Author: Gleixner, E. et al.; Genre: Journal Article; Published in Print: 2008-09; Open Access; Keywords: globin;hyperoxia; hypoxia; respiration; tracheae|br/|; Title: Oxygen-induced changes in hemoglobin expression in Drosophila.

Chromosome conformation capture (3C) technologies can be used to investigate 3D genomic structures. However, high background noise, high costs, and a lack of straightforward noise evaluation in current methods impede the advancement of 3D genomic research. Here we developed a simple digestion-ligation-only Hi-C (DLO Hi-C) technology to explore the 3D landscape of the genome. This method requires only two rounds of digestion and ligation, without the need for biotin labeling and pulldown. Non-ligated DNA was efficiently removed in a cost-effective step by purifying specific linker-ligated DNA fragments. Notably, random ligation could be quickly evaluated in an early quality-control step before sequencing. Moreover, an in situ version of DLO Hi-C using a four-cutter restriction enzyme has been developed. We applied DLO Hi-C to delineate the genomic architecture of THP-1 and K562 cells and uncovered chromosomal translocations. This technology may facilitate investigation of genomic organization, gene

Accumulating evidence converges on the possibility that chromosomes interact with each other to regulate transcription in trans. To systematically explore the epigenetic dimension of such interactions, we devised a strategy termed circular chromosome conformation capture (4C). This approach involves …

We have constructed a minilocus that contains the 5 and 3 flanking regions of the human beta-globin locus and the beta-globin gene. These regions are characterized by erythroid-specific DNAase I-superhypersensitive sites and are normally located approximately 50 kb 5 and 20 kb 3 of the beta-gl …

Takaras Human Beta-globin Control Primer Set contains a set of PCR primers that recognizes the human beta-globin gene at chromosome 11. Beta-globin makes up about half of the human hemoglobin tertrameric protein; in the normal human adult, the hemoglobin tetramer consists of two alpha chains and two beta chains. The Human Beta-globin Control Primer Set may be used as a experimental control during protocols such as PCR ...

Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002 Feb 15;295(5558):1306-11. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 Oct;16(10):1299-309. Fullwood MJ, Han Y, Wei CL, Ruan X, Ruan Y. Chromatin interaction analysis using paired-end tag sequencing. Curr Protoc Mol Biol. 2010 Jan;Chapter 21:Unit 21.15.1-25. Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 2010;11(2):R22. ...

Papillary meningiomas are rare meningeal tumors which are associated with a grim prognosis. These tumors usually recur locally and in some cases they metastasize. The clinical, radiological and histopathological features of a case of a papillary meningioma with a pleural metastasis in a 13-year-old boy are presented. The literature on metastasizing papillary meningiomas is reviewed. Up to now, 131 cases of papillary meningioma have been reported in the literature. Only 8 cases gave rise to metastases outside the central nervous system. The preferential site of metastasis appeared to be the lung. This is the first report of a papillary meningioma giving rise to a metastasis in the pleura.. ...

TY - JOUR. T1 - Modulation of mouse hemoglobin expression by hydroxyurea and erythropoietin in vivo.. AU - Alter, B. P.. AU - Wagner, C. K.. AU - Susser, L. S.. AU - Weinberg, R. S.. PY - 1989. Y1 - 1989. UR - http://www.scopus.com/inward/record.url?scp=0024795799&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=0024795799&partnerID=8YFLogxK. M3 - Article. C2 - 2616578. AN - SCOPUS:0024795799. VL - 316 B. SP - 317. EP - 325. JO - Progress in Clinical and Biological Research. JF - Progress in Clinical and Biological Research. SN - 0361-7742. ER - ...

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Click to launch & play an online audio visual presentation by Dr. Ann Dean on The beta-globin locus, part of a collection of online lectures.

