Classical sickle beta-globin haplotypes exhibit a high degree of long-range haplotype similarity in African and Afro-Caribbean populations

Abstract Manipulating gene regulation to favor gamma-globin transcription over beta-globin transcription has been a goal of research in erythropoiesis for decades because of its relevance to amelioration of the pathophysiology of sickle cell disease and beta-thalassemia. A fundamental unanswered question in biology is how the unique pattern of gene expression, the transcriptome, of the many different individual mammalian cell types arises from the same genome blueprint and changes during development and differentiation. There is a growing appreciation that genome organization and the folding of chromosomes is a key determinant of gene transcription. Within this framework, enhancers function to increase the transcription of target genes over long linear distances. To accomplish this, enhancers engage in close physical contact with target promoters through chromosome folding, or looping. These long range interactions are orchestrated by cell type specific proteins and protein complexes that bind to enhancers and promoters and stabilize their interaction with each other. We have been studying LDB1, a member of an erythroid protein complex containing GATA1, TAL1 and LMO2. The LDB1complex activates erythroid genes through occupancy of virtually all erythroid enhancers. LDB1engages in homo- and heterotypic interactions with proteins occupying the promoters of erythroid genes to bring them into proximity with their enhancers. We find that enhancer long range looping activity can be redirected. Both targeting of the beta-globin locus control region to the gamma-globin gene in adult erythroid cells by the tethering of LDB1 or epigenetic unmasking of a silenced gamma-globin gene lead to increased locus control region (LCR)/gamma-globin contact frequency and reduced LCR/beta-globin contact. The outcome of these manipulations is robust, pan-cellular gamma-globin transcription activation with a concomitant reduction in beta-globin transcription. These examples suggest that chromosome looping can be considered a therapeutic target for gene activation or gene silencing to ameliorate genetic diseases such as sickle cell disease and beta-thalassemia. Disclosures No relevant conflicts of interest to declare.

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The ranges of the α-particles from the radioactive emanations and “A” products and from polonium

Proceedings of the Royal Society of London. Series A, Containing Papers of a Mathematical and Physical Character ◽

10.1098/rspa.1932.0086 ◽

1932 ◽

Vol 136 (829) ◽

pp. 349-363 ◽

Cited By ~ 20

Keyword(s):

Long Range ◽

Point Of View ◽

Counting Methods ◽

Γ Rays ◽

The Mean ◽

High Degree ◽

Α Particles

The analysis of groups of α-particles by new counting methods has been described in previous papers, in which details have been given of the examination of the α-particles emitted by radium-C and -C' thorium-C and -C', and actinium-C and -C', including the long range particles. The methods have the advantage that any appreciable inhomogeneity of a group of α-particles is readily detected, and moreover, the mean range of a group may be directly measured with a high degree of precision. The experiments have now been extended to an examination of the α-particles emitted by the emanations and “A” products of the three radioactive series, and by polonium. The examination of these α-ray groups is not only of great interest from the point of view of the radioactive transformations, but also for the possible connection with the emission of γ-rays.

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CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus

Blood Cells Molecules and Diseases ◽

10.1016/j.bcmd.2006.10.131 ◽

2007 ◽

Vol 38 (2) ◽

pp. 178

Author(s):

Erik Splinter ◽

Helen Heath ◽

Jurgen Kooren ◽

Robert-Jan Palstra ◽

Petra Klous ◽

...

Keyword(s):

Histone Modification ◽

Long Range ◽

Beta Globin ◽

Chromatin Looping

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Dislocation loops on cube planes in long range ordered Cu3Au

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100175545 ◽

1990 ◽

Vol 48 (4) ◽

pp. 482-483

Author(s):

Ch. Rentenberger ◽

H. P. Karnthaler

Keyword(s):

Long Range ◽

Domain Size ◽

Antiphase Boundary ◽

Theoretical Models ◽

Main Role ◽

Gold Content ◽

Dislocation Loops ◽

Thin Foils ◽

Increasing Temperature ◽

High Degree

Long range ordered Cu3Au exhibits like other L12 ordered alloys an anomalous increase in the yield strength with increasing temperature. Dislocations which have an antiphase boundary APB fault on the cube plane play a main role in theoretical models that have been proposed to explain this anomaly. In this investigation two types of loops are studied that occur on cube planes. From the measured dissociaton widths of the superlattice dislocations the value of the APB energy can be determined. Different values have been achieved for octahedral and cube planes; they can be compared with previous measurements and with the theoretical models.Single crystals of Cu3Au were grown under vacuum and subsequently annealed to achieve a high degree of order and a large domain size. The crystals were deformed in tension at room temperature. For the TEM investigation discs were cut parallel to the primary octahedral glide plane and to the cube cross slip plane. The preparation of the thin foils is rather difficult because of the large gold content.

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Long Range Sequencing Shows Improved Resolution in the Detection of Beta Globin Cluster Variants

Blood ◽

10.1182/blood-2019-130652 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 3548-3548

Author(s):

Aruna Rangan ◽

Molly S. Hein ◽

Tejaswi Koganti ◽

William G. Jenkinson ◽

Christopher A. Hilker ◽

...

