1273. High Level, Erythroid Lineage-Specific Gene Expression Using Globin Gene Regulatory Elements Following Lentiviral Vector-Mediated Gene Transfer into Primitive Human and Murine Hematopoietic Cells

Condensins are evolutionarily conserved protein complexes that are required for chromosome segregation during cell division and genome organization during interphase. In Caenorhabditis elegans, a specialized condensin, which forms the core of the dosage compensation complex (DCC), binds to and represses X chromosome transcription. Here, we analyzed DCC localization and the effect of DCC depletion on histone modifications, transcription factor binding, and gene expression using chromatin immunoprecipitation sequencing and mRNA sequencing. Across the X, the DCC accumulates at accessible gene regulatory sites in active chromatin and not heterochromatin. The DCC is required for reducing the levels of activating histone modifications, including H3K4me3 and H3K27ac, but not repressive modification H3K9me3. In X-to-autosome fusion chromosomes, DCC spreading into the autosomal sequences locally reduces gene expression, thus establishing a direct link between DCC binding and repression. Together, our results indicate that DCC-mediated transcription repression is associated with a reduction in the activity of X chromosomal gene regulatory elements.

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Gene-regulatory elements may change the amount, timing, or location of gene expression, cis-Regulation therapy platforms might become a gene therapy to treat many genetic diseases

10.31219/osf.io/xc5a2 ◽

2021 ◽

Author(s):

Moataz Dowaidar

Keyword(s):

Gene Expression ◽

Genetic Diseases ◽

Regulatory Elements ◽

Tissue Type ◽

Gene Promoters ◽

Expression Levels ◽

Cis Regulation ◽

Gene Regulatory Elements ◽

Gene Regulatory ◽

Gene Expression Levels

Changes in gene expression levels above or below a particular threshold may have a dramatic impact on phenotypes, leading to a wide spectrum of human illnesses. Gene-regulatory elements, also known as cis-regulatory elements (CREs), may change the amount, timing, or location (cell/tissue type) of gene expression, whereas mutations in a gene's coding sequence may result in lower or higher gene expression levels resulting in protein loss or gain. Loss-of-function mutations in both genes produce recessive human illness, while haploinsufficient mutations in 65 genes are also known to be deleterious due to function gain, according to the ClinVar1 and ClinGen3 databases. CREs are promoters living near to a gene's transcription start site and switching it on at predefined times, places, and levels. Other distal CREs, like enhancers and silencers, are temporal and tissue-specific control promoters. Enhancers activate promoters, commonly referred to as "promoters," whereas silencers turn them off. Insulators also restrict promiscuous interactions between enhancers and gene promoters. Systematic genomic approaches can help understand the cis-regulatory circuitry of gene expression by highly detecting and functionally defining these CREs. This includes the new use of CRISPR–CRISPR-associated protein 9 (CRISPR–Cas9) and other editing approaches to discover CREs. Cis-Regulation therapy (CRT) provides many promises to heal human ailments. CRT may be used to upregulate or downregulate disease-causing genes due to lower or higher levels of expression, and it may also be used to precisely adjust the expression of genes that assist in alleviating disease features. CRT may employ proteins that generate epigenetic modifications like methylation, histone modification, or gene expression regulation looping. Weighing CRT's advantages and downsides against alternative treatment methods is crucial. CRT platforms might become a practical technique to treat many genetic diseases that now lack treatment alternatives if academics, patient communities, clinicians, regulators and industry work together.

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Dynamic changes in cis-regulatory occupancy by Six1 and its cooperative interactions with distinct cofactors drive lineage-specific gene expression programs during progressive differentiation of the auditory sensory epithelium

Nucleic Acids Research ◽

10.1093/nar/gkaa012 ◽

2020 ◽

Vol 48 (6) ◽

pp. 2880-2896 ◽

Cited By ~ 5

Author(s):

Jun Li ◽

Ting Zhang ◽

Aarthi Ramakrishnan ◽

Bernd Fritzsch ◽

Jinshu Xu ◽

...

