scholarly journals Developmental control of transcription of a retina-specific gene, QR1, during differentiation: involvement of factors from the POU family.

1995 ◽  
Vol 15 (2) ◽  
pp. 642-652 ◽  
Author(s):  
A Pierani ◽  
C Pouponnot ◽  
G Calothy
Keyword(s):  
Transcriptional Control ◽  
Growth Regulation ◽  
Late Phase ◽  
Regulatory Region ◽  
Neural Retina ◽  
Specific Gene ◽  
Postnatal Life ◽  
Developmental Control ◽  
Control Of Gene Expression

Developmental control of gene expression often results from the coupling of growth arrest with the establishment of differentiation programs. QR1 is a gene specifically expressed in retinas during the late phase of embryogenesis. At this stage neuroectodermal precursors have reached terminal mitosis and are undergoing differentiation into distinct cell types. Transcription of the QR1 gene is tightly regulated during retinal development: this gene is expressed between embryonic day 9 (ED9) and ED17 and is completely repressed at hatching in quail. Moreover, QR1 transcription is downregulated when postmitotic neural retina cells are induced to proliferate by pp60v-src. We studied the stage-dependent transcriptional control of this gene during quail neural retina (QNR) cell development. Transient transfection experiments with QR1/CAT constructs at various stages of development showed that a region located between -935 and -1265 bp upstream of the transcription start site is necessary to promote transcription in retina cells during the late phase of embryonal development (QNR9, corresponding to ED9). By in vivo footprinting assays we identified at least two elements that are occupied by DNA-protein complexes in QNR cells: the A and B boxes. The A box allows formation of several biochemically distinct complexes: C1, C2, C3, and C4. Formation of the C2 complex mainly during early stages (ED7) and of C2, C3, and C4 complexes during postnatal life correlates with repression of QR1 transcription, whereas the C1 complex is strongly induced at ED11 when the QR1 gene is expressed. We previously showed that C1 was involved in downregulation of QR1 transcription by pp60v-src. Several complexes are also formed on the B box. We show that these complexes are exclusively present in neural tissues and that they involve members of the POU family of transcription factors. Mutations of each one of the two regions which abolish the binding of the C1 factor(s) on the A box and of the POU factor(s) on the B box also prevent stimulation of QR1 transcription in QNR9. Therefore, both elements appear to be required for the stage-specific transcription of the QR1 gene. We also show that the regulatory region from position -1265 to position -935 is able to confer stage-specific transcription upon a heterologous promoter (thymidine kinase). Indeed, this region stimulates transcription in differentiating retinas (QNR9) and represses transcription in terminally differentiated retinas (QNR17, corresponding to postnatal life). Our results suggest that cell growth regulation and developmental control are coordinated through the A and B boxes in regulating QR1 transcription during retinal differentiation.

scholarly journals Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Taotao Sheng ◽  
Shamaine Wei Ting Ho ◽  
Wen Fong Ooi ◽  
Chang Xu ◽  
Manjie Xing ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Histone Modification ◽  
Cell Fate ◽  
Copy Number ◽  
Regulatory Region ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Functional Assay ◽  
Enhancer Activity

Abstract Background Enhancers are distal cis-regulatory elements required for cell-specific gene expression and cell fate determination. In cancer, enhancer variation has been proposed as a major cause of inter-patient heterogeneity—however, most predicted enhancer regions remain to be functionally tested. Methods We analyzed 132 epigenomic histone modification profiles of 18 primary gastric cancer (GC) samples, 18 normal gastric tissues, and 28 GC cell lines using Nano-ChIP-seq technology. We applied Capture-based Self-Transcribing Active Regulatory Region sequencing (CapSTARR-seq) to assess functional enhancer activity. An Activity-by-contact (ABC) model was employed to explore the effects of histone acetylation and CapSTARR-seq levels on enhancer-promoter interactions. Results We report a comprehensive catalog of 75,730 recurrent predicted enhancers, the majority of which are GC-associated in vivo (> 50,000) and associated with lower somatic mutation rates inferred by whole-genome sequencing. Applying CapSTARR-seq to the enhancer catalog, we observed significant correlations between CapSTARR-seq functional activity and H3K27ac/H3K4me1 levels. Super-enhancer regions exhibited increased CapSTARR-seq signals compared to regular enhancers, even when decoupled from native chromatin contexture. We show that combining histone modification and CapSTARR-seq functional enhancer data improves the prediction of enhancer-promoter interactions and pinpointing of germline single nucleotide polymorphisms (SNPs), somatic copy number alterations (SCNAs), and trans-acting TFs involved in GC expression. We identified cancer-relevant genes (ING1, ARL4C) whose expression between patients is influenced by enhancer differences in genomic copy number and germline SNPs, and HNF4α as a master trans-acting factor associated with GC enhancer heterogeneity. Conclusions Our results indicate that combining histone modification and functional assay data may provide a more accurate metric to assess enhancer activity than either platform individually, providing insights into the relative contribution of genetic (cis) and regulatory (trans) mechanisms to GC enhancer functional heterogeneity.

