Gene Desert Research Articles

A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival

Approximately a quarter of the human genome consists of gene deserts, large regions devoid of genes often located adjacent to developmental genes and thought to contribute to their regulation. However, defining the regulatory functions embedded within these deserts is challenging due to their large size. Here, we explore the cis-regulatory architecture of a gene desert flanking the Shox2 gene, which encodes a transcription factor indispensable for proximal limb, craniofacial, and cardiac pacemaker development. We identify the gene desert as a regulatory hub containing more than 15 distinct enhancers recapitulating anatomical subdomains of Shox2 expression. Ablation of the gene desert leads to embryonic lethality due to Shox2 depletion in the cardiac sinus venosus, caused in part by the loss of a specific distal enhancer. The gene desert is also required for stylopod morphogenesis, mediated via distributed proximal limb enhancers. In summary, our study establishes a multi-layered role of the Shox2 gene desert in orchestrating pleiotropic developmental expression through modular arrangement and coordinated dynamics of tissue-specific enhancers.

Abstract Mo084: Stem Cell-Based Functional Genomics Unravel A Novel Vascular Smooth Muscle Cell State Induced By The 9p21 Coronary Artery Disease Risk Locus

Background: Genome-wide association studies have identified common genetic variants (Single Nucleotide Polymorphisms – SNPs) at ~300 human genomic loci linked to coronary artery disease (CAD) susceptibility. Among these genomic regions, the most impactful is the 9p21.3 CAD risk locus, which spans a 60 kb gene desert and encompasses ~80 SNPs in high linkage disequilibrium. We have previously generated isogenic induced Pluripotent Stem Cells (iPSCs) lines from risk and non-risk donors at 9p21.3 and performed a complete deletion of the locus. By using iPSC-derived vascular smooth muscle cells (iPSC-VSMCs) we demonstrated that the risk haplotype at 9p21.3 causes altered expression of numerous genes essential for muscle function, including contraction and adhesion. Notably, deletion of the risk haplotype restores the non-risk phenotype, suggesting a gain of function effect. Here, we aimed to identify the transcriptomic signature and state trajectories of VSMCs induced by the 9p21.3 risk haplotype and validate them through functional assays and ex-vivo analysis of human coronary arteries. Methods: We have used iPSCs from individuals carrying the risk and non-risk haplotype at 9p21.3 and isogenic knockout lines. After VSMCs differentiation induction, mature VSMCs were used for single cell RNA sequencing using 10X Chromium platform and functional assays. Results: Our analysis revealed that the 9p21.3 risk haplotype prompts VSMCs to acquire a novel cellular state showing reduced plasticity and divergent from other VSMC states previously linked to CAD. We found markers of alternative lineages, including osteogenic and neuronal, coupled with altered expression of genes within other CAD loci, and functional defects. We identified a set of new molecular markers crucial to define risk-associated VSMCs and uncovered their upstream regulators. Conclusions: Our study provides insights into CAD pathogenesis driven by the 9p21.3 risk locus and identified new gene regulatory networks essential for maintaining the normal functionality of the muscle layer of the arteries. Leveraging the power of iPSCs we present novel concepts about the biology of VSMCs and shed light on the impact of the strongest CAD genetic risk factor in preserving a healthy cellular state within the vasculature.

The 9p21.3 coronary artery disease risk locus drives vascular smooth muscle cells to an osteochondrogenic state.

Genome-wide association studies have identified common genetic variants at ~400 human genomic loci linked to coronary artery disease (CAD) susceptibility. Among these genomic regions, the most impactful is the 9p21.3 CAD risk locus, which spans a 60 kb gene desert and encompasses ~80 SNPs in high linkage disequilibrium. Despite nearly two decades since its discovery, the functional mechanism of this genomic region remains incompletely resolved. To investigate the transcriptional gene programs mediated by 9p21.3 risk locus, we applied a model of induced pluripotent stem cells (iPSCs) from risk and non-risk donors at 9p21.3, as well as isogenic lines with a full haplotype deletion. Upon differentiation to vascular smooth muscle cells (VSMC), single-cell transcriptomic profiling demonstrated iPSC-VSMC phenotypes resembling those from native human coronary arteries, confirming the robustness of this model. Remarkably, our analyses revealed that VSMCs harboring the 9p21.3 risk haplotype preferentially adopt an osteochondrogenic state. Importantly, we identified LIMCH1 and CRABP1 as signature genes critical for defining this transcriptional program. Our study provides new insights into the mechanism at the 9p21.3 risk locus and defines its role in driving a disease-prone transcriptional state in VSMCs.