Our chromosome conformation capture kit simplifies chromatin folding studies enabling determination of DNA contact frequencies and chromosome conformation

Imaging and chromosome conformation capture studies have revealed several layers of chromosome organization, including segregation into megabase-sized active

human beta-globin gene inhibits pre-mRNA splicing: a mechanism for beta+-thalassemia. Proc. Natl. Acad. Sci. U.S.A. 86 (3): 1041-5. doi:10.1073/pnas. ...

How is Happy Birthday Brother abbreviated? HBB stands for Happy Birthday Brother. HBB is defined as Happy Birthday Brother very frequently.

Recent evidence suggests that long-range enhancers and gene promoters are in close proximity, which might reflect the formation of chromatin loops. Here, we examined the mechanism for DNA looping at the beta-globin locus. By using chromosome conformation capture (3C), we show that the hematopoietic transcription factor GATA-1 and its cofactor FOG-1 are required for the physical interaction between the beta-globin locus control region (LCR) and the beta-major globin promoter. Kinetic studies reveal that GATA-1-induced loop formation correlates with the onset of beta-globin transcription and occurs independently of new protein synthesis. GATA-1 occupies the beta-major globin promoter normally in fetal liver erythroblasts from mice lacking the LCR, suggesting that GATA-1 binding to the promoter and LCR are independent events that occur prior to loop formation. Together, these data demonstrate that GATA-1 and FOG-1 are essential anchors for a tissue-specific chromatin loop, providing general insights into

Four distinct factors in extracts from murine erythroleukemia (MEL) cells interacted with the human beta-globin gene promoter CAAT box: CP1, GATA-1, and two novel factors, denoted a and b, one of which is highly inducible in the MEL system. GATA-1 binding to the CAAT element was very unstable (half-life | 1 min), whereas bindings of a, b, and CP1 were comparatively stable, with half-lives of 18, 19, and 3.5 min, respectively. Stable transfections of MEL cells showed that in the presence of the beta-globin locus control region (LCR), the wild-type CAAT box, a mutant which bound to GATA-1 with increased stability over the normal sequences, and a mutant which bound a, b, and CP1 specifically could all stimulate transcription greater than ninefold over that induced by a null CAAT mutation in both uninduced and terminally differentiated MEL cells. A mutant which bound the a and b factors specifically gave only a twofold stimulation of promoter activity, and this lower activity correlated with a decrease in

S. Svasti, Suwanmanee, T., Fucharoen, S., Moulton, H. M., Nelson, M. H., Maeda, N., Smithies, O., and Kole, R., RNA repair restores hemoglobin expression in IVS2-654 thalassemic mice., Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 4, pp. 1205-10, 2009. ...

1DXV: High-resolution X-ray study of deoxy recombinant human hemoglobins synthesized from beta-globins having mutated amino termini.

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2006年04月, DNA Structure, Chromatin and Gene Expression, Chapter 14, Involvement of nuclear matrix and chromatin loop formation in the function of insulators., Transworld Research Network, 2006年, 04, 単行本（学術書）, 共編著, Akasaka K. , ...

Reactivation of fetal hemoglobin (HbF) in adults ameliorates the severity of the common β-globin disorders. The transcription factor BCL11A is a critical modulator of hemoglobin switching and HbF silencing, yet the molecular mechanism through which BCL11A coordinates the developmental switch is incompletely understood. Particularly, the identities of BCL11A cooperating protein complexes and their roles in HbF expression and erythroid development remain largely unknown. Here we determine the interacting partner proteins of BCL11A in erythroid cells by a proteomic screen. BCL11A is found within multiprotein complexes consisting of erythroid transcription factors, transcriptional corepressors, and chromatin-modifying enzymes. We show that the lysine-specific demethylase 1 and repressor element-1 silencing transcription factor corepressor 1 (LSD1/CoREST) histone demethylase complex interacts with BCL11A and is required for full developmental silencing of mouse embryonic β-like globin genes and human γ

