Proximal Promoter Research Articles

Mapping Chromatin Occupancy of Ppp1r1b-lncRNA Genome-Wide Using Chromatin Isolation by RNA Purification (ChIRP)-seq.

Long non-coding RNA (lncRNA) mediated transcriptional regulation is increasingly recognized as an important gene regulatory mechanism during development and disease. LncRNAs are emerging as critical regulators of chromatin state; yet the nature and the extent of their interactions with chromatin remain to be fully revealed. We have previously identified Ppp1r1b-lncRNA as an essential epigenetic regulator of myogenic differentiation in cardiac and skeletal myocytes in mice and humans. We further demonstrated that Ppp1r1b-lncRNA function is mediated by the interaction with the chromatin-modifying complex polycomb repressive complex 2 (PRC2) at the promoter of myogenic differentiation transcription factors, TBX5 and MyoD1. Herein, we employed unbiased chromatin isolation by RNA purification (ChIRP) and high throughput sequencing to map the repertoire of Ppp1r1b-lncRNA chromatin occupancy genome-wide in the mouse muscle myoblast cell line. We uncovered a total of 99732 true peaks corresponding to Ppp1r1b-lncRNA binding sites at high confidence (p-value < 1E-5) and enrichment score ≥ 10). The Ppp1r1b-lncRNA-binding sites averaged 558 bp in length and were distributed widely within the coding and non-coding regions of the genome. Approximately 46% of these true peaks were mapped to gene elements, of which 1180 were mapped to experimentally validated promoter sequences. Importantly, the promoter-mapped binding sites were enriched in myogenic transcription factors and heart development while exhibiting focal interactions with known motifs of proximal promoters and transcription initiation by RNA Pol-II, including TATA-box, transcription initiator motif, CCAAT-box, and GC-box, supporting Ppp1r1b-lncRNA role in transcription initiation of myogenic regulators. Remarkably, nearly 40% of Ppp1r1b-lncRNA-binding sites mapped to gene introns were enriched with the Homeobox family of transcription factors and exhibited TA-rich motif sequences, suggesting potential motif-specific Ppp1r1b-lncRNA-bound introns. Lastly, more than 136521 enhancer sequences were detected in Ppp1r1b-lncRNA-occupancy sites at high confidence. Among these enhancers, 3390 (12%) exhibited cell type/tissue-specific enrichment in fetal heart and muscles. Together, our findings provide further insights into the genome-wide Ppp1r1b-lncRNA: Chromatin interactome that may dictate its function in myogenic differentiation and potentially other cellular and biological processes.

Abstract A155: The TGF-β/BMP signaling cascades induce opposing fates in breast cancer and medulloblastoma through chromatin and cell cycle modulation

Abstract The transforming growth factor β (TGF-β) superfamily comprises more than 30 structurally-related proteins, including TGF-β1, TGF-β2, TGF-β3 and bone morphogenesis proteins (BMPs). TGF-β/BMP ligands bind to their respective kinase receptors culminating paradoxically in either tumor-promoting or suppressing outcomes. The former fate is attributed mainly to the induction of the epithelial-mesenchymal transition and microenvironmental remodeling by TGF-β/BMP, whereas the latter outcome is a consequence of various antiproliferative mechanisms. To gain a broader perspective, we studied the fates of different cancer models, including breast cancer and medulloblastoma, either challenged with TGF-β/BMP ligands or depleted of essential transcription factors. In 3D cultures, TGF-β stimulation enhances the genome-wide chromatin accessibility of normal-like and transformed breast epithelial models. Concomitantly, we observed a dramatic increase in accessible regions mapped to transcription start sites and, to less extent, at annotated enhancers. The corresponding transcriptome-wide analyses indicated positive modulation of DNA replication and repair associated with resistance to cyclin-dependent kinase inhibition in breast cancer organoids. Nevertheless, such TGF-β-induced remodeling was partly dependent on the activity of the transcription factor SOX4. Further implementation of whole transcriptome spatial profiling in medulloblastoma PDX tissues identified several cell cycle-related pathways and chromatin remodeling terms that negatively associate with activated BMP signaling. In this context, the stem cell capacity of medulloblastoma spheroids was significantly inhibited by BMP stimulation in vitro. Moreover, we uncovered a regulatory network that maintains the transcriptional activation of BMP receptor type I (ACVR1) through the LHX2 transcription factor that maintains an active chromatin landscape at the ACVR1 proximal promoter. The depletion of LHX2 resulted in reduced tumor formation capacity of medulloblastoma in vivo. Taken together, our extensive studies across multiple model systems suggest that the TGF-β superfamily remodels the chromatin state to alter the cell cycle progression and, subsequently, affect cancer stemness and cell fate. Citation Format: Mohamad Moustafa Ali, Yae Ohata, Carl-Henrik Heldin, Aristidis Moustakas. The TGF-β/BMP signaling cascades induce opposing fates in breast cancer and medulloblastoma through chromatin and cell cycle modulation [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A155.

Transcriptional Targeting of Dendritic Cells Using an Optimized Human Fascin1 Gene Promoter

Deeper knowledge about the role of the tumor microenvironment (TME) in cancer development and progression has resulted in new strategies such as gene-based cancer immunotherapy. Whereas some approaches focus on the expression of tumoricidal genes within the TME, DNA-based vaccines are intended to be expressed in antigen-presenting cells (e.g., dendritic cells, DCs) in secondary lymphoid organs, which in turn induce anti-tumor T cell responses. Besides effective delivery systems and the requirement of appropriate adjuvants, DNA vaccines themselves need to be optimized regarding efficacy and selectivity. In this work, the concept of DC-focused transcriptional targeting was tested by applying a plasmid encoding for the luciferase reporter gene under the control of a derivative of the human fascin1 gene promoter (pFscnLuc), comprising the proximal core promoter fused to the normally more distantly located DC enhancer region. DC-focused activity of this reporter construct was confirmed in cell culture in comparison to a standard reporter vector encoding for luciferase under the control of the strong ubiquitously active cytomegalovirus promoter and enhancer (pCMVLuc). Both plasmids were also compared upon intravenous administration in mice. The organ- and cell type-specific expression profile of pFscnLuc versus pCMVLuc demonstrated favorable activity especially in the spleen as a central immune organ and within the spleen in DCs.

