scholarly journals The Ly-6E.1 (Sca-1) gene requires a 3' chromatin-dependent region for high-level gamma-interferon-induced hematopoietic cell expression

Blood ◽  
1996 ◽  
Vol 87 (7) ◽  
pp. 2750-2761 ◽  
Author(s):  
A Sinclair ◽  
B Daly ◽  
E Dzierzak

The Ly-6E.1/A.2 gene product recognized by the Sca-1 antibody has been found on murine hematopoietic stem cells and some hematopoietic precursors, T lymphocytes, and nonhematopoietic cell lineages, suggesting a complex array of gene regulatory elements. The ability to use the Ly6E.1/A.2 transcriptional regulatory elements to direct expression of heterologous genes will allow for the manipulation of these cells during development and in hematopoietic cell transplantations. To identify the elements necessary for high-level expression, we have made deletion constructs of Ly-6E.1 gene flanking regions containing DNase I hypersensitive sites, tested them for expression in hematopoietic cells, and have performed kinetic analyses to correlate the appearance of hypersensitive sites with gene transcription and protein expression. We show that a 3′ region containing two DNase I hypersensitive sites at +8.7 and +8.9 kb is required for high-level, gamma-interferon (gamma-IFN)-induced expression of the Ly-6E.1 gene and that a consensus sequence for a gamma-IFN-responsive element localizes to the +8.7 site. We also provide a description of allele- and cell-specific DNase I hypersensitive site patterns of the Ly-6E.1 and Ly-6A.2 genes. Taken together, these data indicate that while both 5′ and 3′ hypersensitive sites are rapidly induced with gamma-IFN, the 3′ most distal hypersensitive sites are involved in directing high levels of expression of Sca-1 in hematopoietic cells.

Blood ◽  
1993 ◽  
Vol 82 (10) ◽  
pp. 3052-3062 ◽  
Author(s):  
AM Sinclair ◽  
EA Dzierzak

Abstract The Sca-1 antibody recognizes antigens encoded by members of the Ly-6 multigene family. These antigens are expressed on fetal and adult hematopoietic stem cells, progenitor cells, mature activated T cells, and some nonhematopoietic cells and are most likely encoded by the Ly- 6E.1 and Ly-6A.2 genes. Characterization and isolation of regulatory elements of Ly-6E.1 and A.2 genes that govern tissue-specific and high levels of expression in the cells of the hematopoietic system (particularly stem cells) are of considerable interest. To characterize the control elements of this gene, we have cloned a 30-kb fragment encoding a fully functional Ly-6E.1 gene and 13 kb of 5′ and 13 kb of 3′ flanking sequence. Transfection studies in murine erythroleukemia (MEL) cells show that a 14-kb BamHI fragment from this clone is sufficient to confer Ly-6E.1 gene expression at levels equivalent to those of the endogenous gene. By mapping regions of chromatin sensitive to DNase I digestion, we have located hypersensitive sites in the 5′ and 3′ regions of the gene in FDCP-1 cells, MEL cells, and various T- cell lines. The appearance of two 5′ hypersensitive sites in hematopoietic cells correlates with Ly-6E.1 expression after gamma- interferon induction. We show that the presence of hypersensitive sites in the 5′ and 3′ regions corresponds to Sca-1 expression, and we also discuss the localization of putative regulatory control elements.


Blood ◽  
1993 ◽  
Vol 82 (10) ◽  
pp. 3052-3062 ◽  
Author(s):  
AM Sinclair ◽  
EA Dzierzak

The Sca-1 antibody recognizes antigens encoded by members of the Ly-6 multigene family. These antigens are expressed on fetal and adult hematopoietic stem cells, progenitor cells, mature activated T cells, and some nonhematopoietic cells and are most likely encoded by the Ly- 6E.1 and Ly-6A.2 genes. Characterization and isolation of regulatory elements of Ly-6E.1 and A.2 genes that govern tissue-specific and high levels of expression in the cells of the hematopoietic system (particularly stem cells) are of considerable interest. To characterize the control elements of this gene, we have cloned a 30-kb fragment encoding a fully functional Ly-6E.1 gene and 13 kb of 5′ and 13 kb of 3′ flanking sequence. Transfection studies in murine erythroleukemia (MEL) cells show that a 14-kb BamHI fragment from this clone is sufficient to confer Ly-6E.1 gene expression at levels equivalent to those of the endogenous gene. By mapping regions of chromatin sensitive to DNase I digestion, we have located hypersensitive sites in the 5′ and 3′ regions of the gene in FDCP-1 cells, MEL cells, and various T- cell lines. The appearance of two 5′ hypersensitive sites in hematopoietic cells correlates with Ly-6E.1 expression after gamma- interferon induction. We show that the presence of hypersensitive sites in the 5′ and 3′ regions corresponds to Sca-1 expression, and we also discuss the localization of putative regulatory control elements.


2002 ◽  
Vol 269 (2) ◽  
pp. 553-559 ◽  
Author(s):  
Marios Phylactides ◽  
Rebecca Rowntree ◽  
Hugh Nuthall ◽  
David Ussery ◽  
Ann Wheeler ◽  
...  