Keyword(s):

Long Range ◽

Short Range ◽

Array Cgh ◽

Globin Gene ◽

Consensus Sequence ◽

Read Length ◽

Compound Heterozygous ◽

Beta Globin ◽

Sequencing Technology ◽

Hb S

Introduction: Globin gene sequencing has long been impeded by repetitive regions, homology and structural variation. Currently, long-read sequencing technology has been limited by high cost and error rate. These challenges can be mitigated by sample multiplexing of targeted capture sequencing and the use of consensus reads, respectively. This ongoing study analyzes the utility of long range sequencing technology in identifying historically problematic beta globin cluster mutations. Materials and methods: Long range sequencing was performed on complex beta globin gene cluster cases utilizing the Sequel platform (Pacific Biosciences, Menlo Park, California, United States). Sample input was 1 microgram of DNA extracted from whole blood. Circular Consensus Sequence (CCS) FASTQ sequences files were mapped to reference genome (GRCh37/hg19) using NGMLR, followed by annotation of variants using a custom bioinformatics workflow. Comparison to multiplex ligation-dependent probe amplification (MLPA), Sanger sequencing, array CGH, short-range NGS (300 bp), hemoglobin protein, and clinical data was performed. Results: CCS read length varied from 1 to 10 kb, average 3.5. Analysis of the beta globin cluster region showed impressive superiority and comprehensiveness to Sanger, MLPA, array CGH and short range sequencing technology: 1) single nucleotide variants (SNVs) were identified to a sensitivity and specificity of 99.5%; 2) large structural variants (SVs) such as large deletions, duplications, insertions, crossovers and fusions spanning many kilobases were characterized in the heterozygous, homozygous and compound heterozygous state to a precise genomic coordinate (table 1); 3) phasing SNVs identified Hb S haplotypes (Central African region (CAR), Benin, Senegal, Arab-Indian and Cameroon). Conclusion: 1) Long range sequencing holds significant promise in genotyping hemoglobin disorders. This method improves efficiency with potential for a single test offering with increased resolution, particularly in large deletion analysis. Complex cases greatly benefited from improved range and resolution. 2) The decreased requirement of blood volume for extensive testing is of particular interest for the pediatric population. 3) Genotyping of Hb S patients detected by positive newborn screening will help predict need for prophylaxis or therapy by assessing variant zygosity, phasing and haplotypes. In conclusion, we believe that long range sequencing has immense potential to contribute extensively to thalassemia and hemoglobinopathy diagnostics and is far superior to the currently available technologies for beta globin cluster analysis. Disclosures Jen: Celgene: Employment.

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Tissue section lifting for electron microscopy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100081292 ◽

1978 ◽

Vol 36 (2) ◽

pp. 86-87

Author(s):

Adrian F. van Dellen

Keyword(s):

Infectious Disease ◽

Electron Microscopy ◽

Tissue Culture ◽

Organ System ◽

Surrounding Tissue ◽

Paraffin Sections ◽

Surface Areas ◽

Specific Determination ◽

High Degree ◽

Accuracy And Repeatability

The morphologic pathologist may require information on the ultrastructure of a non-specific lesion seen under the light microscope before he can make a specific determination. Such lesions, when caused by infectious disease agents, may be sparsely distributed in any organ system. Tissue culture systems, too, may only have widely dispersed foci suitable for ultrastructural study. In these situations, when only a few, small foci in large tissue areas are useful for electron microscopy, it is advantageous to employ a methodology which rapidly selects a single tissue focus that is expected to yield beneficial ultrastructural data from amongst the surrounding tissue. This is in essence what "LIFTING" accomplishes. We have developed LIFTING to a high degree of accuracy and repeatability utilizing the Microlift (Fig 1), and have successfully applied it to tissue culture monolayers, histologic paraffin sections, and tissue blocks with large surface areas that had been initially fixed for either light or electron microscopy.

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Electron Microscopy in Molecular Biology

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100060027 ◽

1967 ◽

Vol 25 ◽

pp. 2-3

Author(s):

Cecil E. Hall

Keyword(s):

Electron Microscopy ◽

Molecular Biology ◽

Noise Level ◽

Molecular Structures ◽

Material Structure ◽

The Arts ◽

Shadow Casting ◽

Electron Image ◽

High Degree ◽

Very High

The visualization of organic macromolecules such as proteins, nucleic acids, viruses and virus components has reached its high degree of effectiveness owing to refinements and reliability of instruments and to the invention of methods for enhancing the structure of these materials within the electron image. The latter techniques have been most important because what can be seen depends upon the molecular and atomic character of the object as modified which is rarely evident in the pristine material. Structure may thus be displayed by the arts of positive and negative staining, shadow casting, replication and other techniques. Enhancement of contrast, which delineates bounds of isolated macromolecules has been effected progressively over the years as illustrated in Figs. 1, 2, 3 and 4 by these methods. We now look to the future wondering what other visions are waiting to be seen. The instrument designers will need to exact from the arts of fabrication the performance that theory has prescribed as well as methods for phase and interference contrast with explorations of the potentialities of very high and very low voltages. Chemistry must play an increasingly important part in future progress by providing specific stain molecules of high visibility, substrates of vanishing “noise” level and means for preservation of molecular structures that usually exist in a solvated condition.

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A High Angle, Double Tilting Cold Stage for the AEI EM7

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100052262 ◽

1974 ◽

Vol 32 ◽

pp. 450-451

Author(s):

P.R. Swann ◽

A.E. Lloyd

Keyword(s):

Habit Plane ◽

Temperature Control ◽

Tilt Angle ◽

Cooling System ◽

Thermal Drift ◽

High Angle ◽

Cold Stage ◽

High Degree ◽

Better Than

Figure 1 shows the design of a specimen stage used for the in situ observation of phase transformations in the temperature range between ambient and −160°C. The design has the following features a high degree of specimen stability during tilting linear tilt actuation about two orthogonal axes for accurate control of tilt angle read-out high angle tilt range for stereo work and habit plane determination simple, robust construction temperature control of better than ±0.5°C minimum thermal drift and transmission of vibration from the cooling system.

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