Extrachromosomal circular DNA promotes prostate cancer progression through the FAM84B/CDKN1B/MYC/WWP1 axis

BackgroundExtrachromosomal circular DNA (eccDNA), a kind of circular DNA that originates from chromosomes, carries complete gene information, particularly the oncogenic genes. This study aimed to examine the contributions of FAM84B induced by eccDNA to prostate cancer (PCa) development and the biomolecules involved.MethodsThe presence of eccDNA in PCa cells and the FAM84B transcripts that eccDNA carries were verified by outward and inward PCR. The effect of inhibition of eccDNA synthesis on FAM84B expression in PCa cells was analyzed by knocking down Lig3. The impact of FAM84B on the growth and metastases of PCa cells was verified by Cell Counting Kit-8 (CCK8), EdU, transwell assays, and a xenograft mouse model. Chromatin immunoprecipitation quantitative PCR (ChIP-qPCR) and dual-luciferase reporter assays were carried out to examine the effect of FAM84B/MYC on WWP1 transcription, and a co-immunoprecipitation (Co-IP) assay was conducted to verify the modification of CDKN1B by WWP1. The function of this molecular axis in PCa was explored by rescue assays.ResultsThe inhibited eccDNA synthesis significantly downregulated FAM84B in PCa cells, thereby attenuating the growth and metastasis of PCa. FAM84B promoted the transcription of WWP1 by MYC by activating the expression of MYC coterminous with the 8q24.21 gene desert in a beta catenin-dependent approach. WWP1 transcription promoted by MYC facilitated the ubiquitination and degradation of CDKN1B protein and inversely attenuated the repressive effect of CDKN1B on MYC expression. Exogenous overexpression of CDKN1B blocked FAM84B-activated MYC/WWP1 expression, thereby inhibiting PCa progression.ConclusionsFAM84B promoted by eccDNA mediates degradation of CDKN1B via MYC/WWP1, thereby accelerating PCa progression.

A disease-associated gene desert directs macrophage inflammation through ETS2

Increasing rates of autoimmune and inflammatory disease present a burgeoning threat to human health1. This is compounded by the limited efficacy of available treatments1 and high failure rates during drug development2, highlighting an urgent need to better understand disease mechanisms. Here we show how functional genomics could address this challenge. By investigating an intergenic haplotype on chr21q22—which has been independently linked to inflammatory bowel disease, ankylosing spondylitis, primary sclerosing cholangitis and Takayasu’s arteritis3–6—we identify that the causal gene, ETS2, is a central regulator of human inflammatory macrophages and delineate the shared disease mechanism that amplifies ETS2 expression. Genes regulated by ETS2 were prominently expressed in diseased tissues and more enriched for inflammatory bowel disease GWAS hits than most previously described pathways. Overexpressing ETS2 in resting macrophages reproduced the inflammatory state observed in chr21q22-associated diseases, with upregulation of multiple drug targets, including TNF and IL-23. Using a database of cellular signatures7, we identified drugs that might modulate this pathway and validated the potent anti-inflammatory activity of one class of small molecules in vitro and ex vivo. Together, this illustrates the power of functional genomics, applied directly in primary human cells, to identify immune-mediated disease mechanisms and potential therapeutic opportunities.

Mapping putative enhancers in mouse oocytes and early embryos reveals TCF3/12 as key folliculogenesis regulators.