Suppression of Super-Enhancer-Driven TAL1 Expression By KLF4 in T-Cell Acute Lymphoblastic Leukemia

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy characterized by differentiation arrest and clonal proliferation of immature thymocytes. Many oncogenes in T-ALL are genes encoding transcription factors. TAL bHLH transcription factor 1 ( TAL1) is one of the most frequently dysregulated transcription factors in T-ALL and is ectopically overexpressed in approximately 50% of T-ALL cases, owing to chromosome translocations, SIL (SCL-interrupting locus) -TAL1 fusion, and 5‘ super-enhancer (SE)-generating mutations. TAL1 overexpression caused by 5‘ TAL1 SE is found in 5% of patients with T-ALL and is associated with unfavorable clinical outcomes. However, no clinically available drugs specifically inhibit TAL1 or TAL1 SE components. Kruppel-like factor 4 (KLF4) is a member of the KLF family of transcription factors that exhibits both oncogenic and tumor-suppressive functions in a context-dependent manner. In T-cell malignancies, KLF4 is regarded as a tumor suppressor because KLF4 expression is silenced by promoter methylation, and the induction of KLF4 promotes apoptosis through the BCL-2/BCL-XL pathway. However, whether KLF4 affects the expression of T-ALL-related transcription factors remains unclear. We first analyzed three independent previously reported microarray datasets to explore the essential downstream targets of KLF4 in T-ALL cells. The following groups of genes were extracted: genes upregulated in patients with T-ALL compared to normal thymocytes (GSE46170), genes upregulated in Klf4-deficient T-ALL mice (GSE75663), and genes downregulated in KLF4-overexpressing human T-ALL cells (Li W et al. Mol. Cancer. 2015). Overlapping genes in these groups were identified as potential downstream targets of KLF4. Among these, we focused on TAL1, a well-known oncogenic transcription factor gene in T-ALL. We performed a functional analysis of KLF4 using TAL1-positive T-ALL cell lines (Jurkat, MOLT-3, CCRF-CEM, and RPMI-8402). Genetic induction of KLF4 showed stronger anti-leukemic effects in Jurkat and MOLT-3 cells, 5‘ TAL1 SE-positive T-ALL cell lines, compared with CCRF-CEM and RPMI-8402 cells, SIL-TAL1-positive T-ALL cell lines. KLF4 overexpression significantly reduced mRNA expression levels of TAL1 in Jurkat and MOLT-3 cells but not in CCRF-CEM and RPMI-8402 cells. Thus, we hypothesized that KLF4 specifically suppressed SE-driven TAL1 expression by impairing mutated TAL1 enhancer activity. The luciferase reporter assay confirmed that the activity of the mutated TAL1 enhancer was significantly reduced by the exogenous expression of KLF4, whereas that of the wild-type reporter was not affected. According to previous studies, mutations in TAL1 enhancers in Jurkat and MOLT-3 cells create MYB primary motifs, and MYB binding at this location is essential for the formation of 5‘ TAL1 SE. Therefore, we examined whether KLF4 represses MYB expression. The chromatin immunoprecipitation assay and qPCR analysis revealed that KLF4 bound to the proximal gene promoter of MYB and directly downregulated its expression. The luciferase reporter assay using the MYB promoter showed a significant reduction of reporter activity upon KLF4 overexpression. Finally, we investigated whether pharmacological induction of KLF4 using APTO-253, a small-molecule inducer ofKLF4, could control leukemia. APTO-253 inhibited the growth of all TAL1-positive T-ALL cell lines at nanomolar concentrations. The GI 50 values of APTO-253 for Jurkat and MOLT-3 cells were lower than those for CCRF-CEM and RPMI-8402 cells, which was consistent with the KLF4-overexpression-induced growth inhibition of T-ALL cell lines. APTO-253 induced KLF4 expression and decreased TAL1 and MYB expression in Jurkat and MOLT-3 cells. Furthermore, exogenous MYB expression rescued growth inhibition by APTO-253. Collectively, these results indicated that APTO-253 suppressed the growth of T-ALL cells by targeting SE-driven TAL1 expression via the induction of KLF4. In summary, we revealed that KLF4 suppressed SE-driven TAL1 expression via the direct inhibition of MYB. Moreover, pharmacological induction of KLF4 demonstrated anti-leukemic activity in T-ALL cells. These findings propose a promising strategy for patients with T-ALL and 5' TAL1 SE.

Epigenetic Dissection of Human Blood Group Genes Reveals Unknown Regulatory Elements and Detailed Characteristics of KEL and Other Loci

Accurate blood group typing is essential for compatible blood transfusions and can often be achieved with the combination of serology and genotyping technologies. Currently, most genotyping platforms focus on variants in coding regions. In addition, variants in the non-coding region that can disrupt regulatory motifs in the promoter or enhancer regions are also important for blood group typing, as demonstrated in ABO, FY and XG systems for example. These blood group regulatory regions have yet to be fully characterized for all genes. Recently, we systematically explored the GATA1-dependent blood group regulome in silico and found 193 candidate regulators in 33 blood group genes. As proof of concept, we resolved in vitro the GATA1-dependent mechanism underlying the Helgeson phenotype of the Knops system, where there is very low expression of Complement Receptor 1 (CR1) on red blood cells. Aiming to improve the precision of our global blood group gene regulator prediction, we expanded the analysis to include preexisting epigenetic datasets such as ChIPseq with erythroid transcription factors (TFs; GATA1, KLF1, RUNX1, NFE2), histone modifications (H3K27ac, H3K4me1, H3K4me3), and ATAC-seq. In total, 96 candidate regions were identified where at least 2 TFs were bound. Four genes ( CR1, EMP3, ABCB6 and ABCC4) showed co-localization of ChIPseq peaks for all 4 TFs within their introns 37, 4, 1 and 1, respectively. Functional analysis with luciferase assay of these potential enhancers with their respective promoters showed different levels of enhancement. Among the more well-known and clinically important blood groups, the KEL proximal promoter was shown to co-localize GATA1 and KLF1. Previous studies suggested the presence of 3 GATA1-binding sites and an Sp1 site, but KLF1 was novel to our knowledge. Moreover, decreased KEL expression has been reported in a KLF1-null human and in mouse knockouts. Candidate GATA1 sites near the KLF1 motif were observed, with the GATA1 motif closest to the KLF1 motif having the highest motif score in JASPAR (939 vs. 913 for the 5‘ and 851 for the 3‘ GATA1 motifs using GATA1 logotype MA0035.3). In light of this, and the importance of KEL for transfusion and fetomaternal incompatibility, we carefully examined the KEL promoter region. A decrease in JASPAR score was used to select two natural variants that disrupt TF binding at the GATA1 and KLF1 motifs compared to the wild-type (wt): rs1204402835:A&amp;gt;G for GATA1 (939&amp;gt;815); rs1442994069:G&amp;gt;A for KLF1 (924&amp;gt;801, KLF1 logotype: MA0493.2). We showed binding of KLF1 and GATA1 to the −35 to +1 bp region (NM_000420.3) with electrophoretic mobility shift assay (EMSA) and mass spectrometry (MS) using synthetic probes and nuclear extract from HEL cells. Disruption of the KLF1 and/or GATA1-binding motifs with the aforementioned natural variants led to the loss of bands which, compared to the wt, represented nuclear extract binding to the probes in the EMSAs. The decreased abundance of bound TFs was confirmed by MS (−2.38 for KLF1 and −1.76 for GATA1, log 2-fold changes compared to wt). Luciferase assays of the KEL promoter exhibited the highest activity (set to 100%) with wt GATA1 and KLF1 motifs and omitting Sp1 and 3'-side GATA1 motifs (Figure 1). The whole region including Sp1 and 3' GATA1 sites gave 44% activity whilst the 3' GATA1 alone or with Sp1 site was &amp;lt;10% (similar to vector control). The promoter construct containing the 5' GATA1 site and the central GATA1 and KLF1 sites showed the highest activity, but reduced activity was observed with disrupted GATA1 motif at 44% and KLF1 motif at 48%. Activity decreased to 17% when both variants were present (Figure 1). In summary, we used a combined bioinformatics and experimental approach to unravel regions with potential to regulate blood group expression and explain weak phenotypes that may escape detection in clinical practice. Our studies are limited by the number of available datasets for relevant TFs but were able to detect regions where these TFs co-localize in CR1, EMP3, ABCB6 and ABCC4. Furthermore, we characterized the clinically important KEL blood group gene promoter in greater detail indicating that the central GATA1 motif is the most crucial. For the first time, we described that KLF1 and GATA1 jointly enhance KEL transcription. Finally, our updated pipeline provides multiple candidate regulatory regions to be explored to improve knowledge on the blood group regulome.

