scholarly journals Antisense lncRNA transcription drives stochastic Protocadherin α promoter choice

2018 ◽  
Author(s):  
Daniele Canzio ◽  
Chiamaka L. Nwakeze ◽  
Adan Horta ◽  
Sandy M. Rajkumar ◽  
Eliot L. Coffey ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
Neural Circuit ◽  
Antisense Transcription ◽  
Dna Demethylation ◽  
Ctcf Binding ◽  
Gene Promoters ◽  
Protein Coding ◽  
Close Proximity ◽  
A Cell

SUMMARYStochastic and combinatorial activation of clustered Protocadherin (Pcdh) α, β, and γ gene promoters generates a cell-surface identity code in individual neurons that functions in neural circuit assembly. Here we show that Pcdhα promoter choice requires transcription of a long noncoding RNA (lncRNA) initiated from newly identified promoters located in the protein coding sequence of each Pcdhα exon. Antisense transcription of the lncRNA through the sense promoter results in its activation and in DNA demethylation of the binding sites for the CCCTC-binding protein, CTCF, located in close proximity to both sense and antisense promoters. Increased CTCF binding promotes the assembly of long-range DNA contacts between the activated promoter and a neuron-specific enhancer, thus locking in the epigenetic state of the stochastically chosen Pcdhα promoter. Examination of this hierarchical molecular mechanism in differentiating olfactory sensory neurons, suggests that antisense Pcdhα transcription is a key prerequisite for stochastic Pcdhα promoter choice in vivo.

scholarly journals Angiogenic patterning by STEEL, an endothelial-enriched long noncoding RNA

2018 ◽  
Vol 115 (10) ◽  
pp. 2401-2406 ◽  
Author(s):  
H. S. Jeffrey Man ◽  
Aravin N. Sukumar ◽  
Gabrielle C. Lam ◽  
Paul J. Turgeon ◽  
Matthew S. Yan ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
De Novo ◽  
Feedback Inhibition ◽  
Body Position ◽  
In Vivo Model ◽  
Protein Coding ◽  
Angiogenic Potential ◽  
Hemodynamic Forces

Endothelial cell (EC)-enriched protein coding genes, such as endothelial nitric oxide synthase (eNOS), define quintessential EC-specific physiologic functions. It is not clear whether long noncoding RNAs (lncRNAs) also define cardiovascular cell type-specific phenotypes, especially in the vascular endothelium. Here, we report the existence of a set of EC-enriched lncRNAs and define a role for spliced-transcript endothelial-enriched lncRNA (STEEL) in angiogenic potential, macrovascular/microvascular identity, and shear stress responsiveness. STEEL is expressed from the terminus of the HOXD locus and is transcribed antisense to HOXD transcription factors. STEEL RNA increases the number and integrity of de novo perfused microvessels in an in vivo model and augments angiogenesis in vitro. The STEEL RNA is polyadenylated, nuclear enriched, and has microvascular predominance. Functionally, STEEL regulates a number of genes in diverse ECs. Of interest, STEEL up-regulates both eNOS and the transcription factor Kruppel-like factor 2 (KLF2), and is subject to feedback inhibition by both eNOS and shear-augmented KLF2. Mechanistically, STEEL up-regulation of eNOS and KLF2 is transcriptionally mediated, in part, via interaction of chromatin-associated STEEL with the poly-ADP ribosylase, PARP1. For instance, STEEL recruits PARP1 to the KLF2 promoter. This work identifies a role for EC-enriched lncRNAs in the phenotypic adaptation of ECs to both body position and hemodynamic forces and establishes a newer role for lncRNAs in the transcriptional regulation of EC identity.

scholarly journals The 3′ processing of antisense RNAs physically links to chromatin-based transcriptional control

2020 ◽  
Vol 117 (26) ◽  
pp. 15316-15321 ◽  
Author(s):  
Xiaofeng Fang ◽  
Zhe Wu ◽  
Oleg Raitskin ◽  
Kimberly Webb ◽  
Philipp Voigt ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
Transcriptional Control ◽  
Rna Binding ◽  
Antisense Transcription ◽  
Set Domain ◽  
Antisense Transcripts ◽  
Polycomb Repressive Complex 2 ◽  
Active Transcription ◽  
Transcriptional Output