Dynamic epigenomic reprogramming occurs during mammalian oocyte maturation and early development. However, the underlying transcription circuitry remains poorly characterized. By mapping cis-regulatory elements using H3K27ac, we identified putative enhancers in mouse oocytes and early embryos distinct from those in adult tissues, enabling global transitions of regulatory landscapes around fertilization and implantation. Gene deserts harbour prevalent putative enhancers in fully grown oocytes linked to oocyte-specific genes and repeat activation. Embryo-specific enhancers are primed before zygotic genome activation and are restricted by oocyte-inherited H3K27me3. Putative enhancers in oocytes often manifest H3K4me3, bidirectional transcription, Pol II binding and can drive transcription in STARR-seq and a reporter assay. Finally, motif analysis of these elements identified crucial regulators of oogenesis, TCF3 and TCF12, the deficiency of which impairs activation of key oocyte genes and folliculogenesis. These data reveal distinctive regulatory landscapes and their interacting transcription factors that underpin the development of mammalian oocytes and early embryos.

Ectopic Pitx2 expression and sinoatrial node dysfunction in mice recapitulating a novel cardiac syndrome identified in unrelated families with deletions in a gene desert on chromosome 4q25

Abstract Funding Acknowledgements Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Dutch Research Councin/NWO Introduction Several unrelated families presenting with a complex, heterogeneous cardiac syndrome including sinoatrial node dysfunction and atrial fibrillation were found to share overlapping deletions in a 1.5 Megabase pair gene desert on chromosome 4q25. These overlapping regions contain evolutionarily conserved CTCF binding sites that modulate the separation of topologically associating domains containing the transcription factor-encoding gene PITX2 and noncoding RNA genes. Aim To understand mechanistically how the deletion in the gene desert causes sinoatrial node dysfunction and atrial arrhythmias. Methods Mice lacking the orthologue of the minimally overlapping genomic region deleted in affected patients were generated. Electrophysiology, morphology, tissue composition, and transcriptomes were analysed in this mouse model. Results These mice recapitulated major morpho-functional features of the syndrome, including sinoatrial node dysfunction and atrial arrhythmogenesis . Out of the 15 genes flanking the gene desert, only Pitx2 expression was deregulated in the sinoatrial node. During development, cardiac Pitx2c expression is normally restricted to the left side where it drives left sinus venosus and left atrial morphogenesis and prevents the formation of a left-sided sinoatrial node. The PITX2 locus has also been associated with atrial fibrillation in GWAS. Immunohistochemistry together with 3D volume analysis showed that Pitx2c was ectopically expressed in half of the pacemaker cardiomyocytes of the developing and postnatal sinoatrial node while its expression in the left atrium was maintained. Key transcription factors that drive pacemaker cell differentiation, Tbx3, Isl1 and Shox2, were lost where Pitx2c was ectopically expressed. Moreover, a conserved long non-coding RNA (Playrr) previously linked to Pitx2 regulation in the developing dorsal mesentery, was downregulated in the sinoatrial node of homozygous mutants. The downregulation of the pacemaker gene program additionally coincided with the activation of the atrial myocardial gene program in half of the pacemaker cardiomyocytes. Conclusion We generated a mouse model of a novel human cardiac syndrome including sinoatrial node dysfunction associated with the deletion of critical CTCF binding sites in a gene desert on chromosome 4q25. This deletion induced ectopic Pitx2c expression in the sinoatrial node alongside a substantial loss of pacemaker cardiomyocyte identity and a gain in a working atrial myocardium-like phenotype in the sinoatrial node of affected mice.Loss of pacemaker cardiomyocyte identitySinoatrial node dysfunction in mutants

Regulation of Myc transcription by an enhancer cluster dedicated to pluripotency and early embryonic expression

MYC plays various roles in pluripotent stem cells, including the promotion of somatic cell reprogramming to pluripotency, the regulation of cell competition and the control of embryonic diapause. However, how Myc expression is regulated in this context remains unknown. The Myc gene lies within a ~ 3-megabase gene desert with multiple cis-regulatory elements. Here we use genomic rearrangements, transgenesis and targeted mutation to analyse Myc regulation in early mouse embryos and pluripotent stem cells. We identify a topologically-associated region that homes enhancers dedicated to Myc transcriptional regulation in stem cells of the pre-implantation and early post-implantation embryo. Within this region, we identify elements exclusively dedicated to Myc regulation in pluripotent cells, with distinct enhancers that sequentially activate during naive and formative pluripotency. Deletion of pluripotency-specific enhancers dampens embryonic stem cell competitive ability. These results identify a topologically defined enhancer cluster dedicated to early embryonic expression and uncover a modular mechanism for the regulation of Myc expression in different states of pluripotency.