Localization of distal regulatory domains in the megakaryocyte-specific platelet basic protein/platelet factor 4 gene locus

Blood ◽  
2001 ◽  
Vol 98 (3) ◽  
pp. 610-617 ◽  
Author(s):  
Chunyan Zhang ◽  
Michael A. Thornton ◽  
M. Anna Kowalska ◽  
Bruce S. Sachis ◽  
Michael Feldman ◽  
...  
Keyword(s):  
Gene Locus ◽  
Basic Protein ◽  
Regulatory Region ◽  
Platelet Factor 4 ◽  
Specific Gene ◽  
Sufficient Information ◽  
Specific Expression ◽  
Platelet Factor ◽  
High Level

Abstract The genes for the related human (h) chemokines, PBP (platelet basic protein) and PF4 (platelet factor 4), are within 5.3 kilobases (kb) of each other and form a megakaryocyte-specific gene locus. The hypothesis was considered that the PBP and PF4 genes share a common distal regulatory region(s) that leads to their high-level megakaryocyte-specific expression in vivo. This study examined PBP and PF4 expression in transgenic mice using 4 distinct humanPBP/PF4 gene locus constructs. These studies showed that within the region studied there was sufficient information to regulate tissue-specific expression of both hPBP and hPF4. Indeed this region contained sufficient DNA information to lead to expression levels of PBP and PF4 comparable to the homologous mouse genes in a position-independent, copy number–dependent fashion. These studies also indicated that the DNA domains that led to this expression were distinct for the 2 genes; hPBP expression is regulated by a region that is 1.5 to 4.4 kb upstream of that gene. Expression of hPF4 is regulated by a region that is either intergenic between the 2 genes or immediately downstream of the hPF4 gene. Comparison of the available human and mouse sequences shows conserved flanking region domains containing potential megakaryocyte-related transcriptional factor DNA-binding sites. Further analysis of these regulatory regions may identify enhancer domains involved in megakaryopoiesis that may be useful in the selective expression of other genes in megakaryocytes and platelets as a strategy for regulating hemostasis, thrombosis, and inflammation.

scholarly journals Long-Range Transcriptional Control of theIl2Gene by an Intergenic Enhancer

2015 ◽  
Vol 35 (22) ◽  
pp. 3880-3891 ◽  
Author(s):  
Parul Mehra ◽  
Andrew D. Wells
Keyword(s):  
Autoimmune Disease ◽  
Long Range ◽  
Transcriptional Control ◽  
Regulatory Element ◽  
Interleukin 2 ◽  
Regulatory Region ◽  
Dependent Manner ◽  
Regulatory Architecture

Interleukin-2 (IL-2) is a potent cytokine with roles in both immunity and tolerance. Genetic studies in humans and mice demonstrate a role forIl2in autoimmune disease susceptibility, and for decades the proximalIl2upstream regulatory region has served as a paradigm of tissue-specific, inducible gene regulation. In this study, we have identified a novel long-range enhancer of theIl2gene located 83 kb upstream of the transcription start site. This element can potently enhanceIl2transcription in recombinant reporter assaysin vitro, and the native region undergoes chromatin remodeling, transcribes a bidirectional enhancer RNA, and loops to physically interact with theIl2genein vivoin a CD28-dependent manner in CD4+T cells. Thiscisregulatory element is evolutionarily conserved and is situated near a human single-nucleotide polymorphism (SNP) associated with multiple autoimmune disorders. These results indicate that the regulatory architecture of theIl2locus is more complex than previously appreciated and suggest a novel molecular basis for the genetic association ofIl2polymorphism with autoimmune disease.

