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An Ikaros Promoter Element with Dual Epigenetic and Transcriptional Activities.

Perotti EA, Georgopoulos K, Yoshida T - PLoS ONE (2015)

Bottom Line: Deletion of this binding site increased the percentage of the reporter-expressing mouse lines, indicating that its loss provided a more permissive chromatin environment.However, once transcription was established, the lack of this site decreased transcriptional activity.These findings implicate a dual role for Ikaros/Ets1 binding on Ikzf1 expression that is exerted at least through its promoter.

View Article: PubMed Central - PubMed

Affiliation: Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, United States of America.

ABSTRACT
Ikaros DNA binding factor plays critical roles in lymphocyte development. Changes in Ikaros expression levels during lymphopoiesis are controlled by redundant but also unique regulatory elements of its locus that are critical for this developmental process. We have recently shown that Ikaros binds its own locus in thymocytes in vivo. Here, we evaluated the role of an Ikaros binding site within its major lympho-myeloid promoter. We identified an Ikaros/Ets binding site within a promoter sub-region that was highly conserved in mouse and human. Deletion of this binding site increased the percentage of the reporter-expressing mouse lines, indicating that its loss provided a more permissive chromatin environment. However, once transcription was established, the lack of this site decreased transcriptional activity. These findings implicate a dual role for Ikaros/Ets1 binding on Ikzf1 expression that is exerted at least through its promoter.

No MeSH data available.


Ikaros binding sites on the Ikzf1 locus and its promoter region.(A) The The Ikzf1 locus along with the un-translated exons 1a and 1b[29], and translated exons 2 to 8 [29] are indicated. The known lympho-myeloid specific promoters (A, B), promoter element (p) and enhancers (J, C (D), E, F, H, I) are shown [29,30]. Enrichment for Ikaros bindings on Ikzf1 revealed by ChIP-seq analysis on wild type thymocytes [11] is indicated (published in [30]). The red and brown asterisks indicate Ikaros binding sites in the promoter-B and enhancer-H regions, respectively. (B) The relative locations of the Ikaros and Ets1 binding regions identified by ChIP-seq [29,30] to the mouse-human homology; sub-regions 1, 2, 3; and exon1b on the promoter-B fragment are shown. (C) The sequence of the Ikaros binding area within the promoter-B region (black letters) is shown. The un-translated exon1b is marked in yellow box, and one of the conserved sub-regions (sub-region 1) is underlined with navy lines. Ikaros binding motifs on the plus strand (+) and minus strand (–) are indicated as blue and green squares, respectively. (D) The sequence of conserved sub-region 1 and the deleted region in the promoter-B of the B-p-GFP parental construct are indicated. Ikaros and Ets consensus binding motifs are underlined by blue and purple, respectively.
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pone.0131568.g001: Ikaros binding sites on the Ikzf1 locus and its promoter region.(A) The The Ikzf1 locus along with the un-translated exons 1a and 1b[29], and translated exons 2 to 8 [29] are indicated. The known lympho-myeloid specific promoters (A, B), promoter element (p) and enhancers (J, C (D), E, F, H, I) are shown [29,30]. Enrichment for Ikaros bindings on Ikzf1 revealed by ChIP-seq analysis on wild type thymocytes [11] is indicated (published in [30]). The red and brown asterisks indicate Ikaros binding sites in the promoter-B and enhancer-H regions, respectively. (B) The relative locations of the Ikaros and Ets1 binding regions identified by ChIP-seq [29,30] to the mouse-human homology; sub-regions 1, 2, 3; and exon1b on the promoter-B fragment are shown. (C) The sequence of the Ikaros binding area within the promoter-B region (black letters) is shown. The un-translated exon1b is marked in yellow box, and one of the conserved sub-regions (sub-region 1) is underlined with navy lines. Ikaros binding motifs on the plus strand (+) and minus strand (–) are indicated as blue and green squares, respectively. (D) The sequence of conserved sub-region 1 and the deleted region in the promoter-B of the B-p-GFP parental construct are indicated. Ikaros and Ets consensus binding motifs are underlined by blue and purple, respectively.

Mentions: In our previous studies, we have established two lympho-myeloid specific promoters, a promoter element, and six enhancers of the Ikzf1 locus using in vivo transgenic reporter mouse systems combined with chromatin studies and comparative genome analyses [29,30] (Fig 1A). Up-stream hemo-lymphoid specific trans-factors that bind the Ikzf1 locus in vivo have been identified in hematopoietic lineages [30], however, the actual roles of these factors on Ikzf1 regulation remain unknown. One of these factors is Ikaros itself, suggesting an auto-regulatory function of the locus [30]. Another factor is Ets1 that is implicated in various immune functions [30,31]. Ets1 shares its consensus binding motifs with those of Ikaros [32].


