A compilation of composite regulatory elements affecting gene transcription in vertebrates

Kel, O. V.; Romaschenko, A. G.; Kel, Alexander; Wingender, Edgar; Колчанов, Н. А.

doi:10.1093/nar/23.20.4097

Cited by 83 publications

(41 citation statements)

References 192 publications

(164 reference statements)

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“…Composite elements are transcriptionally active DNA sequences, which bind two or more transcriptional regulators, and they have been found in many vertebrate gene promoters (73). They provide an efficient way of fine-tuning gene expression in different cellular situations, by exploiting either the synergistic or antagonistic effects of the transcription factors they bind to respectively overactivate or down-regulate transcription.…”

Section: Discussionmentioning

confidence: 99%

Nuclear Factor 1 Interferes with Sp1 Binding through a Composite Element on the Rat Poly(ADP-ribose) Polymerase Promoter to Modulate Its Activity in Vitro

Laniel

Poirier

Guérin

2001

Journal of Biological Chemistry

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Poly(ADP-ribose) polymerase-1 (PARP-1) catalyzes the rapid and extensive poly(ADP-ribosyl)ation of nuclear proteins in response to DNA strand breaks, and its expression, although ubiquitous, is modulated from tissue to tissue and during cellular differentiation. PARP-1 gene promoters from human, rat, and mouse have been cloned, and they share a structure common to housekeeping genes, as they lack a functional TATA box and contain multiple GC boxes, which bind the transcriptional activator Sp1. We have previously shown that, although Sp1 is important for rat PARP1 (rPARP) promoter activity, its finely tuned modulation is likely dependent on other transcription factors that bind the rPARP proximal promoter in vitro. In this study, we identified one such factor as NF1-L, a rat liver isoform of the nuclear factor 1 family of transcription factors. The NF1-L site on the rPARP promoter overlaps one of the Sp1 binding sites previously identified, and we demonstrated that binding of both factors to this composite element is mutually exclusive. Furthermore, we provide evidence that NF1-L has no effect by itself on rPARP promoter activity, but rather down-regulates the Sp1 activity by interfering with its ability to bind the rPARP promoter in order to modulate transcription of the rPARP gene.Poly(ADP-ribose) polymerase-1 (PARP-1) 1 is a nuclear enzyme which catalyzes the addition of ADP-ribose units from nicotinamide adenine dinucleotide (NAD ϩ ) onto itself and other nuclear proteins such as histones and topoisomerases (reviewed in Refs. 1 and 2). It is made up of three functional domains, namely the amino-terminal DNA-binding domain, the central automodification domain, and the carboxyl-terminal catalytic domain (3). Although PARP-1 is often associated with DNA repair, because of its rapid and extensive activation following DNA damage (4, 5), it has also been implicated in other major nuclear functions such as transcription (6, 7), DNA replication (8, 9) and recombination (10). PARP-1 is also important for cell differentiation (11-13) and is involved in cell death, likely acting as a molecular switch between apoptosis and necrosis (14).PARP-1 is expressed in all organs, albeit at varying degrees, with highest mRNA expression found in brain, thymus, heart, and testis (15, 16). PARP-1 mRNA level is regulated at the cell cycle level, reaching its peak at either the G 1 (17-20) or the S phases (21, 22). It has also been shown that a decrease in PARP-1 mRNA levels is associated with cellular differentiation (23-26) and senescence (27), whereas an increase is observed upon activation of lymphocytes (17, 28) or peripheral blood mononuclear cells (18). All these studies show that, although PARP-1 is ubiquitously expressed, its modulation, likely through complex transcriptional regulation, is critical to major cellular functions.In order to better understand the transcriptional mechanisms regulating PARP-1 expression, the PARP-1 gene promoter has been identified and cloned from three mammalian species, human (29, 30), rat (31), ...

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Section: Discussionmentioning

confidence: 99%

Nuclear Factor 1 Interferes with Sp1 Binding through a Composite Element on the Rat Poly(ADP-ribose) Polymerase Promoter to Modulate Its Activity in Vitro

Laniel

Poirier

Guérin

2001

Journal of Biological Chemistry

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“…Another feature of many YY1 binding sites is their proximity to recognition sequences for other transcription factors, thus forming composite regulatory elements (25). Often the two single sites overlap, which is reported to result in functional antagonism between YY1 and mammary gland-specific factor, GATA-1, and NF-B in the promoters of the rat ␤-casein (34,45), the human ε-globin (44), and the rat serum amyloid A1 (32) genes, respectively.…”

Section: Discussionmentioning

confidence: 99%

Binding of YY1 to a Site Overlapping a Weak TATA Box Is Essential for Transcription from the Uteroglobin Promoter in Endometrial Cells

Klug

Beato

1996

Molecular and Cellular Biology

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The gene for rabbit uteroglobin codes for a small calcium-, steroid-, and biphenyl metabolite-binding homodimeric protein which is expressed in a variety of epithelial cell types such as Clara cells (lung) and the glandular and luminal cells of the endometrium. One important region mediating its efficient transcription in a human endometrium-derived cell line, Ishikawa, is centered around a noncanonical TATA box. Two factors, TATA core factor (TCF), expressed in cell lines derived from uteroglobin-expressing tissues, and the ubiquitously expressed TATA palindrome factor, bind to the DNA major groove at two adjacent sites within this region. Here, we report the identification of the TATA palindrome factor as the transcription/initiation factor YY1 by microsequencing of the biochemically purified factor from HeLa cells. The binding site for YY1 within the uteroglobin gene is unique in its sequence and its location overlapping a weak TATA box (TACA). Binding of YY1 was required for efficient transcription in TCF-positive Ishikawa cells, which responded only weakly to a change of TACA to TATA, although in vitro binding affinity for the TATA-box-binding protein increased by 1 order of magnitude. In contrast, in CV-1 cells, lacking TCF, binding of YY1 was not required for transcription in the context of a wild-type TACA box, whereas a change from TACA to TATA led to significantly increased reporter gene expression. DNA binding data exclude a role of YY1 in stabilizing the interaction of the TATA-box-binding protein with the uteroglobin promoter. We conclude that cell lines derived from uteroglobin-expressing tissues overcome the weak TATA box with the help of auxiliary factors, one of them being YY1.