Keyword(s):

Gene Expression ◽

Regulatory Elements ◽

Sensory Epithelium ◽

Hair Bundle ◽

Specific Gene ◽

Cell Type ◽

Specific Gene Expression ◽

Wide Range ◽

Cell Type Specific ◽

Lineage Specific Gene

Abstract The transcription factor Six1 is essential for induction of sensory cell fate and formation of auditory sensory epithelium, but how it activates gene expression programs to generate distinct cell-types remains unknown. Here, we perform genome-wide characterization of Six1 binding at different stages of auditory sensory epithelium development and find that Six1-binding to cis-regulatory elements changes dramatically at cell-state transitions. Intriguingly, Six1 pre-occupies enhancers of cell-type-specific regulators and effectors before their expression. We demonstrate in-vivo cell-type-specific activity of Six1-bound novel enhancers of Pbx1, Fgf8, Dusp6, Vangl2, the hair-cell master regulator Atoh1 and a cascade of Atoh1’s downstream factors, including Pou4f3 and Gfi1. A subset of Six1-bound sites carry consensus-sequences for its downstream factors, including Atoh1, Gfi1, Pou4f3, Gata3 and Pbx1, all of which physically interact with Six1. Motif analysis identifies RFX/X-box as one of the most significantly enriched motifs in Six1-bound sites, and we demonstrate that Six1-RFX proteins cooperatively regulate gene expression through binding to SIX:RFX-motifs. Six1 targets a wide range of hair-bundle regulators and late Six1 deletion disrupts hair-bundle polarity. This study provides a mechanistic understanding of how Six1 cooperates with distinct cofactors in feedforward loops to control lineage-specific gene expression programs during progressive differentiation of the auditory sensory epithelium.

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Scavenger receptor A gene regulatory elements target gene expression to macrophages and to foam cells of atherosclerotic lesions.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.92.12.5391 ◽

1995 ◽

Vol 92 (12) ◽

pp. 5391-5395 ◽

Cited By ~ 84

Author(s):

A. Horvai ◽

W. Palinski ◽

H. Wu ◽

K. S. Moulton ◽

K. Kalla ◽

...

Keyword(s):

Gene Expression ◽

Target Gene ◽

Scavenger Receptor ◽

Foam Cells ◽

Regulatory Elements ◽

Target Gene Expression ◽

Atherosclerotic Lesions ◽

Gene Regulatory Elements ◽

Scavenger Receptor A ◽

Gene Regulatory

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Genetic Determinants of Hemolysis in Sickle Cell Anemia.

Blood ◽

10.1182/blood.v120.21.2104.2104 ◽

2012 ◽

Vol 120 (21) ◽

pp. 2104-2104

Author(s):

Jacqueline N Milton ◽

Helen Rooks ◽

Emma Drasar ◽

Elizabeth L McCabe ◽

Clinton T. Baldwin ◽

...

Keyword(s):

Sickle Cell ◽

Sickle Cell Anemia ◽

Globin Gene ◽

Principal Component ◽

Regulatory Elements ◽

Intravascular Hemolysis ◽

Plasma Hemoglobin ◽

Hypersensitive Sites ◽

Gene Regulatory Elements ◽

Gene Regulatory

Abstract Abstract 2104 The phenotype of sickle cell disease is caused by sickle vasoocclusion and hemolytic anemia. Hemolysis in sickle cell anemia has been associated with complications that were presumed to result in part from vascular nitric oxide depletion due to scavenging by free plasma hemoglobin. Though plasma hemoglobin is a specific marker of intravascular hemolysis and red cell survival studies are the most definitive method of establishing the extent of hemolysis, these tests are rarely done and not available in large cohorts. However, the intensity of hemolysis can be estimated by the reticulocyte count, lactate dehydrogenase (LDH), aspartate aminotransaminase (AST) and bilirubin levels, all of which are commonly measured in cohort studies, although none of which is specific for hemolysis. We previously reported the results of a genome-wide association study (GWAS) of hemolysis where we used as a phenotype a new measure of the rate of intravascular hemolysis appropriate for cohort studies and GWAS. Using a principal component analysis of the commonly measured markers of hemolysis we derived a hemolytic score and found that the top SNPs associated with this score included a variant located in the first intron of NPRL3 (rs7203560; chr16p13.3, p=6.04×10−07) This result was replicated in two additional cohorts of 549 and 296 patients. We also established that while rs7203560 was associated with the ∝3.7 thalassemia gene deletion, when adjusted for HbF and ∝ thalassemia the association of NPRL3 with the hemolytic score remained significant (p=0.00375) and this association was also significant when examining only cases without ∝ thalassemia (p=0.02463). To further validate these results we studied 213 additional adult sickle cell anemia patients from King's College Hospital, London, UK. The mean age of these patients was 33 years. None had been treated with hydroxyurea and lab parameters obtained 3 months after, if transfused. Patients had similar clinical characteristics. The hemolytic score was calculated by using principal component analysis of the same markers of hemolysis. The SNPs associated with the hemolytic score in the primary study were genotyped in this cohort using TaqMan SNP genotyping assays according to standard Applied Biosystems protocol and their association with the derived hemolytic score studies using the same additive genetic model. The SNP rs7203560 replicated the association with hemolytic score (p= 0.03674) in this cohort. To examine the linkage disequilibrium (LD) structure of the region, we looked for conserved sequences in the α- globin cluster in multiple divergent species using the Basic Local Alignment Sequencing Tool (BLAST) to identify the approximate locations of the hypersensitive sites that are the major α-globin gene regulatory elements. On examination of the LD structure of SNPs in these regions with rs7203560, we found that rs7203560 was in LD with several SNPs located in and near the hypersensitive sites including rs2238368 (D'=1), rs2541612 (D'=0.89) and rs3331107 (D'=0.61). We hypothesize that rs7203560 is a marker for one or more variants in the major α-globin gene regulatory elements that down-regulate α-globin gene expression and cause a mild α thalassemia-like effect. In sickle cell anemia, perhaps by independently down-regulating expression of the α-globin genes, variants of the major ∝-globin gene regulatory loci reduce HbS concentration, lessen the polymerization potential of deoxy sickle hemoglobin and therefore retard hemolysis. Disclosures: No relevant conflicts of interest to declare.