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Matteo D′Antonio ◽  
Donate Weghorn ◽  
Agnieszka D′Antonio-Chronowska ◽  
Florence Coulet ◽  
Katrina M. Olson ◽  
...  

2017 ◽  
Author(s):  
Balachandran Manavalan ◽  
Tae Hwan Shin ◽  
Gwang Lee

AbstractDNase I hypersensitive sites (DHSs) are genomic regions that provide important information regarding the presence of transcriptional regulatory elements and the state of chromatin. Therefore, identifying DHSs in uncharacterized DNA sequences is crucial for understanding their biological functions and mechanisms. Although many experimental methods have been proposed to identify DHSs, they have proven to be expensive for genome-wide application. Therefore, it is necessary to develop computational methods for DHS prediction. In this study, we proposed a support vector machine (SVM)-based method for predicting DHSs, called DHSpred (DNase I Hypersensitive Site predictor in human DNA sequences), which was trained with 174 optimal features. The optimal combination of features was identified from a large set that included nucleotide composition and di- and trinucleotide physicochemical properties, using a random forest algorithm. DHSpred achieved a Matthews correlation coefficient and accuracy of 0.660 and 0.871, respectively, which were 3% higher than those of control SVM predictors trained with non-optimized features, indicating the efficiency of the feature selection method. Furthermore, the performance of DHSpred was superior to that of state-of-the-art predictors. An online prediction server has been developed to assist the scientific community, and is freely available at:http://www.thegleelab.org/DHSpred.html.


2020 ◽  
Author(s):  
Charles E. Breeze ◽  
John Lazar ◽  
Tim Mercer ◽  
Jessica Halow ◽  
Ida Washington ◽  
...  

AbstractEarly mammalian development is orchestrated by genome-encoded regulatory elements populated by a changing complement of regulatory factors, creating a dynamic chromatin landscape. To define the spatiotemporal organization of regulatory DNA landscapes during mouse development and maturation, we generated nucleotide-resolution DNA accessibility maps from 15 tissues sampled at 9 intervals spanning post-conception day 9.5 through early adult, and integrated these with 41 adult-stage DNase-seq profiles to create a global atlas of mouse regulatory DNA. Collectively, we delineated >1.8 million DNase I hypersensitive sites (DHSs), with the vast majority displaying temporal and tissue-selective patterning. Here we show that tissue regulatory DNA compartments show sharp embryonic-to-fetal transitions characterized by wholesale turnover of DHSs and progressive domination by a diminishing number of transcription factors. We show further that aligning mouse and human fetal development on a regulatory axis exposes disease-associated variation enriched in early intervals lacking human samples. Our results provide an expansive new resource for decoding mammalian developmental regulatory programs.


1984 ◽  
Vol 4 (9) ◽  
pp. 1853-1863 ◽  
Author(s):  
N Costlow ◽  
J T Lis

High-resolution analysis of the chromatin structure of the promoter regions of five Drosophila heat shock genes showed a similar location for the hypersensitive sequences relative to the start of transcription. For each of the five genes examined--those coding for hsp27, hsp26, hsp23, hsp70, and hsp83--the DNase I-hypersensitive sites in Drosophila melanogaster nuclei mapped to two regions upstream of the coding region. These sites occurred on the average, 115 and 17 base pairs upstream from the start of transcription of the five heat shock genes examined. This latter site corresponded to sequences at or near the TATA consensus sequence. Sites even further upstream of the hsp27, hsp26, and hsp83 genes were also evident. Additionally, for the two genes examined--hsp70 and hsp83--the DNase I-hypersensitive sites were preserved, at least within this level of resolution (+/- 10 base pairs), when the Drosophila genes were integrated into the Saccharomyces cerevisiae genome. This result indicates that the signals responsible for generating these hypersensitive sites are inherent in the DNA sequences and, in this case, are not highly species specific.


1984 ◽  
Vol 4 (9) ◽  
pp. 1853-1863
Author(s):  
N Costlow ◽  
J T Lis

High-resolution analysis of the chromatin structure of the promoter regions of five Drosophila heat shock genes showed a similar location for the hypersensitive sequences relative to the start of transcription. For each of the five genes examined--those coding for hsp27, hsp26, hsp23, hsp70, and hsp83--the DNase I-hypersensitive sites in Drosophila melanogaster nuclei mapped to two regions upstream of the coding region. These sites occurred on the average, 115 and 17 base pairs upstream from the start of transcription of the five heat shock genes examined. This latter site corresponded to sequences at or near the TATA consensus sequence. Sites even further upstream of the hsp27, hsp26, and hsp83 genes were also evident. Additionally, for the two genes examined--hsp70 and hsp83--the DNase I-hypersensitive sites were preserved, at least within this level of resolution (+/- 10 base pairs), when the Drosophila genes were integrated into the Saccharomyces cerevisiae genome. This result indicates that the signals responsible for generating these hypersensitive sites are inherent in the DNA sequences and, in this case, are not highly species specific.


Sign in / Sign up

Export Citation Format

Share Document