High-throughput interaction data from novel chromosome interaction assays has become a staple in genomics research. Methods such as high-throughput chromosome conformation capture (Hi-C) and chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) provide researchers with a way of quantifying three-dimensional chromatin architecture, while also gaining insights into which regions in the genome are interacting frequently. A common downstream data-type from these experimental methods is chromatin loop data. Loops are inferred by marking regions in the genome with high frequency of interaction compared to a background. Typically, we are interested in loops because they provide an insulated environment for interaction of genomic regions, as well as a direct mode of contact for regions near the loop anchors. A classic canonical chromatin loop interaction is one that involves enhancer-promoter interactions in the regulation of gene expression. Therefore, a very common workflow involving ...

Chromosomes are folded in the nuclues according to a specific code. This 3D structure of the chromatin directly affects the regulation of genes by facilitating and restricting the contacts regulatory elements can make. Chromosome conformations capture (3C) technologies (4C and HiC) are used by us to measure and visualize chromatin folding and how it is altered by mutations. We study the mechanisms and rules of chromatin folding in vivo in cells/tissues from mouse embryos. This allows us to be a close as possible to the developmental processes and the diseases that are of interest to us. Mutations are produced by genome editing with CRISPR/Cas9 in mouse embryonic stem (ES) cells and mice are then generated by ES cell aggregation. We use the developing limb as a model system to study how gene regulation changes and directs morphogenesis. The limb has many advantages for this sort of study as it is accessible and the developmental steps and the major genes/molecular mechanisms are known. This ...

Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of

In chromosome conformation capture experiments (Hi-C), the accuracy with which contacts are detected varies due to the uneven distribution of restriction

The human HBB complex sequence is a compilation of sequences. Most of the sequences flanking the beta-like globin genes and LCR were determined by Mike Bulger in the Groudine lab, and he generated this compilation. A minimal tiling path of GenBank sequences that in combination will make something close to this compilation (after removing overlaps) is accession numbers AF137396, AF064190, U01317, AF137131, X54282, AF289203 and AF289204. THERE IS A ROUGHLY 6 KB GAP IN THE HUMAN SEQUENCE at position 344746. The gene HOR3beta3 and the 3 breakpoint for the Chinese thalassemia deletion precede this gap, and the 3 breakpoint for HPFH1 and the gene HOR3beta4 follow this gap. This gap was resistant to cloning and sequencing in multiple attempts. The Celera contig also ends in roughly this region. ...

Abstract. Mutations within exon 3 of the beta-globin gene are relatively uncommon, and many of these mutations produce a dominant thalassemia- like phenotype.

Cell-free DNA is detected in blood in many diseases, but also in healthy individuals. Cell-free DNA can originate from necrotic cells or apoptotic …

Question - Medication for Beta-thalassemia. Ask a Doctor about diagnosis, treatment and medication for Thalassemia, Ask a Pediatrician

The HBB gene encodes the β-globin component of hemoglobin. Mutations in this gene affect the shape and functionality of hemoglobin ...

TY - JOUR. T1 - ζ-/-thalassemic mice are affected by two modifying loci and display unanticipated somatic recombination leading to inherited variation. AU - Leder, Aya. AU - McMenamin, Jennifer. AU - Fontaine, Karen. AU - Bishop, Alexander. AU - Leder, Philip. PY - 2005/3/1. Y1 - 2005/3/1. N2 - Thalassemia is a disease caused by a variety of mutations affecting both the adult and embryonic α- and β-globin loci. A mouse strain carrying an embryonic ζ-globin gene disrupted by the insertion of a PGK-Neo cassette displays an α-thalassemia-like syndrome. Embryonic survival of this ζ-null mouse is variable and strongly influenced by genetic background, the 129/SvEv mouse strain displaying a more severe phenotype than C57BL/6. We have identified two modifying loci on C57BL/6 chromosomes 2 and 5, which affect the penetrance of embryonic lethality in the 129/SvEv mouse. Through this work, we were able to observe an interesting effect on somatic recombination events in thalassemic embryos. We show ...