Abstract 2072: The 9p21.3 Coronary Artery Disease Risk Locus Induces Cell State Transitions In Vascular Smooth Muscle Cells

Background: Genome-wide association studies have identified common genetic variants (Single Nucleotide Polymorphisms - SNPs) at ~300 human genomic loci linked to coronary artery disease (CAD) susceptibility. Among these genomic regions, the most impactful is the 9p21.3 CAD risk locus, which spans a 60 kb gene desert and encompasses ~80 SNPs in high linkage disequilibrium. We have previously generated isogenic induced Pluripotent Stem Cells (iPSCs) lines from risk and non-risk donors at 9p21.3 and performed a complete deletion of the locus. By using iPSC-derived vascular smooth muscle cells (iPSC-VSMCs) we demonstrated that the risk haplotype at 9p21.3 causes altered expression of numerous genes essential for muscle function, including contraction and adhesion. Notably, deletion of the risk haplotype restores the non-risk phenotype, suggesting a gain of function effect. Hypothesis: The 9p21.3 risk haplotype alters VSMCs plasticity and induces dedifferentiation and alternative lineage acquisition. Aims: Identify transcriptomic signatures and trajectories of VSMCs induced by the 9p21.3 risk haplotype Methods: We have used iPSCs from individuals carrying the risk and non-risk haplotype at 9p21.3 and isogenic knockout lines. After VSMCs differentiation induction, mature VSMCs were used for single cell RNA sequencing using 10X Chromium platform. Results: Our analysis revealed that the 9p21.3 risk haplotype prompts VSMCs to acquire a novel cellular state showing reduced plasticity and divergent from other VSMC states previously linked to CAD. We found markers of alternative lineages, including osteogenic and neuronal, coupled with altered expression of genes within other CAD loci. We identified a set of new molecular markers crucial to define risk-associated VSMCs and uncovered their upstream regulators. Conclusions: Our study provides insights into CAD pathogenesis driven by the 9p21.3 risk locus and identified new gene regulatory networks essential for maintaining the normal functionality of the muscle layer of the arteries. Leveraging the power of iPSCs we present novel concepts about the biology of VSMCs and shed light on the impact of CAD genetic risk factors in preserving a healthy cellular state within the vasculature.

The genomic history and global migration of a windborne pest.

Many insect pests, including the brown planthopper (BPH), undergo windborne migration that is challenging to observe and track. It remains controversial about their migration patterns and largely unknown regarding the underlying genetic basis. By analyzing 360 whole genomes from around the globe, we clarify the genetic sources of worldwide BPHs and illuminate a landscape of BPH migration showing that East Asian populations perform closed-circuit journeys between Indochina and the Far East, while populations of Malay Archipelago and South Asia undergo one-way migration to Indochina. We further find round-trip migration accelerates population differentiation, with highly diverged regions enriching in a gene desert chromosome that is simultaneously the speciation hotspot between BPH and related species. This study not only shows the power of applying genomic approaches to demystify the migration in windborne migrants but also enhances our understanding of how seasonal movements affect speciation and evolution in insects.

TAD boundary deletion causes PITX2-related cardiac electrical and structural defects

While 3D chromatin organization in topologically associating domains (TADs) and loops mediating regulatory element-promoter interactions is crucial for tissue-specific gene regulation, the extent of their involvement in human Mendelian disease is largely unknown. Here, we identify 7 families presenting a new cardiac entity associated with a heterozygous deletion of 2 CTCF binding sites on 4q25, inducing TAD fusion and chromatin conformation remodeling. The CTCF binding sites are located in a gene desert at 1 Mb from the Paired-like homeodomain transcription factor 2 gene (PITX2). By introducing the ortholog of the human deletion in the mouse genome, we recapitulate the patient phenotype and characterize an opposite dysregulation of PITX2 expression in the sinoatrial node (ectopic activation) and ventricle (reduction), respectively. Chromatin conformation assay performed in human induced pluripotent stem cell-derived cardiomyocytes harboring the minimal deletion identified in family#1 reveals a conformation remodeling and fusion of TADs. We conclude that TAD remodeling mediated by deletion of CTCF binding sites causes a new autosomal dominant Mendelian cardiac disorder.