Noncoding RNA plays essential roles in transcriptional control and chromatin silencing. AtArabidopsis thaliana FLC,antisense transcription quantitatively influences transcriptional output, but the mechanism by which this occurs is still unclear. Proximal polyadenylation of the antisense transcripts by FCA, an RNA-binding protein that physically interacts with RNA 3′ processing factors, reducesFLCtranscription. This process genetically requires FLD, a homolog of the H3K4 demethylase LSD1. However, the mechanism linking RNA processing to FLD function had not been established. Here, we show that FLD tightly associates with LUMINIDEPENDENS (LD) and SET DOMAIN GROUP 26 (SDG26) in vivo, and, together, they prevent accumulation of monomethylated H3K4 (H3K4me1) over theFLCgene body. SDG26 interacts with the RNA 3′ processing factor FY (WDR33), thus linking activities for proximal polyadenylation of the antisense transcripts to FLD/LD/SDG26-associated H3K4 demethylation. We propose this demethylation antagonizes an active transcription module, thus reducing H3K36me3 accumulation and increasing H3K27me3. Consistent with this view, we show that Polycomb Repressive Complex 2 (PRC2) silencing is genetically required by FCA to repressFLC. Overall, our work provides insights into RNA-mediated chromatin silencing.

scholarly journals Synergistic transcriptional activation by CTF/NF-I and the estrogen receptor involves stabilized interactions with a limiting target factor.

1991 ◽  
Vol 11 (6) ◽  
pp. 2937-2945 ◽  
Author(s):  
E Martinez ◽  
Y Dusserre ◽  
W Wahli ◽  
N Mermod
Keyword(s):  
Estrogen Receptor ◽  
Dna Binding ◽  
Transcriptional Activation ◽  
Transcription Initiation ◽  
Limiting Factor ◽  
Gene Promoters ◽  
Protein Coding ◽  
Transcriptional Activation Domain

Transcription initiation at eukaryotic protein-coding gene promoters is regulated by a complex interplay of site-specific DNA-binding proteins acting synergistically or antagonistically. Here, we have analyzed the mechanisms of synergistic transcriptional activation between members of the CCAAT-binding transcription factor/nuclear factor I (CTF/NF-I) family and the estrogen receptor. By using cotransfection experiments with HeLa cells, we show that the proline-rich transcriptional activation domain of CTF-1, when fused to the GAL4 DNA-binding domain, synergizes with each of the two estrogen receptor-activating regions. Cooperative DNA binding between the GAL4-CTF-1 fusion and the estrogen receptor does not occur in vitro, and in vivo competition experiments demonstrate that both activators can be specifically inhibited by the overexpression of a proline-rich competitor, indicating that a common limiting factor is mediating their transcriptional activation functions. Furthermore, the two activators functioning synergistically are much more resistant to competition than either factor alone, suggesting that synergism between CTF-1 and the estrogen receptor is the result of a stronger tethering of the limiting target factor(s) to the two promoter-bound activators.

scholarly journals Ikaros and GATA-1 Combinatorial Effect Is Required for Silencing of Human γ-Globin Genes

2008 ◽  
Vol 29 (6) ◽  
pp. 1526-1537 ◽  
Author(s):  
Stefania Bottardi ◽  
Julie Ross ◽  
Vincent Bourgoin ◽  
Nasser Fotouhi-Ardakani ◽  
El Bachir Affar ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Globin Gene ◽  
Gene Promoters ◽  
Globin Genes ◽  
Close Proximity ◽  
Transcriptional Switch ◽  
Globin Gene Regulation ◽  
First Time ◽  
Globin Gene Expression

ABSTRACT During development and erythropoiesis, globin gene expression is finely modulated through an important network of transcription factors and chromatin modifying activities. In this report we provide in vivo evidence that endogenous Ikaros is recruited to the human β-globin locus and targets the histone deacetylase HDAC1 and the chromatin remodeling protein Mi-2 to the human γ-gene promoters, thereby contributing to γ-globin gene silencing at the time of the γ- to β-globin gene transcriptional switch. We show for the first time that Ikaros interacts with GATA-1 and enhances the binding of the latter to different regulatory regions across the locus. Consistent with these results, we show that the combinatorial effect of Ikaros and GATA-1 impairs close proximity between the locus control region and the human γ-globin genes. Since the absence of Ikaros also affects GATA-1 recruitment to GATA-2 promoter, we propose that the combinatorial effect of Ikaros and GATA-1 is not restricted to globin gene regulation.

scholarly journals Allele-Specific Binding of CTCF to the Multipartite Imprinting Control Region KvDMR1

2007 ◽  
Vol 27 (7) ◽  
pp. 2636-2647 ◽  
Author(s):  
Galina V. Fitzpatrick ◽  
Elena M. Pugacheva ◽  
Jong-Yeon Shin ◽  
Ziedulla Abdullaev ◽  
Youwen Yang ◽  
...  
Keyword(s):  
Control Region ◽  
Binding Sites ◽  
Noncoding Rna ◽  
Specific Binding ◽  
Ctcf Binding ◽  
Luciferase Reporter ◽  
Imprinting Control Region ◽  
Enhancer Blocking ◽  
Functional Components