DHT and Insulin Upregulate Secretion of the Soluble Decoy Receptor of IL-33 From Decidualized Endometrial Stromal Cells.

Interleukin 33 (IL-33) signaling regulates most of the key processes of pregnancy, including decidualization, trophoblast proliferation and invasion, vascular remodeling, and placental growth. Accordingly, dysregulation of IL-33, its membrane-bound receptor (ST2L, transducer of IL-33 signaling), and its soluble decoy receptor (sST2, inhibitor of IL-33 signaling) has been linked to a wide range of adverse pregnancy outcomes that are common in women with obesity and polycystic ovary syndrome, that is, conditions associated with hyperandrogenism, insulin resistance, and compensatory hyperinsulinemia. To reveal if androgens and insulin might modulate uteroplacental IL-33 signaling, we investigated the effect of dihydrotestosterone (DHT) and/or insulin on the expression of ST2L and sST2 (along with the activity of their promoter regions), IL-33 and sIL1RAP (heterodimerization partner of sST2), during in vitro decidualization of endometrial stromal cells from 9 healthy women. DHT and insulin markedly upregulated sST2 secretion, in addition to the upregulation of its messenger RNA (mRNA) expression, while the proximal ST2 promoter, from which the sST2 transcript originates, was upregulated by insulin, and in a synergistic manner by DHT and insulin combination treatment. On the other hand, sIL1RAP was slightly downregulated by insulin and IL-33 mRNA expression was not affected by any of the hormones, while ST2L mRNA expression and transcription from its promoter region (distal ST2 promoter) could not be detected or showed a negligibly low level. We hypothesize that high levels of androgens and insulin might lead to subfertility and pregnancy complications, at least partially, through the sST2-dependent downregulation of uteroplacental IL-33 signaling.

Molecular cloning of the gene promoter encoding the human CaVγ2/Stargazin divergent transcript (CACNG2-DT): characterization and regulation by the cAMP-PKA/CREB signaling pathway.

CaVγ2 (Stargazin or TARPγ2) is a protein expressed in various types of neurons whose function was initially associated with a decrease in the functional expression of voltage-gated presynaptic Ca2+ channels (CaV) and which is now known to promote the trafficking of the postsynaptic α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors (AMPAR) towards the cell membrane. Alterations in CaVγ2 expression has been associated with several neurological disorders, such as absence epilepsy. However, its regulation at the transcriptional level has not been intensively addressed. It has been reported that the promoter of the Cacng2 gene, encoding the rat CaVγ2, is bidirectional and regulates the transcription of a long non-coding RNA (lncRNA) in the antisense direction. Here, we investigate the proximal promoter region of the human CACNG2 gene in the antisense direction and show that this region includes two functional cAMP response elements that regulate the expression of a lncRNA called CACNG2-DT. The activity of these sites is significantly enhanced by forskolin, an adenylate cyclase activator, and inhibited by H89, a protein kinase A (PKA) antagonist. Therefore, this regulatory mechanism implies the activation of G protein-coupled receptors and downstream phosphorylation. Interestingly, we also found that the expression of CACNG2-DT may increase the levels of the CaVγ2 subunit. Together, these data provide novel information on the organization of the human CACNG2-DT gene promoter, describe modulatory domains and mechanisms that can mediate various regulatory inputs, and provide initial information on the molecular mechanisms that regulate the functional expression of the CaVγ2 protein.

Differential usage of DNA modifications in neurons, astrocytes, and microglia

BackgroundCellular identity is determined partly by cell type-specific epigenomic profiles that regulate gene expression. In neuroscience, there is a pressing need to isolate and characterize the epigenomes of specific CNS cell types in health and disease. In this study, we developed an in vivo tagging mouse model (Camk2a-NuTRAP) for paired isolation of neuronal DNA and RNA without cell sorting and then used this model to assess epigenomic regulation, DNA modifications in particular, of gene expression between neurons and glia.ResultsAfter validating the cell-specificity of the Camk2a-NuTRAP model, we performed TRAP-RNA-Seq and INTACT-whole genome oxidative bisulfite sequencing (WGoxBS) to assess the neuronal translatome and epigenome in the hippocampus of young mice (4 months old). WGoxBS findings were validated with enzymatic methyl-Seq (EM-Seq) and nanopore sequencing. Comparing neuronal data to microglial and astrocytic data from NuTRAP models, microglia had the highest global mCG levels followed by astrocytes and then neurons, with the opposite pattern observed for hmCG and mCH. Differentially modified regions between cell types were predominantly found within gene bodies and distal intergenic regions, rather than proximal promoters. Across cell types there was a negative correlation between DNA modifications (mCG, mCH, hmCG) and gene expression at proximal promoters. In contrast, a negative correlation of gene body mCG and a positive relationship between distal promoter and gene body hmCG with gene expression was observed. Furthermore, we identified a neuron-specific inverse relationship between mCH and gene expression across promoter and gene body regions.ConclusionsNeurons, astrocytes, and microglia demonstrate different genome-wide levels of mCG, hmCG, and mCH that are reproducible across analytical methods. However, modification-gene expression relationships are conserved across cell types. Enrichment of differential modifications across cell types in gene bodies and distal regulatory elements, but not proximal promoters, highlights epigenomic patterning in these regions as potentially greater determinants of cell identity. These findings also demonstrate the importance of differentiating between mC and hmC in neuroepigenomic analyses, as up to 30% of what is conventionally interpreted as mCG can be hmCG, which often has a different relationship to gene expression than mCG.