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“…Like PD-L1, the PD-L2 5Ј regulatory region includes an ISRE/IRF1 module and degenerate STAT binding sites (supplemental data). However, the spacing of ISRE and IRF1 elements in the predicted module was larger than that seen in other transcription regulatory elements, 33 including the 5Ј PD-L1 sequence, and there were fewer degenerate STAT binding sites (supplemental data). Consistent with these findings, JAK2 inhibition decreased PD-L2 transcript abundance and PD-L2 promoter-driven luciferase expression less than PD-L1 (supplemental data).…”

Section: Jak2-associated Induction Of Pd-l1 In Hlsmentioning

confidence: 97%

Integrative analysis reveals selective 9p24.1 amplification, increased PD-1 ligand expression, and further induction via JAK2 in nodular sclerosing Hodgkin lymphoma and primary mediastinal large B-cell lymphoma

Green

Monti

Rodig

et al. 2010

Blood

1,166

1,064

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Classical Hodgkin lymphoma (cHL) and mediastinal large B-cell lymphoma (MLBCL) are lymphoid malignancies with certain shared clinical, histologic, and molecular features. Primary cHLs and MLBCLs include variable numbers of malignant cells within an inflammatory infiltrate, suggesting that these tumors escape immune surveillance. Herein, we integrate high-resolution copy number data with transcriptional profiles and identify the immunoregulatory genes, PD-L1 and PD-L2, as key targets at the 9p24.1 amplification peak in HL and MLBCL cell lines. We extend these findings to lasercapture microdissected primary Hodgkin Reed-Sternberg cells and primary MLBCLs and find that programmed cell death-1 (PD-1) ligand/9p24.1 amplification is restricted to nodular sclerosing HL, the cHL subtype most closely related to MLBCL. Using quantitative immunohistochemical methods, we document the association between 9p24.1 copy number and PD-1 ligand expression in primary tumors. In cHL and MLBCL, the extended 9p24.1 amplification region also included the Janus kinase 2 (JAK2) locus. Of note, JAK2 amplification increased protein expression and activity, specifically induced PD-1 ligand transcription and enhanced sensitivity to JAK2 inhibition. Therefore, 9p24.1 amplification is a disease-specific structural alteration that increases both the gene dosage IntroductionClassical Hodgkin lymphoma (cHL) is a B-cell malignancy that occurs frequently in Western countries and commonly affects young adults. 1 These tumors are characterized by small numbers of neoplastic Reed-Sternberg (RS) cells within an extensive inflammatory/immune cell infiltrate. There are 4 subtypes of cHL, 2 of which comprise Ϸ 90% of cases: nodular sclerosing Hodgkin lymphoma (NSHL; 60% of cases) and mixed cellularity Hodgkin lymphoma (MCHL; 30% of cases). cHLs lack surface immunoglobulin expression and B-cell receptor-mediated signals and rely on alternative survival pathways, including aberrant nuclear factorB signaling. 1 In previous studies, we and others have defined shared molecular features of cHL and a specific subtype of diffuse large B-cell lymphoma (DLBCL), primary mediastinal large B-cell lymphoma (MLBCL). 2,3 Like cHL, MLBCLs have a T-helper cell type 2 (Th2)-skewed cytokine profile, decreased expression of B-cell receptor signaling pathway components, and constitutive activation of nuclear factorB. 2 MLBCL also exhibits certain clinical and histologic similarities to cHL, particularly the NSHL subtype. 4,5 For example, both diseases are most common in young adults and often present as an anterior mediastinal or localized nodal mass. 2,4,5 In addition, both MLBCLs and NSHLs include bands of sclerotic tissue and immune/inflammatory cell infiltrates. 4,5 However, the inflammatory infiltrate is less prominent in MLBCLs, which have a more diffuse growth pattern. 4 Although cHLs have an extensive polymorphous inflammatory infiltrate, there is little evidence of an effective host antitumor immune response. In fact, recent studies indicate that Hodgkin RS cells pro...

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A compilation of composite regulatory elements affecting gene transcription in vertebrates

Abstract: ABSTRACT

Cited by 83 publications

References 192 publications

Nuclear Factor 1 Interferes with Sp1 Binding through a Composite Element on the Rat Poly(ADP-ribose) Polymerase Promoter to Modulate Its Activity in Vitro

Nuclear Factor 1 Interferes with Sp1 Binding through a Composite Element on the Rat Poly(ADP-ribose) Polymerase Promoter to Modulate Its Activity in Vitro

Binding of YY1 to a Site Overlapping a Weak TATA Box Is Essential for Transcription from the Uteroglobin Promoter in Endometrial Cells

Integrative analysis reveals selective 9p24.1 amplification, increased PD-1 ligand expression, and further induction via JAK2 in nodular sclerosing Hodgkin lymphoma and primary mediastinal large B-cell lymphoma

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