An Ikaros Promoter Element with Dual Epigenetic and Transcriptional Activities.

Perotti EA, Georgopoulos K, Yoshida T - PLoS ONE (2015)

Ikaros binding sites on the Ikzf1 locus and its promoter region.(A) The The Ikzf1 locus along with the un-translated exons 1a and 1b[29], and translated exons 2 to 8 [29] are indicated. The known lympho-myeloid specific promoters (A, B), promoter element (p) and enhancers (J, C (D), E, F, H, I) are shown [29,30]. Enrichment for Ikaros bindings on Ikzf1 revealed by ChIP-seq analysis on wild type thymocytes [11] is indicated (published in [30]). The red and brown asterisks indicate Ikaros binding sites in the promoter-B and enhancer-H regions, respectively. (B) The relative locations of the Ikaros and Ets1 binding regions identified by ChIP-seq [29,30] to the mouse-human homology; sub-regions 1, 2, 3; and exon1b on the promoter-B fragment are shown. (C) The sequence of the Ikaros binding area within the promoter-B region (black letters) is shown. The un-translated exon1b is marked in yellow box, and one of the conserved sub-regions (sub-region 1) is underlined with navy lines. Ikaros binding motifs on the plus strand (+) and minus strand (–) are indicated as blue and green squares, respectively. (D) The sequence of conserved sub-region 1 and the deleted region in the promoter-B of the B-p-GFP parental construct are indicated. Ikaros and Ets consensus binding motifs are underlined by blue and purple, respectively.
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pone.0131568.g001: Ikaros binding sites on the Ikzf1 locus and its promoter region.(A) The The Ikzf1 locus along with the un-translated exons 1a and 1b[29], and translated exons 2 to 8 [29] are indicated. The known lympho-myeloid specific promoters (A, B), promoter element (p) and enhancers (J, C (D), E, F, H, I) are shown [29,30]. Enrichment for Ikaros bindings on Ikzf1 revealed by ChIP-seq analysis on wild type thymocytes [11] is indicated (published in [30]). The red and brown asterisks indicate Ikaros binding sites in the promoter-B and enhancer-H regions, respectively. (B) The relative locations of the Ikaros and Ets1 binding regions identified by ChIP-seq [29,30] to the mouse-human homology; sub-regions 1, 2, 3; and exon1b on the promoter-B fragment are shown. (C) The sequence of the Ikaros binding area within the promoter-B region (black letters) is shown. The un-translated exon1b is marked in yellow box, and one of the conserved sub-regions (sub-region 1) is underlined with navy lines. Ikaros binding motifs on the plus strand (+) and minus strand (–) are indicated as blue and green squares, respectively. (D) The sequence of conserved sub-region 1 and the deleted region in the promoter-B of the B-p-GFP parental construct are indicated. Ikaros and Ets consensus binding motifs are underlined by blue and purple, respectively.
Mentions: In our previous studies, we have established two lympho-myeloid specific promoters, a promoter element, and six enhancers of the Ikzf1 locus using in vivo transgenic reporter mouse systems combined with chromatin studies and comparative genome analyses [29,30] (Fig 1A). Up-stream hemo-lymphoid specific trans-factors that bind the Ikzf1 locus in vivo have been identified in hematopoietic lineages [30], however, the actual roles of these factors on Ikzf1 regulation remain unknown. One of these factors is Ikaros itself, suggesting an auto-regulatory function of the locus [30]. Another factor is Ets1 that is implicated in various immune functions [30,31]. Ets1 shares its consensus binding motifs with those of Ikaros [32].

Bottom Line: Deletion of this binding site increased the percentage of the reporter-expressing mouse lines, indicating that its loss provided a more permissive chromatin environment.However, once transcription was established, the lack of this site decreased transcriptional activity.These findings implicate a dual role for Ikaros/Ets1 binding on Ikzf1 expression that is exerted at least through its promoter.

View Article: PubMed Central - PubMed

Affiliation: Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, United States of America.

ABSTRACT
Ikaros DNA binding factor plays critical roles in lymphocyte development. Changes in Ikaros expression levels during lymphopoiesis are controlled by redundant but also unique regulatory elements of its locus that are critical for this developmental process. We have recently shown that Ikaros binds its own locus in thymocytes in vivo. Here, we evaluated the role of an Ikaros binding site within its major lympho-myeloid promoter. We identified an Ikaros/Ets binding site within a promoter sub-region that was highly conserved in mouse and human. Deletion of this binding site increased the percentage of the reporter-expressing mouse lines, indicating that its loss provided a more permissive chromatin environment. However, once transcription was established, the lack of this site decreased transcriptional activity. These findings implicate a dual role for Ikaros/Ets1 binding on Ikzf1 expression that is exerted at least through its promoter.

No MeSH data available.