MHC-II insulators also bind cohesin, but the functional role of cohesin in regulating this system is not known. In this article, we show that the binding of cohesin to MHC-II insulators occurred irrespective of MHC-II expression but was required for optimal expression of the HLA-DR and HLA-DQ genes. In a DNA-dependent manner, cohesin subunits interacted with CCCTC-binding factor and the MHC-II-specific transcription factors regulatory factor X and CIITA. Intriguingly, cohesin subunits were important for DNA looping interactions between the HLA-DRA promoter region and a 5' MHC-II insulator but were not required for interactions between the MHC-II insulators themselves. This latter observation introduces cohesin as a regulator of MHC-II expression by initiating or stabilizing MHC-II promoter regulatory element interactions with the MHC-II insulator elements, events that are required for maximal MHC-II transcription.

P63 regulates Satb1 to control tissue-specific chromatin remodeling during development of the epidermis

During development, multipotent progenitor cells establish tissue-specific programs of gene expression. In this paper, we show that p63 transcription factor, a master regulator of epidermal morphogenesis, executes its function in part by directly regulating expression of the genome organizer Satb1 in progenitor cells. p63 binds to a proximal regulatory region of the Satb1 gene, and p63 ablation results in marked reduction in the Satb1 expression levels in the epidermis. Satb1(-/-) mice show impaired epidermal morphology. In Satb1-null epidermis, chromatin architecture of the epidermal differentiation complex locus containing genes associated with epidermal differentiation is altered primarily at its central domain, where Satb1 binding was confirmed by chromatin immunoprecipitation-on-chip analysis. Furthermore, genes within this domain fail to be properly activated upon terminal differentiation. Satb1 expression in p63(+/-) skin explants treated with p63 small interfering ribonucleic acid partially restored the epidermal phenotype of p63-deficient mice. These data provide a novel mechanism by which Satb1, a direct downstream target of p63, contributes in epidermal morphogenesis via establishing tissue-specific chromatin organization and gene expression in epidermal progenitor cells.

Strategies to identify genes for complex disorders

Bipolar disorder, also termed manic-depression, is a genetically based neuropsychiatric disorder with heritability estimates of 80%. Over 25 genome-wide linkage studies have been completed for bipolar disorder and results are not all randomly distributed but appear to converge on several chromosomal regions. Recently, several genome-wide association studies have been reported using thousands of cases and controls and meta-analyses of combined studies have implicated at least two common alleles predisposing to illness. Taken together, genome-wide linkage and genome-wide association results indicate that both rare and common variants likely underlie the genetic architecture of bipolar disorder. Larger genome-wide association studies using tens of thousands of cases and controls will be required to map additional common loci that presumably have smaller effect sizes. Although genome-wide sequencing using thousands of cases and controls (at least 2000 cases and 2000 controls) will likely be needed to map the full range of rare variants predisposing to bipolar disorder, it is not currently technically or financially feasible for most groups using 'third generation' technology. Advances in sequencing and annotation methods are anticipated, however, and 'fourth generation' methods should make large-scale high throughput sequencing feasible for most investigators. In the meantime, however, high throughput sequencing can be used to scan tens-to-hundreds of genes mapping under linkage peaks or around association signals. We review the linkage evidence implicating the chromosome 16p region in bipolar disorder. Although linkage regions are by nature relatively large (approximately 10-20 Mb) for complex disorders it is currently possible to sequence all coding and proximal regulatory regions. Systematic re-sequencing under linkage peaks could be a valuable strategy for mapping some rare variants underlying bipolar disorder. Advantages of this approach, compared to large case-control sequencing samples, include smaller sample sizes, enrichment of certain alleles in the study group, and the ability to check for co-segregation.

Enhancers regulate progression of development in mammalian cells

During development and differentiation of an organism, accurate gene regulation is central for cells to maintain and balance their differentiation processes. Transcriptional interactions between cis-acting DNA elements such as promoters and enhancers are the basis for precise and balanced transcriptional regulation. We identified modules of combinations of binding sites in proximal and distal regulatory regions upstream of all transcription start sites (TSSs) in silico and applied these modules to gene expression time-series of mouse embryonic development and differentiation of human stem cells. In addition to tissue-specific regulation controlled by combinations of transcription factors (TFs) binding at promoters, we observed that in particular the combination of TFs binding at promoters together with TFs binding at the respective enhancers regulate highly specifically temporal progression during development: whereas 40% of TFs were specific for time intervals, 79% of TF pairs and even 97% of promoter–enhancer modules showed specificity for single time intervals of the human stem cells. Predominantly SP1 and E2F contributed to temporal specificity at promoters and the forkhead (FOX) family of TFs at enhancer regions. Altogether, we characterized three classes of TFs: with binding sites being enriched at the TSS (like SP1), depleted at the TSS (like FOX), and rather uniformly distributed.