Enhancer Arrays Regulating Developmental Genes: Sox2 Enhancers as a Paradigm.

Enhancers are the primary regulatory DNA sequences in eukaryotes and are mostly located in the non-coding sequences of genes, namely, intergenic regions and introns. The essential characteristic of an enhancer is the ability to activate proximal genes, e.g., a reporter gene in a reporter assay, regardless of orientation, relative position, and distance from the gene. These characteristics are ascribed to the interaction (spatial proximity) of the enhancer sequence and the gene promoter via DNA looping, discussed in the latter part of this chapter.Developmentally regulated genes are associated with multiple enhancers carrying distinct cell and developmental stage specificities, which form arrays on the genome. We discuss the array of enhancers regulating the Sox2 gene as a paradigm. Sox2 enhancers are the best studied enhancers of a single gene in developmental regulation. In addition, the Sox2 gene is located in a genomic region with a very sparse gene distribution (no other protein-coding genes in ~1.6Mb in the mouse genome), termed a "gene desert," which means that most identified enhancers in the region are associated with Sox2 regulation. Furthermore, the importance of the Sox2 gene in stem cell regulation and neural development justifies focusing on Sox2-associated enhancers.

OR22-06 Functional Characterization Of X-linked Genes In Regulating Epigenetic Landscape In Endocrine-resistant Breast Cancer

Abstract Disclosure: E.I. Ramos: None. B. Yang: None. M. Sedano: None. V. Reid: None. K. Diwa: None. A. Hidalgo: None. A. Beard: None. J. Patel: None. S.S. Gadad: None. Studies show that genes transcribed from chromosome X play critical roles in several biological processes. X-linked genes are tightly regulated and expressed in tissues protected from immune surveillance. However, several of them get dysregulated in diseases such as cancer. Intriguingly, genome-wide analyses showed their presence in the previously considered gene deserts in the human genome. Their direct role in estrogen transcription in tamoxifen-resistant breast cancer and biological outcomes are still unknown. To this end, we leveraged the power of functional genomics, including RNA with 4-thiouridine (4sU) coupled with RNA-sequencing and CRISPR-based genetic screening, to identify X-linked genes with a potential role in tamoxifen-directed estrogen-regulated transcription. Through a series of phenotypic assays, we selected a poorly studied transcript, “H19X,” with limited protein-coding potential; RNA-In-Situ-Hybridization revealed its localization to the nucleus. In the current study, we have identified the H19X-controlled estrogen-dependent gene regulatory mechanisms in tamoxifen-resistant estrogen receptor-positive (ER+) breast cancer cells. We manipulated the levels of H19X in tamoxifen-resistant ER+ breast cancer cells to generate a comprehensive list of direct transcripts using 4sU-RNA-seq. Interestingly, H19X regulates the expression of estrogen-driven intergenic, divergent, and antisense transcripts whose promoters are bound by ER-alpha (ERα) binding sites. Mechanistically, ‘Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq)’ revealed that H19X modulates chromatin structure at target regions to control gene expression. In addition, ‘chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing ChIP-seq’ (H3K27ac, H3K27me3) identified a critical role for H19X in controlling the epigenetic landscape in tamoxifen-resistant ER+ breast cancer cells. Collectively, our study sheds light on the molecular functions of X-linked genes and allows us to identify new diagnostic and therapeutic targets in tamoxifen-resistant ER+ breast cancer.S.S.G. is supported by grants from a) The Cancer Prevention and Research Institute of Texas (CPRIT; RR170020); b) Lizanell and Colbert Coldwell foundation; c) The Edward N. and Margaret G. Marsh Foundation; d) The American Cancer Society Presentation: Saturday, June 17, 2023

Identification and characterization of Hand2 upstream genomic enhancers active in developing stomach and limbs.