Characterizing the Function of an RNA Binding Protein, IGF2BP3, in Hematopoiesis

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 3664-3664
Author(s):  
Tiffany M Tran ◽  
Jayanth Kumar Palanichamy ◽  
Jonathan Howard ◽  
Jorge R. Contreras ◽  
Thilini Fernando ◽  
...  
Keyword(s):  
Transcriptional Control ◽  
High Throughput Sequencing ◽  
Rna Binding ◽  
Conflicts Of Interest ◽  
Rna Binding Proteins ◽  
Lymphoblastic Leukemia ◽  
Control Of Gene Expression ◽  
Hematopoietic Stem ◽  
Murine Bone Marrow

Abstract Post-transcriptional control of gene expression plays important roles in defining normal and pathological cellular phenotypes. Amongst mechanisms of post-transcriptional regulation, RNA binding proteins (RBPs) have recently been shown to play important roles. However, in vivo roles for RBPs are not well understood. Here, we identified the RBP IGF2BP3 to be specifically overexpressed in MLL-rearranged B-acute lymphoblastic leukemia (B-ALL), which constitutes a subtype of this malignancy associated with poor prognosis and a risk of high relapse. IGF2BP3 was required for the survival of B-ALL cell lines, and knockdown led to decreased proliferation and increase apoptosis. In addition, enforced expression of IGF2BP3 in murine bone marrow transplant assays caused a proliferation of hematopoietic stem and progenitor cells and a skewing of hematopoietic development to the B-cell/myeloid lineage. Using cross-link immunoprecipitation and high-throughput sequencing, we uncovered the transcriptome regulated by IGF2BP3; including novel direct targets, MYC and CDK6. These were regulated following experimental alteration of IGF2BP3 expression in vivo, and are regulated via elements within their 3'untranslated regions. Hence, IGF2BP3 mediated targeting of oncogenic transcripts may represent a critical pathogenetic mechanism operant in MLL-rearranged B-ALL, highlighting IGF2BP3 and its cognate RNA binding partners as potential therapeutic targets in this disease. Disclosures No relevant conflicts of interest to declare.

scholarly journals Tfe3 and Tfeb Transcriptionally Regulate Peroxisome Proliferator-Activated Receptor γ2 Expression in Adipocytes and Mediate Adiponectin and Glucose Levels in Mice

2017 ◽  
Vol 37 (15) ◽  
Author(s):  
Nunciada Salma ◽  
Jun S. Song ◽  
Akinori Kawakami ◽  
Suprabha P. Devi ◽  
Mehdi Khaled ◽  
...  
Keyword(s):  
Transcriptional Control ◽  
Regulatory Region ◽  
Whole Body ◽  
Peroxisome Proliferator ◽  
Peroxisome Proliferator Activated Receptor ◽  
Fed State ◽  
Glucose Levels ◽  
E Boxes

ABSTRACT Members of the MiT transcription factor family are pivotal regulators of several lineage-selective differentiation programs. We show that two of these, Tfeb and Tfe3, control the regulator of adipogenesis, peroxisome proliferator-activated receptor γ2 (Pparγ2). Knockdown of Tfeb or Tfe3 expression during in vitro adipogenesis causes dramatic downregulation of Pparγ2 expression as well as adipogenesis. Additionally, we found that these factors regulate Pparγ2 in mature adipocytes. Next, we demonstrated that Tfeb and Tfe3 act directly by binding to consensus E-boxes within the Pparγ transcriptional regulatory region. This transcriptional control also exists in vivo, as we discovered that wild-type mice in the fed state increased their expression of Tfe3, Tf3b, and Pparγ in white adipose tissue. Furthermore, Tfe3 knockout (Tfe3KO) mice in the fed state failed to upregulate Pparγ and the adiponectin gene, a Pparγ-dependent gene, confirming the in vivo role for Tfe3. Lastly, we found that blood glucose is elevated and serum adiponectin levels are suppressed in the Tfe3KO mice, indicating that the Tfe3/Tfeb/Pparγ2 axis may contribute to whole-body energy balance. Thus, we offer new insights into the upstream regulation of Pparγ by Tfe3/Tf3b and propose that targeting these transcription factors may offer opportunities to complement existing approaches for the treatment of diseases that have dysregulated energy metabolism.

scholarly journals Novel Binding Sites for Regulatory Factors in the Human Papillomavirus Type 18 Enhancer and Promoter Identified by In Vivo Footprinting

1998 ◽  
Vol 72 (1) ◽  
pp. 708-716 ◽  
Author(s):  
Paula H. Bednarek ◽  
Betty J. Lee ◽  
Sanjay Gandhi ◽  
Edward Lee ◽  
Benette Phillips
Keyword(s):  
Transcriptional Control ◽  
Regulatory Region ◽  
Regulatory Elements ◽  
Human Papillomaviruses ◽  
Regulatory Factors ◽  
Dnase I Footprinting ◽  
E6 And E7 ◽  
In Vivo Footprinting