Abstract 18828: Generation and Characterization of a Novel Myh11 Knock-In Smooth Muscle Cell-Specific CreEr T2 Mouse Model

Background: MYH11 is the most specific and robust marker for differentiated smooth muscle cells (SMCs) and its proximal promoter has been used as a SMC Cre-driver to investigate SMC-specific roles of floxed target genes. Two distinct Myh11-CreER T2 ( Myh11-CreER T2 -Off and -RAD ) mouse lines have been used widely for inducible SMC-specific Cre/loxP-mediated recombination in conditional mutagenesis or lineage tracing. However, both mouse lines were generated using bacterial artificial chromosome (BAC), which were randomly integrated into the genome, potentially resulting in multiple copies of the transgene and the unpredictable disruption of endogenous genes. An additional limitation of the Myh11-CreER T2 -Off mouse is its only works on the male mice. To address these limitations, we generated and characterized a new Myh11-CreER T2 mouse ( Myh11-CreER T2 -KI ), which results from integration of a CreER T2 cassette into the endogenous Myh11 gene locus, enabling faithful SMC-specific lineage tracing or specific gene knockout in SMC in vivo in both sexes. Method: A tamoxifen-inducible, CreER T2 cassette was inserted into one of the Myh11 gene alleles after the initiation codon of Myh11 . To validate the Myh11 CreERT2/+ -mediated gene recombination in SMCs, Myh11-CreER T2 -KI mice were crossed with mTmG dual reporter mice or the lncRNA Carmn GFP knock-in reporter/knockout mice to trace SMC lineages or generate SMC-specific inducible Carmn knockout mice. The recombination specificity in SMCs was analyzed by GFP fluorescence analysis. Results: The CreER T2 cassette inserted into the Myh11 gene locus negligibly affects endogenous MYH11 protein expression. In mTmG / Myh11-CreER T2 -KI reporter mice, GFP expression was detected specifically in both vascular and visceral SMCs in various tissues after tamoxifen mediated Cre activation. Moreover, Myh11-CreER T2 -KI -mediated Carmn SMC-specific deletion in adult female mice recapitulated the lethal intestinal pseudo-obstructive phenotype observed in male Myh11-CreER T2 -Off Carmn KO mice. Conclusions: Our new Myh11-CreER T2 -KI mouse model provides an additional genetic tool using the fidelity of an endogenous SMC gene locus to trace SMC lineages and delete genes in the SMC of both sexes of mice.

Integrated Genomic Analysis Identifies a Downstream Regulatory Element Oncogenically Activating Hematopoietically Expressed Homeobox ( HHEX) in ETP-ALL

Hematopoietically-expressed Homeobox ( HHEX) is required for the maintenance of hematopoietic stem cells (HSPCs) and common lymphoid progenitor cells. HHEX is also the second most frequent integration site in retroviral insertional mutagenesis screens of leukemias and lymphomas arising in AKXD recombinant inbred mouse strains, implying that it is an important oncogene. Enforced expression of HHEX induces T-cell acute lymphoblastic leukemias (T-ALL) in murine bone marrow transplantation models. In human studies, HHEXmRNA expression is upregulated in human T-ALL studies, especially in Early T-cell Precursor (ETP-) ALL subtypes where it is concordantly expressed with LMO2. The HHEX locus is not rearranged in ETP-ALL where it is upregulated so the mechanism of HHEX activation is not clear. We analyzed T-ALL induced by retroviral mutagenesis and found an intergenic site of frequent integration, 65kb 3‘ of the Hhex coding exons. Integrations clustered within a 3 kb genomic area that is also an open chromatin region (OCR) by ATAC-seq analysis and that induced Hhex upregulation. The syntenic human region was highly enriched for H3K27 acetylation and for occupancy by multiple transcription factors, notably GATA1 and TAL1, per ENCODE. Our prior data had shown that HHEX was a downstream target of the LMO2 complex comprised of GATA1/2, TAL1 or LYL1, and nucleated by the scaffolding protein, LIM domain binding protein 1 (LDB1). We had previously shown by ChIP-PCR that the LMO2 complex was bound to the intron 1 enhancer. Thus, we performed ChIP-exonuclease analysis of LDB1 in the human ETP-ALL model cell line, LOUCY. We confirmed its occupancy at the intron 1 enhancer but we also observed LDB1 occupancy 68kb 3‘ of the HHEX coding exons, in the exact region syntenic to the murine common insertion sites. ChIP-exo analysis allowed us to pinpoint a core element with composite GATA/E box sites that was highly conserved across multiple mammalian species. LDB1 occupancy at intron 1 and at +68kb of the HHEX locus was reminiscent of LDB1's occupancy at the beta globin locus where LDB1's occupancy and homodimerization mediates chromatin looping between composite E box/GATA sites in the locus control region (LCR) and the beta globin proximal promoters. To test whether a similar interaction was occurring at the HHEX locus, we analyzed virtual 4C (chromatin conformation capture) data. We confirmed looping between the +68kb element and the proximal promoter of HHEX in human ETP-ALL primary samples and in human HSPCs. The experiments showed that looping occurs in certain developmental contexts in HSPCs and is recapitulated in ETP-ALL and mediated by the LMO2/LDB1 protein complex. HHEX is a downstream oncogene of the LMO2/LDB1 complex and is activated through this distal +68kb regulatory element. Our studies raise the possibility that dissection of this regulatory element and interference with chromatin looping are potential therapeutic mechanisms that could disrupt oncogene expression.