The bHLH transcription factor HAND2 plays important roles in the development of the embryonic heart, face, limbs, and sympathetic and enteric nervous systems. To define how and when HAND2 regulates these developmental systems, requires understanding the transcriptional regulation of Hand2. Remarkably, Hand2 is flanked by an extensive upstream gene desert containing a potentially diverse enhancer landscape. Here, we screened the regulatory interval 200 kb proximal to Hand2 for putative enhancers using evolutionary conservation and histone marks in Hand2-expressing tissues. H3K27ac signatures across embryonic tissues pointed to only two putative enhancer regions showing deep sequence conservation. Assessment of the transcriptional enhancer potentialof these elementsusing transgenic reporter lines uncovered distinct in vivo enhancer activities in embryonic stomach and limb mesenchyme, respectively. Activity of the identified stomach enhancer was restricted to the developing antrum and showed expression within the smooth muscle and enteric neurons. Surprisingly, the activity pattern of the limb enhancer did not overlap Hand2 mRNA but consistently yielded a defined subectodermal anterior expression pattern within multiple transgenic lines. Together, these results start to uncover the diverse regulatory potential inherent to the Hand2 upstream regulatory interval.

A desert lncRNA HIDEN regulates human endoderm differentiation via interacting with IMP1 and stabilizing FZD5 mRNA

BackgroundExtensive studies have revealed the function and mechanism of lncRNAs in development and differentiation, but the majority have focused on those lncRNAs adjacent to protein-coding genes. In contrast, lncRNAs located in gene deserts are rarely explored. Here, we utilize multiple differentiation systems to dissect the role of a desert lncRNA, HIDEN (human IMP1-associated "desert" definitive endoderm lncRNA), in definitive endoderm differentiation from human pluripotent stem cells.ResultsWe show that desert lncRNAs are highly expressed with cell-stage-specific patterns and conserved subcellular localization during stem cell differentiation. We then focus on the desert lncRNA HIDEN which is upregulated and plays a vital role during human endoderm differentiation. We find depletion of HIDEN by either shRNA or promoter deletion significantly impairs human endoderm differentiation. HIDEN functionally interacts with RNA-binding protein IMP1 (IGF2BP1), which is also required for endoderm differentiation. Loss of HIDEN or IMP1 results in reduced WNT activity, and WNT agonist rescues endoderm differentiation deficiency caused by the depletion of HIDEN or IMP1. Moreover, HIDEN depletion reduces the interaction between IMP1 protein and FZD5 mRNA and causes the destabilization of FZD5 mRNA, which is a WNT receptor and necessary for definitive endoderm differentiation.ConclusionsThese data suggest that desert lncRNA HIDEN facilitates the interaction between IMP1 and FZD5 mRNA, stabilizing FZD5 mRNA which activates WNT signaling and promotes human definitive endoderm differentiation.

OR16-3 Analysis of Testis-Enriched Genes in Estrogen-Dependent Genome Regulation in Breast Cancer