ABCA1 impacts athero-thrombotic risk and 10-year survival in a contemporary secondary prevention setting

ObjectivesWe prospectively investigated the effects of ATP-binding cassette protein-1 (ABCA1) variants on long-term clinical outcome in patients with coronary artery disease (CAD). BackgroundABCA1 is implicated in the etiology of atherothrombosis and may offer a target to reduce cardiovascular risk. However, the impact of ABCA1 on recurrent cardiovascular disease in a secondary prevention setting is as of yet unknown. MethodsWe studied cause-specific 10-year mortality and quantitative coronary angiography data from the Regression GRowth Evaluation Statin Study (REGRESS), comprising 884 male CAD patients genotyped for promoter variants encompassing a proximal regulatory region (rs2422493, rs1800976, rs2740483 and rs1800977). Kaplan–Meier, proportional hazards and haplotype analyses were used to ascertain single-variant and multi-marker effects on absolute risk and extent of CAD. ResultsProtection from 10-year vascular death could be attributed to the rs2422493 genotype (available in 639 patients) T allele with absolute risk decreasing stepwise from 12.2% to 8.6% to 4.7% per each added allele copy, HR 0.64, p=0.03 and HR 0.53, p=0.04 in the TGCC haplotype context. The TGCC (p=0.04) and TCCT (p=0.003) haplotypes exhibited less extensive CAD. ConclusionsOn a background of contemporary secondary prevention, variation in the ABCA1 promoter influences 10-year risk of vascular death and angiographic extent of CAD in men. These insights contribute to identification of patients sharing a specific prognosis, understanding of its etiological basis and development of strategies of risk reduction in CAD.

Role of serum response factor in the pathogenesis of disease

Serum response factor (SRF) is a ubiquitously expressed transcription factor that binds to a DNA cis element known as the CArG box, which is found in the proximal regulatory regions of over 200 experimentally validated target genes. Genetic deletion of SRF is incompatible with life in a variety of animals from different phyla. In mice, loss of SRF throughout the early embryo results in gastrulation defects precluding analyses in individual organ systems. Genetic inactivation studies using conditional or inducible promoters directing the expression of the bacteriophage Cre recombinase have shown a vital role for SRF in such cellular processes as contractility, cell migration, synaptic activity, inflammation, and cell survival. A growing number of experimental and human diseases are associated with changes in SRF expression, suggesting that SRF has a role in the pathogenesis of disease. This review summarizes data from experimental model systems and human pathology where SRF expression is either deliberately or naturally altered.

Characterization of the 11S Globulin Gene Family in the Castor PlantRicinus communisL.

The 11S globulin (legumin) gene family has been characterized in the castor plant Ricinus communis L. Phylogenetic analysis reveals the presence of two diverged subfamilies (RcLEG1 and RcLEG2) comprising a total of nine genes and two putative pseudogenes. The expression of castor legumin genes has been studied, indicating that it is seed specific and developmentally regulated, with a maximum at the stage when cellular endosperm reaches its full expansion (around 40-45 DAP). However, conspicuous differences are appreciated in the expression timing of individual genes. A characterization of the 5'-proximal regulatory regions for two genes, RcLEG1-1 and RcLEG2-1, representative of the two legumin subfamilies, has also been performed by fusion to the GUS reporter gene. The results obtained from heterologous expression in tobacco and transient expression in castor, indicating seed-specific regulation, support the possible utility of these promoters for biotechnological purposes.

Myocardin-dependent Activation of the CArG Box-rich Smooth Muscle γ-Actin Gene

Serum response factor (SRF) is a ubiquitously expressed transcription factor that binds a 10-bp element known as the CArG box, located in the proximal regulatory region of hundreds of target genes. SRF activates target genes in a cell- and context-dependent manner by assembling unique combinations of cofactors over CArG elements. One particularly strong SRF cofactor, myocardin (MYOCD), acts as a component of a molecular switch for smooth muscle cell (SMC) differentiation by activating cytoskeletal and contractile genes harboring SRF-binding CArG elements. Here we report that the human ACTG2 promoter, containing four conserved CArG elements, displays SMC-specific basal activity and is highly induced in the presence of MYOCD. Stable transfection of a non-SMC cell type with Myocd elicits elevations in endogenous Actg2 mRNA. Gel shift and luciferase assays reveal a strong bias for MYOCD-dependent transactivation through CArG2 of the human ACTG2 promoter. Substitution of CArG2 with other CArGs, including a consensus CArG element, fails to reconstitute full MYOCD-dependent ACTG2 promoter stimulation. Mutation of an adjacent binding site for NKX3.1 reduces MYOCD-dependent transactivation of the ACTG2 promoter. Co-immunoprecipitation, glutathione S-transferase pulldown, and luciferase assays show a physical and functional association between MYOCD and NKX3.1; no such functional relationship is evident with the related NKX2.5 transcription factor despite its interaction with MYOCD. These results demonstrate the ability of MYOCD to discriminate among several juxtaposed CArG elements, presumably through its novel partnership with NKX3.1, to optimally transactivate the human ACTG2 promoter.