Differential Chromatin Organization between t(4;14) and Non-t(4;14) Multiple Myeloma Driven By the Histone Methyltransferase NSD2

Background: The incidence of multiple myeloma (MM) with t(4;14) translocation is ~15% of newly diagnosed MM (NDMM), and is associated with poor prognosis and high-risk disease. Recent analysis of t(4;14) genomics indicate that the location of the chromosome 4 (chr4) breakpoint can significantly segregate patient outcome regardless of therapeutic intervention. Translocation of IGH regulatory elements from chr14, drive the expression of NSD2 (chr4), a histone (H3) methyltransferase responsible for di-methylation of H3 lysine 36 (H3K36me2), a mark of active chromatin. Depending upon the location of the chr4 breakpoint, different isoforms of NSD2 are expressed, including full-length (NSD2-FL) and various N-terminus truncations (NSD2-TR). The mechanisms of how the location of the chr4 breakpoint and the functionalities of NSD2 isoforms may contribute to a higher risk biology in t(4;14) MM patients is not known. Here we compare and contrast the 3D chromosomal organization of t(4;14)-NSD2-FL, t(4;14)-NSD2-TR and non-t(4;14) in pre-clinical MM models. Results: Comparative analysis of chromosome conformation capture (Hi-C) indicates that there is a decrease in medium-to-long range chromosomal looping interactions accompanied by an increase in short-range interactions from t(4;14) vs. non-t(4;14) models (Figure A). Accordingly, relative quantification of chromosomal contact probabilities of intra-chromosomal (cis) contacts increase in frequency from non-t(4;14) (77%) vs. t(4;14)-NSD2-FL (87%) vs. t(4;14)-NSD2-TR (89%). Evaluation of active/inactive (A/B) 3D genomic compartments between non-t(4;14) and t(4;14) models suggest significant compartment switches (~30% genome; combined A-to-B and B-to-A). Analysis of gene neighborhoods through topologically associated domains (TADs) suggests that there are decreases in contacts at the TAD boundary regions in t(4;14)-NSD2-TR vs. t(4;14)-NSD2-FL vs. non-t(4;14) models. TAD sizes are also generally smaller in size, from t(4;14)-NSD2-TR vs. t(4;14)-NSD2-FL vs. non-t(4;14). Complimentary analysis of activity by contact (ABC) to assess the potential influence of proximal and distal enhancers on gene activity confirms there is a decrease in ABC scores when comparing t(4;14) vs. non-t(4;14). Assessment of global chromatin accessibility (ATAC-Seq) indicate significant consensus open peaks (~135k), differentially accessible (DA) peaks (~2.6k), and differential closed peaks (~8.8k) in t(4;14) vs. non-t(4;14). Principal component (PC) analysis demonstrated a unique grouping of t(4;14) models compared to a very heterogenous distribution of non-t(4;14) models. DA regions in t(4;14) were found to be primarily more enriched in both intronic and intergenic regions, and within proximal and distal promoters. Analysis of histone marks was used to assess differences in global active enhancers (H3K4me1, H3K27ac), repressive chromatin (H3K9me3, H3K27me3), and active transcription (H3K36me2/3, H3K4me3) between non-t(4;14) and t(4;14). Active marks were shown to be increased, and repressive marks decreased in t(4;14) vs. non-t(4;14) models that also correlated with DA peaks. Enhancer ranking suggests the frequency of potentially poised superenhancers increase in t(4;14) vs. non-t(4;14). Differential expression (DE) analysis between t(4;14) and non-t(4;14) was highly correlative with DA peaks (Figure B). In addition, distinctive transcriptional signatures between non-t(4;14), t(4;14)-NSD2-FL, and t(4;14)-NSD2-TR were identified. Conservative (DA+DE) pathway enrichment suggests multiple and distinct biological processes including cell adhesion through adherens junctions, cell-cycle regulation through mitotic checkpoints, chromosomal reorganization through depolymerization of the nuclear lamina, and epithelial to mesenchymal transition. Conclusions: Systematic chromosomal re-arrangement and accessibility driven by differential epigenetic deposition of histone regulatory marks, differentiates t(4;14) from non-t(4;14) MM biology. These analyses suggest that given the nature of the translocation, and additionally the location of the chr4 breakpoint, result in major 3D chromosomal structural rearrangement, mediating biological programs that may explain the differences between successful and poor interventional therapies for this subset of MM disease.

The Ingenious Multiple Efficacies of the Integrated Gene Fragment of Torque Teno Mini Virus in Orchestrating Promyelocytic Leukemogenesis Via Hijacking Rara

Introduction Torque teno mini virus (TTMV) is a ubiquitous virus which symbiotic with humans, but it has recently been reported to cause acute promyelocytic leukemia (APL) through a unique form of genome fragment integration and forming the TTMV::RARA fusion gene, with 4 cases reported till now. However, the leukemogenesis mechanism of TTMV::RARA-APL has not been explored. Methods We recruited transcriptome sequencing (RNA-seq) data of 7 TTMV::RARA-APL cases, 3 of them also with whole genome sequencing (WGS) data, to analyze the properties of the TTMV integrated sequences. Clinical information was analyzed. In vitro cell experiments were performed to verify the functions of the conserved regulatory sequences and the fusion protein. Results These cases were collected from 4 centers, 5 males and 2 females, aged 3 to 35 (median 9) years, with 6 pediatric cases. Of which 3 pediatric cases were identified from a continuous acute myeloid leukemia (AML) cohort. In this cohort, 3 TTMV::RARA-APL were identified in 205 AML cases under 14 years, but no cases in another 930 AML cases, showing a strong tendency towards pediatrics (p=0.00022). Moreover, we totally identified 85 PML::RARA-APL and 3 TTMV::RARA-APL, and no other X::RAR cases in this cohort, indicating TTMV::RARA is the most common X::RAR fusion besides PML::RARA. All cases manifested typical APL morphological features, and RNA-seq expression analysis showed clustering with PML::RARA-APL cases. Initial effect and remission can be achieved with chemotherapy regimens containing all-trans retinoic acid (ATRA), but early recurrence is prone to occur. RARA-I387T mutation was observed in case #TR4, who relapsed after treatment with ATRA, suggesting that the leukemic cells were responsive to ATRA. However, primary resistance to ATRA and extensive resistance to various agents were observed in case #TR5, who was initially diagnosed with myeloid sarcoma and transformed into APL at relapse. The TTMV integrated sequences of 3 cases with WGS data were 1164bp, 2113bp, and 2859bp (Fig. 1A), respectively, and the common feature was the involvement of the transcription regulatory region and the open reading frame 2 (ORF2). Alignment of TTMV transcription regulatory sequences (Fig. 1B) revealed a highly conserved basal transcription factor region, including the canonical TATA box and GC box. While in the proximal promoter region showing sequence diversity, all 3 cases carried 4 RUNX1 binding elements and 1 octamer motif. In vitro experiments (Fig. 1C) showed that TTMV basal transcription element can initiate basal expression in 293T cells, while RUNX1 can significantly enhance the expression in response to the RUNX1 binding elements. RUNX1 is an important transcription factor protein in the differentiation of myeloid cells, and the 4 RUNX1 binding elements might explain the myelotropic of TTMV and confer an important basis in promyelocytic leukemogenesis. The TTMV-ORF2 coding sequences of all 7 cases were analyzed, with the common region being the N-terminus 58 amino acids, of which 20 were highly conserved (Fig. 1D, 1E). Co-Immunoprecipitation analysis confirmed that the TTMV::RARA protein forms homopolymers and heteropolymers with RXRA (Fig.1F), which is the property shared by all X::RARA proteins. Serine/Threonine protein phosphatase (S/T PPase) assays showed that the fusion protein exhibits strong S/T PPase activity (Fig. 1G). UAS/GAL4 reporter experiment showed that TTMV::RARA protein exhibited a constrained but concentration-dependent response to ATRA compared to RARA (Fig. 1H). However, fusion proteins with ORF2-C32A/C34A mutation and impaired phosphatase activity were significantly more responsive to ATRA (Fig. 1H). This suggests that the S/T PPase activity of the ORF2 coding region plays a role in retarded ATRA response. Conclusions This is the first systematic report on this novelty disease. Data suggests that TTMV::RARA-APL may be more common in children, which may be related to the ubiquity of TTMV and its acquisition early in life. The clinical manifestations and treatment responses are diverse, with overall dismal prognosis. Molecular investigation indicated the multifunctional TTMV integrated molecular machinery in orchestrating RUNX1 enforced myelotropic, aberrant priming expression, homodimer formation, and S/T PPase activity, and confer promyelocytic leukemogenesis via hijacking RARA.