Abstract Emerging studies show that testis-enriched genes play critical roles in several biological processes. The expression of these genes is tightly regulated and limited to immune-privileged organs; however, many of them escape regulation and are aberrantly expressed in several diseases such as cancer. Intriguingly, our genomic analysis revealed that many of them are transcribed from previously considered gene deserts. We also found that a significant number of them are robustly regulated by estrogen and other peptide hormones such as Tumor Necrosis Factor-alpha (TNF alpha). However, their direct role in estrogen-dependent transcriptional regulation and biological outcomes remains unstudied. In this regard, our integrated genomic approach, including RNA with 4-thiouridine (4sU) coupled with RNA-sequencing and CRISPR-based genetic screening, has identified key estrogen-regulated testis-enriched genes that may modulate estrogen-signaling. Through a series of molecular and phenotypic assays, we selected a potential but understudied transcript, which is predominantly localized to the nucleus. Furthermore, in the current study, we have interrogated the functional mechanisms by which selected transcript controls estrogen-dependent gene regulation in estrogen receptor-positive (ER+) breast cancer. We found that the transcript controls estrogen-dependent cell and tumor growth. Additionally, we have manipulated the levels of the transcript in estrogen-receptor-positive (ER+) breast cancer cells employing gain- and loss-of-function studies and performed 4sU-RNA-seq. Interestingly, the transcript modulates the expression of estrogen-driven transcripts that are transcribed from ER-alpha (ERa) binding sites. Mechanistically, the transcript is localized in the nucleus and interacts with chromatin-associated proteins. In addition, our integrated genomic analyses comprising 'Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq)' and 'chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing ChIP-seq' (H3K27ac, H3K27me3) identified a critical role for the transcript in controlling the epigenetic landscape at target gene promoters and enhancers in ER+ breast cancer. Collectively, our data support a functional role for testis-enriched genes in enhancer transcription and chromatin organization. This study sheds light on the molecular functions of testis-enriched genes and presents an opportunity to identify new diagnostic and develop treatment strategies in ER+ breast cancer. S.S.G. is supported by a grant from the Cancer Prevention and Research Institute of Texas (CPRIT; RR170020). S.S.G. is also supported by a grant from Lizanell and Colbert Coldwell foundation. Presentation: Sunday, June 12, 2022 11:30 a.m. - 11:45 a.m.

Cis-regulatory architecture and functions of a gene desert controlling pleiotropic expression and cardiac pacemaker development

Abstract Gene deserts are extensive genomic regions spanning more than 500 kilobases and enriched near developmental genes. Despite their proposed critical roles in development, the enhancer architecture, and biological functions of most gene deserts in mammalian genomes remain unknown. The Shox2 transcription factor is a key regulator of cardiac pacemaker differentiation and at the genomic level is flanked by a centromeric gene desert harboring a multitude of predicted cis-regulatory modules (CRMs). Using CRISPR-Cas9 we demonstrate a requirement of this gene desert for pleiotropic expression and embryonic survival through full control of Shox2 in the sinoatrial node (SAN). To decode the underlying chromatin architecture and CRM logic, we performed region-specific chromatin conformation capture, epigenomic analysis and transgenic in vivo reporter assays. While the Shox2 regulatory landscape was found partitioned into largely tissue-invariant chromatin loops, we identified a surprising cardiac-specific contact domain within the gene desert. Subsequent transgenic analysis revealed clustering of non-cardiac enhancers with activities in limb, craniofacial or neuronal populations in this domain, pointing to a potential tissue-specific 3D-mechanism for enhancer attenuation. In addition, SAN-chromatin assessment and H3K27ac profiling from human fetal cardiac compartments enabled the identification of a unique cardiac enhancer located outside of the contact domain and essential for robust Shox2 levels during cardiac pacemaker development. In summary, our results serve as a blueprint to investigate gene desert function in context to cardiac defects and identify the Shox2 gene desert as a robust cis-regulatory hub indispensable for pleiotropic patterning, cardiac pacemaker differentiation and embryonic survival. Funding Acknowledgement Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Swiss National Science Foundation (SNSF),National Institutes of Health (NIH)

Syndromic cardiac disorder is associated with a non-coding deletion that induces a 3D chromatin remodeling and PITX2 expression dysregulation