Lactogenic Hormonal Induction of Long Distance Interactions between β-Casein Gene Regulatory Elements

Lactogenic hormone regulation of beta-casein gene expression in mammary epithelial cells provides an excellent model in which to study the mechanisms by which steroid and peptide hormone signaling control gene expression. Prolactin- and glucocorticoid-mediated induction of beta-casein gene expression involves two principal regulatory regions, a proximal promoter and a distal enhancer located in the mouse approximately -6 kb upstream of the transcription start site. Using a chromosome conformation capture assay and quantitative real time PCR, we demonstrate that a chromatin loop is created in conjunction with the recruitment of specific transcription factors and p300 in HC11 mammary epithelial cells. Stimulation with both prolactin and hydrocortisone is required for the induction of these long range interactions between the promoter and enhancer, and no DNA looping was observed in nontreated cells or cells treated with each of the hormones separately. The lactogenic hormone-induced interaction between the proximal promoter and distal enhancer was confirmed in hormone-treated primary three-dimensional mammary acini cultures. In addition, the developmental regulation of DNA looping between the beta-casein regulatory regions was observed in lactating but not in virgin mouse mammary glands. Furthermore, beta-casein mRNA induction and long range interactions between these regulatory regions were inhibited in a progestin-dependent manner following stimulation with prolactin and hydrocortisone in HC11 cells expressing human PR-B. Collectively, these data suggest that the communication between these regulatory regions with intervening DNA looping is a crucial step required to both create and maintain active chromatin domains and regulate transcription.

The human CD6 gene is transcriptionally regulated by RUNX and Ets transcription factors in T cells

CD6 is a lymphocyte surface receptor involved in lymphocyte activation and differentiation processes that is constitutively expressed on developing and mature T cells and on the B1a cells. To define the molecular basis for the tissue-specific expression of CD6 we have identified the transcription factors that control the activity of the proximal regulatory region of the human CD6 gene. The TATA-less CD6 promoter contains multiple transcriptional start sites, and its preferential activity in human T lymphocytes is dependent on RUNX- and Ets-binding sites located within a highly conserved region. RUNX and Ets-1 factors transactivated the CD6 promoter through recognition of the −215 and −230 binding sites, respectively. Chromatin immunoprecipitation assays revealed that RUNX1 constitutively occupies the CD6 promoter in vivo, and knockdown experiments demonstrated that the steady-state level of CD6 mRNA is dependent on the expression of RUNX1, RUNX3 and Ets-1 transcription factors. Therefore, RUNX1/3 and Ets1 control the expression of CD6 in human T lymphocytes, thus expanding the range of T-cell specific and developmentally regulated lymphocyte gene targets involved in T-cell activation and differentiation.

The pathogen receptor liver and lymph node sinusoidal endotelial cell C‐type lectin is expressed in human Kupffer cells and regulated by PU.1†

Human LSECtin (liver and lymph node sinusoidal endothelial cell C‐type lectin, CLEC4G) is a C‐type lectin encoded within the L‐SIGN/DC‐SIGN/CD23 gene cluster. LSECtin acts as a pathogen attachment factor for Ebolavirus and the SARS coronavirus, and its expression can be induced by interleukin‐4 on monocytes and macrophages. Although reported as a liver and lymph node sinusoidal endothelial cell‐specific molecule, LSECtin could be detected in the MUTZ‐3 dendritic‐like cell line at the messenger RNA (mRNA) and protein level, and immunohistochemistry analysis on human liver revealed its presence in Kupffer cells coexpressing the myeloid marker CD68. The expression of LSECtin in myeloid cells was further corroborated through the analysis of the proximal regulatory region of the human LSECtin gene, whose activity was maximal in LSECtin+ myeloid cells, and which contains a highly conserved PU.1‐binding site. PU.1 transactivated the LSECtin regulatory region in collaboration with hematopoietic‐restricted transcription factors (Myb, RUNX3), and was found to bind constitutively to the LSECtin proximal promoter. Moreover, knockdown of PU.1 through the use of small interfering RNA led to a decrease in LSECtin mRNA levels in THP‐1 and monocyte‐derived dendritic cells, thus confirming the involvement of PU.1 in the myeloid expression of the lectin. Conclusion: LSECtin is expressed by liver myeloid cells, and its expression is dependent on the PU.1 transcription factor. (Hepatology 2009;49:287–296.)