Transcription Defects in SF3B1K700E Induce Targetable Alterations in the Chromatin Landscape

Introduction: Acquired mutations, most commonly in RNA splicing factors and epigenetic regulators are thought to be disease drivers of clonal myeloid disorders such as MDS and AML. Both MDS and AML are amenable to epigenetic therapies regardless of underlying mutational subtypes. This prompted our hypothesis that alterations to epigenetic and chromatin landscape is important in pathobiology of clonal myeloid disorders driven by splicing factor mutations. In this study, we demonstrate that SF3B1 mutations induce distinct changes to epigenetic landscape and chromatin organization by altering RNA Polymerase II (Pol2) transcription kinetics. Critically, such epigenetic changes are also targetable - inhibiting components in the H3K4me/Sin3/HDAC pathway reverses Pol2 transcription defects and downstream effects on chromatin organization and genomic integrity. Methods: We generated inducible isogenic K562 cell lines that express single mutant allele of SF3B1 K700Ecombining two genome editing approaches (AAV-intron trap with CRISPR/Cas9 (Boddu et al, Comms Biol, 2021)) (Fig1A). RNAPII transcription kinetics changes were assessed using ChIP-seq for Pol2 and nascent-transcriptome assays (including GRO-seq and transient transcriptome-time lapse sequencing (TT-TL-seq). Chromatin accessibility/nucleosome density and histone marks (H3K4me3, H3K27ac, H3K27me3) were assessed using ATAC-seq and low-input CUT&amp;RUN, respectively. Key results were replicated in patient samples with SF3B1 mutations and in a Sf3b1K700E mouse model. Results: Combining genome-wide approaches (ChIP-seq (Fig1B), GRO-seq, and TT-TL seq (Fig1C)), we found that Pol2 in SF3B1 K700E redistributes into the gene body due to a primary gene-body elongation defect. This transcriptional dysregulation was reflected in downstream effects such as excess R-loops (S9.6 microscopy; Fig1D), transcription-replication conflicts (proximity ligation assay for PCNA-Pol2; Fig1E), and S-phase arrest (flow cytometry; Fig1F). Importantly, normalized Pol2 density at proximal-promoter (p-p) region was reduced in SF3B1 K700E (Fig1G). This correlated with a reduction in p-p H3K4me3 in SF3B1 K700E determined by Cut and Run (Fig1H). ATAC-seq showed a reduction in promoter accessibility (Fig1I) and increased nucleosome promoter density (Fig1J). ChIP-seq for CDK9, a component of p-TEFb pause release complex, showed higher occupancy at promoters in SF3B1 K700E (Fig1K), suggesting that premature promoter pause release of Pol2 is the major driver for the observed reduction in p-p Pol2 density. Consistent with the importance of p-p Pol2 in maintaining accessible chromatin states, our findings suggest that depletion of p-p Pol2 leads to nucleosome repositioning at promoters and loss of chromatin accessibility (Gilchrist et al, Cell, 2010). Given the extensive cross talk between chromatin and transcription, we speculated that modulating epigenetic regulators might improve Pol2 elongation defects and rescue cells from downstream effects. An unbiased shRNA rescue screen, targeting epigenetic regulators and chromatin modifier protein classes, enriched for proteins in the Sin3/HDAC pathway (ING2, HDAC2) (Fig1L). Conversely, knocking down (KD) for WDR5 (H3K4me3 writer complex) further worsened survival. HDAC2 and ING2 KD cells showed reduced R-loops and DNA damage, lower gene-body Pol2 ChIP densities (Fig1M), normalization of p-p H3K4me3 densities (Fig1N), and rescue from S-phase arrest. These effects of WDR5 and HDAC2/ING2 KD on survival in SF3B1-mutant isogenic cells was confirmed in both MDS patient samples (Fig1O)- and Sf3b1K700E murine models (Fig1P)- contexts, using in vitro colony assays. Conclusion: Our findings show that SF3B1 K700E-induced disruption of Pol2 elongation kinetics is reflected in reduced Pol2 density at proximal promoter sites and results in a corresponding reduction in chromatin accessibility and promoter H3K4me3. Through an unbiased shRNA screen, we identified epigenetic factors in the Sin3/HDAC/H3K4me pathway, which, when modulated, improved the transcription defects and their downstream effects. Our findings shed light on the mechanisms by which oncogenic mutant spliceosomes affect chromatin organization through their effects on Pol II transcription elongation and present a rationale for targeting the Sin3/HDAC complex as a potential therapeutic strategy.