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Cis-Regulatory Elements Required for a Lineage-Specific Gene Expression in the Sea Urchin Embryo

American Zoologist ◽

10.1093/icb/31.3.490 ◽

1991 ◽

Vol 31 (3) ◽

pp. 490-492

Author(s):

ROBERTA R. FRANKS

Keyword(s):

Gene Expression ◽

Sea Urchin ◽

Regulatory Elements ◽

Specific Gene ◽

Specific Gene Expression ◽

Sea Urchin Embryo ◽

Lineage Specific Gene

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BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome

10.1101/2020.11.13.381251 ◽

2020 ◽

Author(s):

Nadezda A. Fursova ◽

Anne H. Turberfield ◽

Neil P. Blackledge ◽

Emma L. Findlater ◽

Anna Lastuvkova ◽

...

Keyword(s):

Gene Expression ◽

Histone Modifications ◽

Transcription Initiation ◽

Target Genes ◽

Regulatory Elements ◽

Polycomb Group ◽

Gene Promoters ◽

Histone H2a ◽

Gene Regulatory Elements ◽

Gene Regulatory

AbstractHistone-modifying systems play fundamental roles in gene regulation and the development of multicellular organisms. Histone modifications that are enriched at gene regulatory elements have been heavily studied, but the function of modifications that are found more broadly throughout the genome remains poorly understood. This is exemplified by histone H2A mono-ubiquitylation (H2AK119ub1) which is enriched at Polycomb-repressed gene promoters, but also covers the genome at lower levels. Here, using inducible genetic perturbations and quantitative genomics, we discover that the BAP1 deubiquitylase plays an essential role in constraining H2AK119ub1 throughout the genome. Removal of BAP1 leads to pervasive accumulation of H2AK119ub1, which causes widespread reductions in gene expression. We show that elevated H2AK119ub1 represses gene expression by counteracting transcription initiation from gene regulatory elements, causing reductions in transcription-associated histone modifications. Furthermore, failure to constrain pervasive H2AK119ub1 compromises Polycomb complex occupancy at a subset of Polycomb target genes leading to their derepression, therefore explaining the original genetic characterisation of BAP1 as a Polycomb group gene. Together, these observations reveal that the transcriptional potential of the genome can be modulated by regulating the levels of a pervasive histone modification, without the need for elaborate gene-specific targeting mechanisms.

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The interdependence of gene-regulatory elements and the 3D genome

The Journal of Cell Biology ◽

10.1083/jcb.201809040 ◽

2018 ◽

Vol 218 (1) ◽

pp. 12-26 ◽

Cited By ~ 20

Author(s):

Marit W. Vermunt ◽

Di Zhang ◽

Gerd A. Blobel

Keyword(s):

Gene Expression ◽

Molecular Mechanisms ◽

Regulatory Elements ◽

3D Genome ◽

Gene Positioning ◽

Transcriptional Changes ◽

Gene Regulatory Elements ◽

Chromatin Folding ◽

Gene Regulatory ◽

Relationship Of

Imaging studies, high-resolution chromatin conformation maps, and genome-wide occupancy data of architectural proteins have revealed that genome topology is tightly intertwined with gene expression. Cross-talk between gene-regulatory elements is often organized within insulated neighborhoods, and regulatory cues that induce transcriptional changes can reshape chromatin folding patterns and gene positioning within the nucleus. The cause–consequence relationship of genome architecture and gene expression is intricate, and its molecular mechanisms are under intense investigation. Here, we review the interdependency of transcription and genome organization with emphasis on enhancer–promoter contacts in gene regulation.

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