Animal models of β-hemoglobinopathies: utility and limitations Bradley McColl, Jim Vadolas Cell and Gene Therapy Laboratory, Murdoch Childrens Research Institute, Royal Childrens Hospital, Parkville, VIC, Australia Abstract: The structural and functional conservation of hemoglobin throughout mammals has made the laboratory mouse an exceptionally useful organism in which to study both the protein and the individual globin genes. Early researchers looked to the globin genes as an excellent model in which to examine gene regulation - bountifully expressed and displaying a remarkably consistent pattern of developmental activation and silencing. In parallel with the growth of research into expression of the globin genes, mutations within the β-globin gene were identified as the cause of the β-hemoglobinopathies such as sickle cell disease and β-thalassemia. These lines of enquiry stimulated the development of transgenic mouse models, first carrying individual human globin genes and then substantial

To test whether human GATA-1 (hGATA-1) is involved in the transcriptional control of globin gene switching, transgenic mice were produced overexpressing hGATA-1. These were crossed with mice carrying a human beta-globin locus yeast artificial chromosome (beta YAC), and globin gene expression was analyzed in their progeny. Mice carrying both the hGATA-1 and the beta YAC transgenes have normal levels of gamma- and beta-globin mRNA, with no distortion in the rate or in the timing of gamma-to-beta switch, indicating that hGATA-1 is not involved in the developmental control of gamma- and beta-globin genes. In contrast, mice carrying the hGATA-1 and the beta YAC transgenes have 5- to 6-fold lower expression of the human epsilon globin gene compared with beta YAC mice lacking the hGATA-1 transgene. These results provide direct in vivo evidence that hGATA-1 is a specific repressor of human epsilon gene expression. These findings also suggest that binary transgenic mouse systems based on overexpression ...

[Molecular mechanisms of globin gene regulation and disregulation].: Human globin genes are expressed in tissue and developmental stage specific manners. Variou

For a molecule with two titrateable groups ($ \mathrm{HB_\alpha B_\beta H}$) and the following equilibrium constants $$ \mathrm{HBBH \rightleftharpoons BBH + H^+} \ \ K_{\alpha1}$$ $$\mathrm{HBBH \rightleftharpoons HBB + H^+} \ \ K_{\beta1}$$ $$ \mathrm{HBB \rightleftharpoons BB + H^+} \ \ K_{\alpha0}$$ $$\mathrm{BBH \rightleftharpoons BB + H^+} \ \ K_{\beta0}$$ The probability of, for example, $\mathrm{BBH}$ is $$ f_{\mathrm{BBH}} =\mathrm{\frac{[BBH]}{[BB]+[BBH]+[HBB]+[HBBH]}= \frac{[BBH]}{\textit{P}}} $$ $f_{\mathrm{BBH}}$ can be rewritten in terms of pK values $$f_{\mathrm{BBH}} = \mathrm{\frac{[BBH]/[BB]}{\textit{P}/[BB]} = \frac{10^{p\textit{K}_{\beta0}-pH}}{\textit{P}/[BB]}} $$ where $$ \mathrm{ \textit{P}/[BB] = 1+10^{p\textit{K}_{\alpha0}-pH}+10^{p\textit{K}_{\beta0}-pH}+ 10^{p\textit{K}_{\alpha0}+p\textit{K}_{\beta1}-2pH}} $$ Similarly, $$ f_{\mathrm{HBB}} = \mathrm{\frac{10^{p\textit{K}_{\alpha0}-pH}}{\textit{P}/[BB]}} $$ and $$ f_{\mathrm{HBBH}} = ...