Hells (LSH) Controls Gene Expression in T-Cell Lymphomas By Regulating RNA Polymerase II with a Bimodal Function

Chromatin modifiers are emerging as determinants of many types of cancer, including anaplastic large cell lymphoma (ALCL), a family of highly heterogeneous T-cell lymphomas for which therapeutic options are still limited. We recently identified the DNA helicase HELLS - a member of the SWI/SNF2 family- as a genetic vulnerability of ALK - ALCLs. HELLS is a multifunctional chromatin remodeler that affects genomic instability. Although its transcriptional function has been suggested, no clues on how HELLS controls transcription are currently available. To explore its transcriptional function in ALCLs, we integrated HELLSChromatin immunoprecipitation-sequencing (ChIP-seq) analysis in the TLBR-2 cell line with RNA-sequencing data TLBR-2 HELLS KD and control cells. Out of 729 genes significantly affected by HELLS KD, 467 genes (64% of the total) resulted directly bound by HELLS. We termed these genes HELLS-direct genes (HDGs). Analysis of HELLS binding profile at HDGs site showed that 67% of HELLS binding sites at HDGs has intragenic localization being associated with promoters, introns, and exons. Gene-set enrichment analysis of HDGs revealed several pathogenic processes associated with deregulated genes including JAK/STAT signaling pathway, inflammation mediated by chemokines, and cytokines signaling pathway. To assess the contribution of HELLS to the transcription of its HDGs, the distribution of RNA-PolymeraseII (RNAPII) was investigated by ChIP-seq in TLBR-2 HELLS KD and control cells. We observed that HELLSdepletion caused a bimodal alteration of RNAPII. On genes belonging to biological processes involved in the dysregulation of circuitries that controls T-cells dependent host interactions (n=195, 40% of HDG promoters), the depletion of HELLS caused a significant impairment of RNAPII recruitment suggesting that HELLS partakes in transcription regulation of these pathways acting as a co-transcriptional factor. Whereas, on the remaining 60% of HDGs (n=272), which are enriched for selective biological functions including cytoskeleton regulation and DNA metabolic processes, we observed a selective loss of RNAPII signal in the regions immediately downstream of the TSS coherent with a potential proximal promoter pausing of RNAPII. Target analysis of phospho-CTD modification ser2P of RNAPII confirmed the RNAPII pausing after HELLS depletion. Stacked RNAPII during elongation drives DNA-RNA hybrids (R-loops) formation and it is a primary source of DNA break accumulation. We hypothesized that HELLS could promote RNAPII elongation by relieving R-loops, thereby decreasing potential obstacles to the transcription machinery. We investigated the effect of HELLS depletion on R-loops accumulation by performing immunofluorescences using the S9.6 antibody to detect R-loops in control and HELLS KD cells. We observed a significant increase in the nuclear intensity of R-loops in several models of ALCL HELLS KD cells. The increased S9.6 signal was accompanied by a different pattern of nuclear Ser2P-RNAPII with clusters adjacent to R-loop structures suggesting that R-loops are associated with stalled transcription. After HELLS KD, we also observed an overall increase in the intensity of the nuclear γH2AX signal - used as a readout of DNA damage accumulation- and a significant increase in the formation of γH2AX foci in all cell lines tested. The increase in γH2AX foci was found in S9.6 positive cells andwasassociated with a distinctive pattern of ser2P-RNAPII. By using reporter-GFP-based assays, we investigated which pathway mediates HELLS ability to repair DNA damage discovering that the loss of HELLS results in decreased NHEJ and MMEJ efficiency (37% and 36% respectively over time). To validate the clinical impact of HELLS in vivo, we interrogated a cohort of 44 ALCL patients using the NCounter platform. Gene expression analysis showed that HELLS was significantly associated with its HDGs showing a positive correlation with 68% of genes and a negative correlation with 32% of genes in ALK -ALCL samples. Our data indicate that i) HELLS works with a bi-modal function in controlling gene expression by regulating both the initiation and the elongation of RNAPII and ii) the different work modalities underline different biological consequences. At the crossroads between transcription and DNA repair, HELLS is as an attractive target for developing novel treatments in hematological malignancies

Genetic variations in G-quadruplex forming sequences affect the transcription of human disease-related genes.

Guanine-rich DNA strands can fold into non-canonical four-stranded secondary structures named G-quadruplexes (G4s). G4s folded in proximal promoter regions (PPR) are associated either with positive or negative transcriptional regulation. Given that single nucleotide variants (SNVs) affecting G4 folding (G4-Vars) may alter gene transcription, and that SNVs are associated with the human diseases' onset, we undertook a novel comprehensive study of the G4-Vars genome-wide (G4-variome) to find disease-associated G4-Vars located into PPRs. We developed a bioinformatics strategy to find disease-related SNVs located into PPRs simultaneously overlapping with putative G4-forming sequences (PQSs). We studied five G4-Vars disturbing in vitro the folding and stability of the G4s located into PPRs, which had been formerly associated with sporadic Alzheimer's disease (GRIN2B), a severe familiar coagulopathy (F7), atopic dermatitis (CSF2), myocardial infarction (SIRT1)and deafness (LHFPL5). Results obtained in cultured cells for these five G4-Vars suggest that the changes in the G4s affect the transcription, potentially contributing to the development of the mentioned diseases. Collectively, data reinforce the general idea that G4-Vars may impact on the different susceptibilities to human genetic diseases' onset, and could be novel targets for diagnosis and drug design in precision medicine.

CRISPR Activation of PKD1 in Immortalized Cell Lines Is Limited by Its Heterochromatinized Proximal Promoter

CRISPR Activation of PKD1 in Immortalized Cell Lines Is Limited by Its Heterochromatinized Proximal Promoter

Novel Insights on the Role of Epigenetics in Androgen Receptor's Expression in Prostate Cancer.

The androgens/androgen receptor (AR) axis is the main therapeutic target in prostate cancer (PCa). However, while initially responsive, a subset of tumors loses AR expression through mechanisms putatively associated with epigenetic modifications. In this study, we assessed the link between the presence of CpG methylation in the 5'UTR and promoter regions of AR and loss of AR expression. Hence, we characterized and compared the methylation signature at CpG resolution of these regulatory regions in vitro, both at basal levels and following treatment with 5-aza-2-deoxycytidine (DAC) alone, or in combination with Trichostatin A (TSA). Our results showed heterogeneity in the methylation signature of AR negative cell lines and pinpointed the proximal promoter region as the most consistently methylated site in DU-145. Furthermore, this region was extremely resistant to the demethylating effects of DAC and was only significantly demethylated upon concomitant treatment with TSA. Nevertheless, no AR re-expression was detected at the mRNA or protein level. Importantly, after treatment, there was a significant increase in repressive histone marks at AR region 1 in DU-145 cells. Altogether, our data indicate that AR region 1 genomic availability is crucial for AR expression and that the inhibition of histone methyltransferases might hold promise for AR re-expression.