ABSTRACT Paternal deletion of the imprinting control region (ICR) KvDMR1 results in loss of expression of the Kcnq1ot1 noncoding RNA and derepression of flanking paternally silenced genes. Truncation of Kcnq1ot1 also results in the loss of imprinted expression of these genes in most cases, demonstrating a role for the RNA or its transcription in gene silencing. However, enhancer-blocking studies indicate that KvDMR1 also contains chromatin insulator or silencer activity. In this report we demonstrate by electrophoretic mobility shift assays and chromatin immunoprecipitation the existence of two CTCF binding sites within KvDMR1 that are occupied in vivo only on the unmethylated paternally derived allele. Methylation interference and mutagenesis allowed the precise mapping of protein-DNA contact sites for CTCF within KvDMR1. Using a luciferase reporter assay, we mapped the putative transcriptional promoter for Kcnq1ot1 upstream and to a site functionally separable from enhancer-blocking activity and CTCF binding sites. Luciferase reporter assays also suggest the presence of an additional cis-acting element in KvDMR1 upstream of the putative promoter that can function as an enhancer. These results suggest that the KvDMR1 ICR consists of multiple, independent cis-acting modules. Dissection of KvDMR1 into its functional components should help elucidate the mechanism of its function in vivo.

scholarly journals The molecular chaperone Ydj1 is required for the p34CDC28-dependent phosphorylation of the cyclin Cln3 that signals its degradation.

1996 ◽  
Vol 16 (7) ◽  
pp. 3679-3684 ◽  
Author(s):  
J A Yaglom ◽  
A L Goldberg ◽  
D Finley ◽  
M Y Sherman
Keyword(s):  
Molecular Chaperone ◽  
Terminal Segment ◽  
Direct Role ◽  
Yeast Saccharomyces Cerevisiae ◽  
Free System ◽  
Close Proximity ◽  
Ubiquitin Proteasome ◽  
A Cell ◽  
Histone Kinase

The G1 cyclin Cln3 of the yeast Saccharomyces cerevisiae is rapidly degraded by the ubiquitin-proteasome pathway. This process is triggered by p34CDC28-dependent phosphorylation of Cln3. Here we demonstrate that the molecular chaperone Ydj1, a DnaJ homolog, is required for this phosphorylation. In a ydj1 mutant at the nonpermissive temperature, both phosphorylation and degradation of Cln3 were deficient. No change was seen upon inactivation of Sis1, another DnaJ homolog. The phosphorylation defect in the ydj1 mutant was specific to Cln3, because no reduction in the phosphorylation of Cln2 or histone H1, which also requires p34CDC28, was observed. Ydj1 was required for Cln3 phosphorylation and degradation rather than for the proper folding of this cyclin, since Cln3 produced in the ydj1 mutant was fully active in the stimulation of p34CDC28 histone kinase activity. Moreover, Ydj1 directly associates with Cln3 in close proximity to the segment that is phosphorylated and signals degradation. Thus, binding of Ydj1 to this domain of Cln3 seems to be essential for the phosphorylation and breakdown of this cyclin. In a cell-free system, purified Ydj1 stimulated the p34CDC28-dependent phosphorylation of the C-terminal segment of Cln3 and did not affect phosphorylation of Cln2 (as was found in vivo). The reconstitution of this process with pure components provides evidence of a direct role for the chaperone in the phosphorylation of Cln3.

scholarly journals MicroRNAs: Diverse Mechanisms of Action and Their Potential Applications as Cancer Epi-Therapeutics

Biomolecules ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1285
Author(s):  
Anna Sadakierska-Chudy
Keyword(s):  
Tumor Suppressor ◽  
Cancer Progression ◽  
Therapeutic Potential ◽  
Translation Regulation ◽  
Gene Promoters ◽  
Protein Coding ◽  
Mirna Genes ◽  
Potential Applications

Usually, miRNAs function post-transcriptionally, by base-pairing with the 3′UTR of target mRNAs, repressing protein synthesis in the cytoplasm. Furthermore, other regions including gene promoters, as well as coding and 5′UTR regions of mRNAs are able to interact with miRNAs. In recent years, miRNAs have emerged as important regulators of both translational and transcriptional programs. The expression of miRNA genes, similar to protein-coding genes, can be epigenetically regulated, in turn miRNA molecules (named epi-miRs) are able to regulate epigenetic enzymatic machinery. The most recent line of evidence indicates that miRNAs can influence physiological processes, such as embryonic development, cell proliferation, differentiation, and apoptosis as well as pathological processes (e.g., tumorigenesis) through epigenetic mechanisms. Some tumor types show repression of tumor-suppressor epi-miRs resulting in cancer progression and metastasis, hence these molecules have become novel therapeutic targets in the last few years. This review provides information about miRNAs involvement in the various levels of transcription and translation regulation, as well as discusses therapeutic potential of tumor-suppressor epi-miRs used in in vitro and in vivo anti-cancer therapy.