For a molecule with two titrateable groups ($ \mathrm{HB_\alpha B_\beta H}$) and the following equilibrium constants $$ \mathrm{HBBH \rightleftharpoons BBH + H^+} \ \ K_{\alpha1}$$ $$\mathrm{HBBH \rightleftharpoons HBB + H^+} \ \ K_{\beta1}$$ $$ \mathrm{HBB \rightleftharpoons BB + H^+} \ \ K_{\alpha0}$$ $$\mathrm{BBH \rightleftharpoons BB + H^+} \ \ K_{\beta0}$$ The probability of, for example, $\mathrm{BBH}$ is $$ f_{\mathrm{BBH}} =\mathrm{\frac{[BBH]}{[BB]+[BBH]+[HBB]+[HBBH]}= \frac{[BBH]}{\textit{P}}} $$ $f_{\mathrm{BBH}}$ can be rewritten in terms of pK values $$f_{\mathrm{BBH}} = \mathrm{\frac{[BBH]/[BB]}{\textit{P}/[BB]} = \frac{10^{p\textit{K}_{\beta0}-pH}}{\textit{P}/[BB]}} $$ where $$ \mathrm{ \textit{P}/[BB] = 1+10^{p\textit{K}_{\alpha0}-pH}+10^{p\textit{K}_{\beta0}-pH}+ 10^{p\textit{K}_{\alpha0}+p\textit{K}_{\beta1}-2pH}} $$ Similarly, $$ f_{\mathrm{HBB}} = \mathrm{\frac{10^{p\textit{K}_{\alpha0}-pH}}{\textit{P}/[BB]}} $$ and $$ f_{\mathrm{HBBH}} = ...

For a molecule with two titrateable groups ($ \mathrm{HB_\alpha B_\beta H}$) and the following equilibrium constants $$ \mathrm{HBBH \rightleftharpoons BBH + H^+} \ \ K_{\alpha1}$$ $$\mathrm{HBBH \rightleftharpoons HBB + H^+} \ \ K_{\beta1}$$ $$ \mathrm{HBB \rightleftharpoons BB + H^+} \ \ K_{\alpha0}$$ $$\mathrm{BBH \rightleftharpoons BB + H^+} \ \ K_{\beta0}$$ The probability of, for example, $\mathrm{BBH}$ is $$ f_{\mathrm{BBH}} =\mathrm{\frac{[BBH]}{[BB]+[BBH]+[HBB]+[HBBH]}= \frac{[BBH]}{\textit{P}}} $$ $f_{\mathrm{BBH}}$ can be rewritten in terms of pK values $$f_{\mathrm{BBH}} = \mathrm{\frac{[BBH]/[BB]}{\textit{P}/[BB]} = \frac{10^{p\textit{K}_{\beta0}-pH}}{\textit{P}/[BB]}} $$ where $$ \mathrm{ \textit{P}/[BB] = 1+10^{p\textit{K}_{\alpha0}-pH}+10^{p\textit{K}_{\beta0}-pH}+ 10^{p\textit{K}_{\alpha0}+p\textit{K}_{\beta1}-2pH}} $$ Similarly, $$ f_{\mathrm{HBB}} = \mathrm{\frac{10^{p\textit{K}_{\alpha0}-pH}}{\textit{P}/[BB]}} $$ and $$ f_{\mathrm{HBBH}} = ...

Adult White Leghorn chickens were rendered anemic by injection with 1-acetyl-2-phenylhydrazine and then treated with parenteral 5-azacytidine, and levels of embryonic globin RNA in circulating reticulocytes were measured. A very small but detectable amount of correctly initiated embryonic p-type globin RNA was detected in reticulocytes from birds treated with 5-azacytidine, while none was detected in reticulocytes from those receiving only phenylhydrazine or phenylhydrazine plus 1-beta-D-arabinofuranosylcytosine (cytosine arabinonucleoside). An attempt to increase embryonic globin RNA induction by treatment with parenteral sodium butyrate after 7 days of 5-azacytidine administration resulted in a 5- to 10-fold increase in the level of embryonic globin RNA. However, sodium butyrate did not induce embryonic gene expression when given alone or after treatment with cytosine arabinonucleoside. Sodium butyrate treatment also caused a DNase I-hypersensitive site to be exposed at the 5 end of the ...