The KIR2DL1 intermediate upstream element participates in gene activation

The human KIR genes encode a family of class I MHC receptors that are expressed on subsets of NK cells. The expression of KIR proteins is controlled by a stochastic process, and competition between sense and antisense promoter elements has been suggested to program the variegated expression of these genes. Previous studies have demonstrated distinct roles of distal, intermediate, and proximal sense promoter/enhancer elements in gene activation and expression. Conversely, proximal and intronic antisense promoter transcripts have been associated with gene silencing at different stages of NK cell development. In the current study, we examine the effect of intermediate promoter deletion on KIR2DL1 expression in the YTS cell line. Homozygous deletion of the KIR2DL1 intermediate element did not affect proximal promoter activity but resulted in increased detection of upstream transcripts. No significant changes in alternative mRNA splicing or expression levels of KIR2DL1 protein were observed. However, intermediate element deletion was associated with a reduced frequency of gene activation by 5-azacytidine. Taken together, these results indicate that the intermediate element is not an enhancer required for KIR expression; however, it is required for the efficient activation of the gene.

THU625 Med12 Mutation Activates Tryptophan-Kynurenine-ahr Pathway To Promote Growth Of Uterine Leiomyoma

Abstract Disclosure: A. Zuberi: None. Y. Huang: None. A. Dotts: None. H. Wei: None. J. Coon V: None. T. Lizuka: None. O. Wu: None. O. Sotos: None. D. Chakravarti: None. Y. Dai: None. S.E. Bulun: None. P. Yin: None. A.Z. and Y.H. contributed equally to this work.† Y.D., S.E.B., and P.Y. are co-senior authors. ‡To whom correspondence should be addressed: Serdar E. Bulun, M.D.Division of Reproductive Science in MedicineDepartment of Obstetrics and Gynecology Feinberg School of Medicine at Northwestern University 250 E. Superior Street, Suite 03-2306 Chicago, Illinois 60611-2914 Tel: 312-472-3636 Fax: 312-472-3740 Email: s-bulun@northwestern.edu Ping Yin, M.D., Ph.D. Division of Reproductive Science in Medicine Department of Obstetrics and Gynecology Feinberg School of Medicine at Northwestern University 303 E. Superior Street, Suite 10-111 Chicago, Illinois 60611 Tel: 312-503-1831 Fax: 312-503-0095 Email: p-yin@northwestern.edu. Conflict of interest: The authors have declared that no conflict of interest exists. Uterine leiomyomas (LM) cause heavy menstrual bleeding, anemia and pregnancy loss in approximately 10 million US women. Driver mutations in the mediator complex subunit 12 (MED12) gene in uterine myometrial cells initiate 70% LM tumors that grow in a progesterone-dependent manner. We showed a distinct chromatin occupancy landscape of MED12 and a shift of binding sites from proximal promoters to intronic/intergenic regions in mutant (mut-MED12) vs wild-type LM tissues. Integration of cistrome and transcriptome data identified tryptophan 2,3-dioxygenase (TDO2) as the top mut-MED12 target gene, which was massively upregulated in mut-MED12 LM. TDO2 catalyzes the conversion of tryptophan to kynurenine, which is an aryl hydrocarbon receptor (AHR) ligand and significantly elevated in mut-MED12 LM. Incubation of primary mut-MED12 LM cells with tryptophan or kynurenine stimulated AHR nuclear translocation, increased proliferation, inhibited apoptosis and induced AHR-target gene expression, whereas blocking the TDO2-kynurenine-AHR pathway by siRNA or pharmacologically abolished these effects. Progesterone receptor regulated the expression of AHR and its target genes. In vivo, TDO2 expression positively correlated with the expression of genes crucial for LM growth. In summary, activation of the TDO2-kynurenine-AHR pathway selectively in mut-MED12 LM induces tumor growth and may inform the development of targeted treatments and precision medicine. Presentation: Thursday, June 15, 2023

OR2801 Novel Cis-Regulatory Mechanisms Of Lhb Transcription By Non-Coding RNAs And Non-Canonical DNA Structures

Abstract Disclosure: T. Refael: None. H. Gruber: None. G. Golan: None. L. Pnueli: None. P. Melamed: None. Expression of the Lhb gene was shown previously to be directed by synergistic actions of lineage-specific transcription factors at conserved regions of the proximal promoter. However extensive genomic analysis during the last few decades has expanded the repertoire of factors we now know to be involved in transcriptional regulation, revealing roles for distal transcriptional enhancers and long non-coding RNAs (lncRNAs), whose modes of action are only beginning to be elucidated1. Recently it has also become evident that regulatory regions of the genome are enriched with non-canonical DNA structures. These include G-quadruplexes (G4s) which form on guanine-rich stretches of single-stranded DNA and iMotifs (iMs) on the complementary strand, and are reported to bind various proteins which presumably regulate and mediate their actions. We identified in available mice pituitary scATAC-seq data a region of gonadotrope-specific open chromatin upstream of the Lhb gene, and chromatin conformation capture (3C) in murine gonadotrope cell lines indicated the distal sites that are in physical proximity to the Lhb promoter. Further, we show by chromatin immunoprecipitation (ChIP) a peak of H3K4 monomethylation (H3K4me1) ∼3 kbp upstream of the Lhb TSS, and transcription of two bi-directional non-coding enhancer RNAs (eRNAs), both of which are characteristic of transcriptional enhancers. One of the eRNAs was found to direct open chromatin at the Lhb promoter and is required for Lhb transcription, while guide RNA-mediated recruitment of dCas9- KRAB or dCas9-VP64 to this locus altered Lhb mRNA levels accordingly, confirming its functional enhancer activity. However this enhancer activity is not sufficient for optimal Lhb transcription, and we found that splicing in situ of a distinct downstream lncRNA is also required. The DNA at the central non-coding region of the enhancer, and at the promoter of this lncRNA, forms G4 and iM structures, seen by circular dichroism and ChIP. These DNA structures are affected differentially by local conditions including changes in pH or hormonal treatments, and appear to have diverse effects. HMGB2, which is known to bind structured DNA, was found to bind the enhancer iM in cells and in vitro. Further, HMGB2 knockdown reduced the iM signal and Lhb mRNA, eRNA and lncRNA expression levels quite dramatically. We thus present novel elements involved in the regulation of Lhb transcription through various classes of non-coding RNAs and DNA structures, while emphasizing the complexity of transcriptional regulation via context-dependent cis-acting elements.