Abstract In a first family (family#1), we identified 53 members of whom 17 present a syndromic cardiac disorder characterized by electrical disorders (sinus node dysfunction, atrial fibrillation...) and developmental defects (atrial septal defect, valvopathy, left ventricle non-compaction...) following an autosomal dominant model. Among the affected family members, 6 are implanted with a pacemaker and one experienced a sudden death at 43yo. Despite a strong linkage pointing to the 4q25 region, exome sequencing failed to identify causal variant. Interestingly, 6 additional non-related families presenting the same phenotype have been also identified. Our aims are to identity the causal mutation and the molecular mechanism underlying this complex cardiac syndrome. Genetic study has been performed using whole genome sequencing (WGS). Based on transgenic mouse strains, we assessed the impact of Family#1 mutation on the phenotype and on gene expression. Then, we generated human cardiomyocytes derived iPS cells (CM-iPS) isogenic models to evaluate the epigenome (CUT&RUN and ATAC-seq), transcriptome (RNA-seq) and topological associated domain (TAD) remodelling (Hi-C). By WGS we uncovered a deletion of 15kb in a gene desert area on 4q25, segregating in all affected relatives of Family#1. The 6 other families present overlapping deletions. Mouse model recapitulates the cardiac phenotype and exhibit a dysregulation of Pitx2 expression in cardiac specific compartments. Based on human CM-iPS models, epigenetic data highlight among the 15kb deletion a unique open region containing a CTCF binding site, crucial for delimiting TAD boundaries. Hi-C assay reveals the fusion of 2 TADs and highlights new interactions between PITX2 and atrial specific regulatory elements. We identified a deletion located within a gene desert area associated with a complex cardiac disorder. The CTCF binding site contained in the deletion seems key in the TAD border. The TAD remodelling leads to new (regulatory) interactions and expression dysregulation of PITX2. We describe a new molecular mechanism implying a yet unidentified non-coding regulatory element of PITX2 and responsible for a complex electrical and developmental cardiac syndrome. Funding Acknowledgement Type of funding sources: Public Institution(s). Main funding source(s): Nantes UniversitéFrench national reserch agency (ANR)

Transcriptional regulation of INK4/ARF locus by cis and trans mechanisms.

9p21 locus is one of the most reproducible regions in genome-wide association studies (GWAS). The region harbors CDKN2A/B genes that code for p16INK4a, p15INK4b, and p14ARF proteins, and it also harbors a long gene desert adjacent to these genes. The polymorphisms that are associated with several diseases and cancers are present in these genes and the gene desert region. These proteins are critical cell cycle regulators whose transcriptional dysregulation is strongly linked with cellular regeneration, stemness, aging, and cancers. Given the importance of this locus, intense scientific efforts on understanding the regulation of these genes via promoter-driven mechanisms and recently, via the distal regulatory mechanism have provided major insights. In this review, we describe these mechanisms and propose the ways by which this locus can be targeted in pathologies and aging.

The role of Bcl11b in vascular smooth muscle cell death

Arterial stiffening is a strong independent risk factor for cardiovascular disease. B-cell leukaemia 11b (BCL11B) is a transcription factor known as an essential regulator in T lymphocytes differentiation and neuronal development. Several genome-wide association studies showed that single nucleotide polymorphisms (SNPs) in the 3’gene desert of Bcl11b are associated with a higher susceptibility for aortic stiffness and blood pressure control. However, its role in smooth muscle cells and mechanism of action remains to be uncovered. Our aims are: (1) to analyse the role of Bcl11b in vascular system; (2) to characterize the signalling pathways related to Bcl11b in cell death. Morphological, cellular and molecular analysis were carried out on the arteries of smooth muscle cell-specific Bcl11b-knockout mice at 3, 7, 28 days after tamoxifen injections as well as on the smooth muscle cells isolated from the aorta of Bcl11b-floxed mice that were cultured and inactivated by Cre recombinase using adenoviral vectors. We analysed mice with Bcl11b deletion in vascular SMC (Bcl11b-SMKO). There is no difference between control and mutant mice at the macroscopic level 3 days after Bcl11b KO induction, however, 7 days after Bcl11b inactivation, 70% of the Bcl11b-SMKO mice showed signs of haemorrhage in the distal part of the thoracic aorta near the abdominal aorta. The histological examination of thoracic aorta at day 7 indicated the presence of “bumpy region” in the mutant aorta, these areas seem to be covered by a thicker layer of extracellular matrix and the presence of IgG positive cells, indicating that cell death via necroptosis is occurring in this tissue. Our preliminary results from smooth muscle cell culture indicate higher cell death rate in the mutant cells compared to control cells. Our data suggest a primary effect of Bcl11b inactivation on cell death, probably through necroptosis. The mechanisms linked to cell death induced by Bcl11b loss is under investigation.