The oxygen transport function of hemoglobin (HB) is thought to have arisen ∼500 million years ago, roughly coinciding with the divergence between jawless (Agnatha) and jawed (Gnathostomata) vertebrates. Intriguingly, extant HBs of jawless and jawed vertebrates were shown to have evolved twice, and independently, from different ancestral globin proteins. This raises the question of whether erythroid-specific expression of HB also evolved twice independently. In all jawed vertebrates studied to date, one of the HB gene clusters is linked to the widely expressed NPRL3 gene. Here we show that the nprl3-linked hb locus of a jawless vertebrate, the river lamprey (Lampetra fluviatilis), shares a range of structural and functional properties with the equivalent jawed vertebrate HB locus. Functional analysis demonstrates that an erythroid-specific enhancer is located in intron 7 of lamprey nprl3, which corresponds to the NPRL3 intron 7 MCS-R1 enhancer of jawed vertebrates. Collectively, our findings signify

The oxygen-transport function of hemoglobin (HB) is thought to have arisen ~500 million years ago, roughly coinciding with the divergence between jawless (Agnatha) and jawed (Gnathostomata) vertebrates. Intriguingly, extant HBs of jawless and jawed vertebrates were shown to have evolved twice, and independently, from different ancestral globin proteins. This raises the question whether erythroid-specific expression of HB also evolved twice independently. In all jawed vertebrates studied to date, one of the Hb gene clusters is linked to the widely expressed Nprl3 gene. Here we show that the nprl3-linked hb locus of a jawless vertebrate, the river lamprey (Lampetra fluviatilis), shares a range of structural and functional properties with the equivalent jawed vertebrate Hb locus. Functional analysis demonstrates that an erythroid-specific enhancer is located in intron 7 of lamprey nprl3, which corresponds to the NPRL3 intron 7 MCS-R1 enhancer of jawed vertebrates. Collectively, our findings signify ...

Levels of fetal hemoglobin (HbF) bearing reticulocytes (F reticulocytes) range from 2% to 50% in patients with sickle cell (SS) anemia. To learn whether any portion of such variation in F cell production is regulated by loci genetically separable from the beta- globin gene cluster, percentages of F reticulocytes were compared in 59 sib pairs composed solely of SS members, including 40 pairs from Jamaica and 19 from the United States. We reasoned that differences in F reticulocyte levels might arise (1) from any of several kinds of artifact, (2) via half-sib status, or (3) because one or more genes regulating F cell production segregate separately from beta S. We minimized the role of artifact by assay of fresh samples from 84 SS individuals, including both members of 38 sib pairs. In 78 of the 84 subjects, serial values for percent F reticulocytes fell within 99.9% confidence limits or were alike by t test (P greater than or equal to .05). This left 32 sib pairs for which F reticulocyte levels ...

951 1234 DNase hypersensitive site 4 4550 4775 DNase hypersensitive site 3 8486 8860 DNase hypersensitive site 2 12752 13769 DNase hypersensitive site 1 116 431 Right Alu 1968 2258 Left Alu 5605 5918 Right Alu 8019 8314 Right Alu 10612 10924 Right Alu 12912 13066 Left L1 14836 15071 Right L1 16918 17218 Left Alu 17940 18231 Right Alu 19486 21080 epsilon-globin gene 19486 19632 Exon 1 19755 19977 Exon 2 20833 21080 Exon 3 23118 31136 Left L1 25885 27987 Left InnerL1 32407 32711 Right Alu 32986 33101 Left L1 34478 36069 G-gamma-globin gene 34478 34622 Exon 1 34745 34967 Exon 2 35854 36069 Exon 3 37921 38039 Left L1 39414 40985 A-gamma-globin gene 39414 39558 Exon 1 39681 39903 Exon 2 40770 40985 Exon 3 42695 43274 Left L1 44788 45108 Right Alu 45658 47272 eta-globin pseudo gene 45658 45800 Exon 1 45922 46144 Exon 2 46997 47272 Exon 3 50895 51198 Left Alu 51976 52276 Right Alu 53222 53540 Left L1 54740 56389 delta-globin gene 54740 54881 Exon 1 55010 55232 Exon 2 56131 56389 Exon 3 62137 63742 ...