ABSTRACT The E6 and E7 genes of human papillomaviruses (HPVs) associated with anogenital cancers are largely responsible for the oncogenic activity of these viruses, and regulation of these genes has been intensively studied. Transcription of the E6 and E7 genes is controlled by the viral upstream regulatory region (URR). We have used in vivo footprinting to examine the occupancy by regulatory factors of the HPV type 18 (HPV18) URR enhancer and promoter in the cervical carcinoma cell lines HeLa and C4-II. While corroborating occupancy in vivo of all of the elements previously implicated in the transcriptional control of the HPV18 E6 and E7 genes by in vitro DNase I footprinting, gel retardation assays, and transfection studies, we also detect occupancy in vivo of several enhancer and promoter sequences which have not been previously identified as HPV18 URR regulatory elements. Our data suggest that the HPV18 enhancer and promoter are more densely occupied by DNA-binding proteins than previously thought and raise the possibility that additional, possibly novel factors contribute to transcription of the HPV18 early genes.

Maturation Stage-Specific Regulation of Megakaryocytic Genes by Pointed-Domain Ets Proteins.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 1737-1737
Author(s):  
Liyan Pang ◽  
Xun Wang ◽  
Yuhuan Wang ◽  
Gerd Blobel ◽  
Mortimer Poncz
Keyword(s):  
Gene Expression ◽  
Fetal Liver ◽  
Critical Role ◽  
Regulatory Region ◽  
Maturation Stage ◽  
Specific Gene ◽  
Mrna Levels ◽  
Specific Regulation

Abstract The pointed-domain Ets transcription factor Fli-1 has a critical role during megakaryocyte-specific gene expression. Previously, we demonstrated that Fli-1 occupies the early megakaryocyte-specific gene αIIb in vivo. Moreover, our work suggested a mechanism for Fli-1 function by showing that Fli-1 facilitates GATA-1/FOG-1 dependent expression of the αIIb gene. However, studies by others with a targeted disruption of the Fli-1 gene in mice showed that while Fli-1 is essential for normal megakaryocyte maturation, αIIb mRNA levels were not significantly reduced in the resulting megakaryocytes, suggesting that a related Ets factor(s) might compensate for the loss of Fli-1. Here we show that the widely expressed pointed domain Ets protein GABPα specifically binds in vitro to Ets elements from two early megakaryocyte-specific genes, αIIb and c-mpl. Chromatin immunoprecipitation (ChIP) experiments using primary murine fetal liver-derived megakaryocytes reveal that GABPα associates with αIIb and c-mpl in vivo. Moreover, GABPα is capable of mediating GATA-1/FOG-1 synergy in the context of αIIb promoter constructs. These results suggest that GABPα contributes to megakaryocyte-restricted gene expression and is capable of at least partially compensating for the loss of Fli-1. However, loss of Fli-1 leads to a pronounced decrease in the expression of the late megakaryocyte-specific gene GPIX, indicating that compensation by GABPα is incomplete. Consistent with this observation, ChIP experiments fail to detect significant levels of GABPα at the regulatory region of GPIX while Fli-1 is readily detected there. Together, these results point to a model in which Fli-1 and GABPα serve overlapping, but distinct roles, during the development of megakaryocytes. GABPα may be important during early megakaryopoiesis, but Fli-1 exerting an essential role during late stages of maturation.

scholarly journals Similarities and differences in the transcriptional control of expression of the mouse TSLP gene in skin epidermis and intestinal epithelium

2017 ◽  
Vol 114 (6) ◽  
pp. E951-E960 ◽  
Author(s):  
Krishna Priya Ganti ◽  
Atish Mukherji ◽  
Milan Surjit ◽  
Mei Li ◽  
Pierre Chambon
Keyword(s):  
Retinoic Acid ◽  
Rna Polymerase Ii ◽  
Promoter Region ◽  
Transcriptional Control ◽  
Retinoic Acid Receptor ◽  
Regulatory Region ◽  
Mouse Skin ◽  
Wild Type Mouse ◽  
Epidermal Keratinocytes