scholarly journals Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5’ ends

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wojciech Rosikiewicz ◽  
Jarosław Sikora ◽  
Tomasz Skrzypczak ◽  
Magdalena R. Kubiak ◽  
Izabela Makałowska
Keyword(s):  
Gene Expression ◽  
Antisense Transcription ◽  
Changing Environment ◽  
Antisense Gene ◽  
Protein Coding ◽  
Normal Tissues ◽  
Regulatory Processes ◽  
Elevated Expression ◽  
A Cell ◽  
Cancerous Cells

AbstractDespite the number of studies focused on sense-antisense transcription, the key question of whether such organization evolved as a regulator of gene expression or if this is only a byproduct of other regulatory processes has not been elucidated to date. In this study, protein-coding sense-antisense gene pairs were analyzed with a particular focus on pairs overlapping at their 5’ ends. Analyses were performed in 73 human transcription start site libraries. The results of our studies showed that the overlap between genes is not a stable feature and depends on which TSSs are utilized in a given cell type. An analysis of gene expression did not confirm that overlap between genes causes downregulation of their expression. This observation contradicts earlier findings. In addition, we showed that the switch from one promoter to another, leading to genes overlap, may occur in response to changing environment of a cell or tissue. We also demonstrated that in transfected and cancerous cells genes overlap is observed more often in comparison with normal tissues. Moreover, utilization of overlapping promoters depends on particular state of a cell and, at least in some groups of genes, is not merely coincidental.

scholarly journals A molecular logic of sensory coding revealed by optical tagging of physiologically-defined neuronal types

2019 ◽  
Author(s):  
Donghoon Lee ◽  
Maiko Kume ◽  
Timothy E Holy
Keyword(s):  
Neural Circuit ◽  
Strong Predictor ◽  
Ectopic Expression ◽  
Cell Types ◽  
Specific Cell ◽  
Molecular Logic ◽  
Neuronal Types ◽  
A Cell ◽  
Circuit Function

Neural circuit analysis relies on having molecular markers for specific cell types. However, for a cell type identified only by its circuit function, the process of identifying markers remains laborious. Here, we report physiological optical tagging sequencing (PhOTseq), a technique for tagging and expression-profiling cells based on their functional properties. We demonstrate that PhOTseq is capable of selecting rare cell types and enriching them by nearly one hundred-fold. We applied PhOTseq to the challenge of mapping receptor-ligand pairings among vomeronasal pheromone-sensing neurons in mice. Together with in vivo ectopic expression of vomeronasal chemoreceptors, PhOTseq identified the complete combinatorial receptor code for a specific set of ligands, and revealed that the primary sequence of a chemoreceptor was an unexpectedly strong predictor of functional similarity.

scholarly journals Cell-Surface Proteomic Profiling in the Fly Brain Uncovers New Wiring Regulators

2019 ◽  
Author(s):  
Jiefu Li ◽  
Shuo Han ◽  
Hongjie Li ◽  
Namrata D. Udeshi ◽  
Tanya Svinkina ◽  
...  
Keyword(s):  
Cell Surface ◽  
Neural Development ◽  
Neural Circuit ◽  
Single Cells ◽  
Projection Neurons ◽  
Proteomic Profiling ◽  
A Cell ◽  
Cell Type Specific ◽  
Multicellular Organisms

SUMMARYMolecular interactions at the cellular interface mediate organized assembly of single cells into tissues, and thus govern the development and physiology of multicellular organisms. Here, we developed a cell-type-specific, spatiotemporally-resolved approach to profile cell-surface proteomes in intact tissues. Quantitative profiling of cell-surface proteomes of Drosophila olfactory projection neurons (PNs) in pupae and adults revealed a global down-regulation of wiring molecules and an up-regulation of synaptic molecules in the transition from developing to mature PNs. A proteome-instructed in vivo screen identified 20 new cell-surface molecules regulating neural circuit assembly, many of which belong to evolutionarily conserved protein families not previously linked to neural development. Genetic analysis further revealed that the lipoprotein receptor LRP1 cell-autonomously controls PN dendrite targeting, contributing to the formation of a precise olfactory map. These findings highlight the power of temporally-resolved in situ cell-surface proteomic profiling in discovering new regulators of brain wiring.

Sign in / Sign up

Export Citation Format

Share Document