Looking for online definition of beta-thalassemia in the Medical Dictionary? beta-thalassemia explanation free. What is beta-thalassemia? Meaning of beta-thalassemia medical term. What does beta-thalassemia mean?

Applications of adenine base editors (ABEs) have been constrained by the limited compatibility of the deoxyadenosine deaminase component with Cas homologs other than SpCas9. We evolved the deaminase component of ABE7.10 using phage-assisted non-continuous and continuous evolution (PANCE and PACE), which resulted in ABE8e. ABE8e contains eight additional mutations that increase activity (kapp) 590-fold compared with that of ABE7.10. ABE8e offers substantially improved editing efficiencies when paired with a variety of Cas9 or Cas12 homologs. ABE8e is more processive than ABE7.10, which could benefit screening, disruption of regulatory regions and multiplex base editing applications. A modest increase in Cas9-dependent and -independent DNA off-target editing, and in transcriptome-wide RNA off-target editing can be ameliorated by the introduction of an additional mutation in the TadA-8e domain. Finally, we show that ABE8e can efficiently install natural mutations that upregulate fetal hemoglobin expression

Cancer researchers have an exciting new tool at their disposal: circulating cell-free DNA (ccfDNA) collected in minimally invasive liquid biopsies. With the potential to provide real-time mutational information about primary and metastatic tumors, cfDNA has significant potential for the detection and monitoring of biomarkers for cancer and other diseases. ...

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According to this latest study, the 2021 growth of Glass Insulators will have significant change from previous year. By the most conservative estimates of globa

TY - JOUR. T1 - Secretory factors from OP9 stromal cells delay differentiation and increase the expansion potential of adult erythroid cells in vitro. AU - Trakarnsanga, Kongtana. AU - Wilson, Marieangela C.. AU - Heesom, Kate J.. AU - Andrienko, Tatyana N.. AU - Srisawat, Chatchawan. AU - Frayne, Jan. PY - 2018/1/31. Y1 - 2018/1/31. N2 - Development of in vitro culture systems for the generation of red blood cells is a goal of scientists globally with the aim of producing clinical grade products for transfusion. Although mature reticulocytes can be efficiently generated by such systems, the numbers produced fall short of that required for therapeutics, due to limited proliferative capacity of the erythroblasts. To overcome this hurdle, approaches are required to increase the expansion potential of such culture systems. The OP9 mouse stromal cell line is known to promote haematopoietic differentiation of pluripotent stem cells, however an effect of OP9 cells on erythropoiesis has not been ...

TY - JOUR. T1 - Variation in gamma-globin expression before and after induction with hydroxyurea associated with BCL11A, KLF1 and TAL1. AU - Grieco, Amanda J.. AU - Billett, Henny H.. AU - Green, Nancy S.. AU - Driscoll, M. Catherine. AU - Bouhassira, Eric E.. N1 - Publisher Copyright: © 2015 Grieco et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.. PY - 2015/6/8. Y1 - 2015/6/8. N2 - The molecular mechanisms governing γ-globin expression in a subset of fetal hemoglobin (α2γ2: HbF) expressing red blood cells (F-cells) and the mechanisms underlying the variability of response to hydroxyurea induced γ-globin expression in the treatment of sickle cell disease are not completely understood. Here we analyzed intra-person clonal populations of basophilic erythroblasts (baso-Es) derived from bone marrow ...