We previously reported that selective ablation of the nuclear receptors retinoid X receptor (RXR)-α and RXR-β in mouse epidermal keratinocytes (RXR-αβep−/−) or a topical application of active vitamin D3 (VD3) and/or all-trans retinoic acid (RA) on wild-type mouse skin induces a human atopic dermatitis-like phenotype that is triggered by an increased expression of the thymic stromal lymphopoietin (TSLP) proinflammatory cytokine. We demonstrate here that in epidermal keratinocytes, unliganded heterodimers of vitamin D receptor (VDR)/RXR-α and retinoic acid receptor-γ (RAR-γ)/RXR-β are bound as repressing complexes to their cognate DNA-binding sequence(s) (DBS) in the TSLP promoter regulatory region. Treatments with either an agonistic VD3 analog or RA dissociate the repressing complexes and recruit coactivator complexes and RNA polymerase II, thereby inducing transcription. Furthermore, we identified several functional NF-κB, activator protein 1 (AP1), STAT, and Smad DBS in the TSLP promoter region. Interestingly, many of these transcription factors and DBS present in the TSLP promoter region are differentially used in intestinal epithelial cell(s) (IEC). Collectively, our study reveals that, in vivo within their heterodimers, the RXR and RAR isotypes are not functionally redundant, and it also unveils the combinatorial mechanisms involved in the tissue-selective regulation of TSLP transcription in epidermal keratinocytes and IEC.

scholarly journals Characterizing a distal muscle enhancer in the mouse Igf2 locus

2016 ◽  
Vol 48 (2) ◽  
pp. 167-172 ◽  
Author(s):  
Damir Alzhanov ◽  
Peter Rotwein
Keyword(s):  
Skeletal Muscle ◽  
Transcriptional Control ◽  
Fluorescent Protein ◽  
Artificial Chromosome ◽  
Control Element ◽  
Specific Gene ◽  
Reporter System ◽  
Chromosomal Locus ◽  
Igf2 Gene

Insulin-like growth factor-2 (IGF2) is highly expressed in skeletal muscle and was identified as a quantitative trait locus for muscle mass. Yet little is known about mechanisms of its regulation in muscle. Recently, a DNA segment found ∼100 kb from the Igf2 gene was identified as a possible muscle transcriptional control element. Here we have developed an in vivo reporter system to assess this putative enhancer by substituting nuclear (n) EGFP for Igf2 coding exons in a bacterial artificial chromosome containing the mouse Igf2 - H19 chromosomal locus. After stable transfection into a mesenchymal stem cell line, individual clones were converted to myoblasts and underwent progressive muscle-specific gene expression and myotube formation in differentiation medium. Transgenic mRNA and nuclear-targeted enhanced green fluorescent protein were produced coincident with endogenous Igf2 mRNA, but only in lines containing an intact distal conserved DNA element. Our results show that a 294 bp DNA fragment containing two E-boxes is a necessary and sufficient long-range enhancer for induction of Igf2 gene transcription during skeletal muscle differentiation and provides a robust experimental platform for its further functional dissection.

scholarly journals Type III-A CRISPR systems as a versatile gene knockdown technology

2020 ◽  
Author(s):  
Walter T. Woodside ◽  
Nikita Vantsev ◽  
Michael P. Terns
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Bacterial Species ◽  
Distinct Type ◽  
Gene Knockdown ◽  
Control Of Gene Expression ◽  
Type Iii ◽  
Dna And Rna ◽  
Pathway Analyses

AbstractCRISPR-Cas systems are functionally diverse prokaryotic anti-viral defense systems, which encompass six distinct types (I-VI) that each encode different effector Cas nucleases with distinct nucleic acid cleavage specificities. By harnessing the unique attributes of the various CRISPR-Cas systems, a range of innovative CRISPR-based DNA and RNA targeting tools and technologies have been developed. Here, we exploit the ability of type III-A CRISPR-Cas systems to carry out RNA-guided and sequence-specific target RNA cleavage for establishment of research tools for post-transcriptional control of gene expression. Type III-A systems from three bacterial species (L. lactis, S. epidermidis and S. thermophilus) were each expressed on a single plasmid in E. coli and the efficiency and specificity of gene knockdown was assessed by Northern blot analysis. We show that engineered type III-A modules can be programmed using tailored CRISPR RNAs to efficiently knock down gene expression of both coding and non-coding RNAs in vivo. Moreover, simultaneous degradation of multiple cellular mRNA transcripts can be directed by utilizing a CRISPR array expressing corresponding gene-targeting crRNAs. Our results demonstrate the utility of distinct type III-A modules to serve as effective gene knockdown platforms in heterologous cells. This transcriptome engineering technology has the potential to be further refined and exploited for key applications including gene discovery and gene pathway analyses in additional prokaryotic and perhaps eukaryotic cells and organisms.

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