Current models suggest that tissue-specific genes are arranged in discrete, independently controlled segments of chromatin referred to as regulatory domains. Transition from a closed to open chromatin structure may be an important step in the regulation of gene expression. To determine whether the human alpha-globin cluster, like the beta-globin cluster, lies within a discrete, erythroid-specific domain, we have examined the long-range genomic organization and chromatin structure around this region. The alpha genes lie adjacent to at least four widely expressed genes. The major alpha-globin regulatory element lies 40 kb away from the cluster within an intron of one of these genes. Therefore, unlike the beta cluster, cis-acting sequences controlling alpha gene expression are dispersed within a region of chromatin that is open in both erythroid and nonerythroid cells. This implies a difference in the hierarchical control of alpha- and beta-globin expression.

The KLF1 gene encodes a key transcription factor regulating the developmental switch from fetal to adult globin. Based on previous and recent experimental data it has been hypothesized that after birth high levels of KLF1 activate the HBB gene and BCL11A expression, which in turn suppresses HBG1/HBG2 expression, while in the fetus reduced KLF1 levels result in very low HBB and BCL11A gene expression and therefore in low beta and high gamma globin levels.6 It is interesting to note that subjects II-1 and II-2, with genetic compound for the two KLF1 mutations, have unbalanced alpha/beta globin chain synthesis ratio (i.e. in the beta-thalassemia carrier range), despite having normal beta globin gene sequence and not increased HbA2 levels. The reduced beta globin production and the excess of G-gamma chains partly resembles a late fetal or newborn condition, consistent with the key role of KLF1 in the globin switching. The milder imbalance in II-2 as compared to II-1 is due to the coinheritance of ...

BACKGROUND: The CCTC-binding factor (CTCF) protein is involved in genome organization, including mediating three-dimensional chromatin interactions. Human patient lymphocytes with mutations in a single copy of the CTCF gene have reduced expression of enhancer-associated genes involved in response to stimuli. We hypothesize that CTCF interactions stabilize enhancer-promoter chromatin interaction domains, facilitating increased expression of genes in response to stimuli. Here we systematically investigate this model using computational analyses. RESULTS: We use CTCF ChIA-PET data from the ENCODE project to show that CTCF-associated chromatin loops have a tendency to enclose regions of enhancer-regulated stimulus responsive genes, insulating them from neighboring regions of constitutively expressed housekeeping genes. To facilitate cell type-specific CTCF loop identification, we develop an algorithm to predict CTCF loops from ChIP-seq data alone by exploiting the CTCF motif directionality in loop ...

Here we present HiC-DC, a principled method to estimate the statistical significance (P values) of chromatin interactions from Hi-C experiments. HiC-DC uses hurdle negative binomial regression account for systematic sources of variation in Hi-C read counts-for example, distance-dependent random polymer ligation and GC content and mappability bias-and model zero inflation and overdispersion. Applied to high-resolution Hi-C data in a lymphoblastoid cell line, HiC-DC detects significant interaction

Insulation for direct current transmission is totally different from that of AC transmission. The behavior of local discharge on the insulator is different from that of AC transmission. The problems of ion migration and thermal runaway in the material of the body of the insulator are matters to be considered only in the case of DC applications. To suppress the problems unique to DC and enable the reliable operation of DC power systems, insulators for DC applications require design and materials different from AC applications.. ...

Common coordinate-based workflows involving processed chromatin loop and genomic element data are considered and packaged into appropriate customizable functions. Includes methods for linking element sets via chromatin loops and creating consensus loop datasets. ...

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Instantly find & access educational materials and complete eLearning activities at your leisure. Native iPad/iPhone/Android Apps are available for the convenience of on-the-go users.

/PRNewswire/ -- Natera, Inc. (NASDAQ: NTRA), a leader in non-invasive genetic testing and the analysis of circulating cell-free DNA, today reported financial...