scholarly journals Syntaxin 1A Gene Is Negatively Regulated in a Cell/Tissue Specific Manner by YY1 Transcription Factor, Which Binds to the −183 to −137 Promoter Region Together with Gene Silencing Factors Including Histone Deacetylase

Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 146
Author(s):  
Takahiro Nakayama ◽  
Toshiyuki Fukutomi ◽  
Yasuo Terao ◽  
Kimio Akagawa
Keyword(s):  
Transcription Factor ◽  
Gene Silencing ◽  
Protein Complex ◽  
Promoter Region ◽  
Neuronal Cell ◽  
Syntaxin 1A ◽  
Tissue Specific ◽  
Cell Tissue ◽  
Specific Manner ◽  
A Cell

The HPC-1/syntaxin 1A (Stx1a) gene, which is involved in synaptic transmission and neurodevelopmental disorders, is a TATA-less gene with several transcription start sites. It is activated by the binding of Sp1 and acetylated histone H3 to the −204 to +2 core promoter region (CPR) in neuronal cell/tissue. Furthermore, it is depressed by the association of class 1 histone deacetylases (HDACs) to Stx1a–CPR in non-neuronal cell/tissue. To further clarify the factors characterizing Stx1a gene silencing in non-neuronal cell/tissue not expressing Stx1a, we attempted to identify the promoter region forming DNA–protein complex only in non-neuronal cells. Electrophoresis mobility shift assays (EMSA) demonstrated that the −183 to −137 OL2 promoter region forms DNA–protein complex only in non-neuronal fetal rat skin keratinocyte (FRSK) cells which do not express Stx1a. Furthermore, the Yin-Yang 1 (YY1) transcription factor binds to the −183 to −137 promoter region of Stx1a in FRSK cells, as shown by competitive EMSA and supershift assay. Chromatin immunoprecipitation assay revealed that YY1 in vivo associates to Stx1a–CPR in cell/tissue not expressing Stx1a and that trichostatin A treatment in FRSK cells decreases the high-level association of YY1 to Stx1a-CPR in default. Reporter assay indicated that YY1 negatively regulates Stx1a transcription. Finally, mass spectrometry analysis showed that gene silencing factors, including HDAC1, associate onto the −183 to −137 promoter region together with YY1. The current study is the first to report that Stx1a transcription is negatively regulated in a cell/tissue-specific manner by YY1 transcription factor, which binds to the −183 to −137 promoter region together with gene silencing factors, including HDAC.

scholarly journals Myostatin/SMAD4 signaling-mediated regulation of miR-124-3p represses glucocorticoid receptor expression and inhibits adipocyte differentiation

2019 ◽  
Vol 316 (4) ◽  
pp. E635-E645 ◽  
Author(s):  
Kaiqing Liu ◽  
Xinbao Zhang ◽  
Wei Wei ◽  
Xin Liu ◽  
Ye Tian ◽  
...  
Keyword(s):  
Glucocorticoid Receptor ◽  
Muscle Tissue ◽  
Promoter Region ◽  
Adipocyte Differentiation ◽  
Adipogenic Differentiation ◽  
Intramuscular Fat ◽  
Fat Deposition ◽  
Receptor Expression ◽  
Tissue Specific ◽  
Specific Manner

The mechanism of adipocyte regulation specifically in muscle and the influence of muscle tissue on intramuscular fat deposition are unknown. Our previous studies have shown that myostatin, a myokine, is involved in inhibiting the differentiation of preadipocytes and may be a potential regulator that affects the deposition of intramuscular fat. Myostatin inhibited adipogenesis by downregulating the expression of glucocorticoid receptor (GR) in porcine preadipocytes. However, the mechanism of regulation is not yet clear. In this study, we demonstrate microRNA (miR-124-3p) mediates regulation of GR by myostatin. We found that miR-124-3p can target GR 3'-UTR and negatively regulate GR expression. We demonstrate that overexpression of miR-124-3p can reduce differentiation of 3T3-L1 cells by inhibiting GR, and vice versa. The expression of miR-124-3p was upregulated in 3T3-L1 cells treated with myostatin. Further study revealed that myostatin also promotes the expression of SMAD4 and its transfer and localization to the nucleus. The activated myostatin/SMAD4 signal promotes the expression of miR-124-3p by SMAD4 binding to the promoter region of miR-124-3p. When myostatin or SMAD4 activity is inhibited, the upregulation of miR-124-3p is also inhibited. All of these findings suggested that myostatin could inhibit adipogenic differentiation of 3T3-L1 cells by activating miR-124-3p to inhibit GR. These data may provide an explanation for how myostatin signaling affects intramuscular fat deposition in a tissue-specific manner.

scholarly journals Cell and tissue type independent age-associated DNA methylation changes are not rare but common

2018 ◽  
Author(s):  
Tianyu Zhu ◽  
Shijie C Zheng ◽  
Dirk S. Paul ◽  
S. Horvath ◽  
Andrew E. Teschendorff
Keyword(s):  
Dna Methylation ◽  
Cell Types ◽  
Tissue Type ◽  
Tissue Cell ◽  
Cell Type ◽  
Tissue Specific ◽  
Cell Tissue ◽  
A Cell ◽  
High Degree ◽  
Do So

AbstractAge-associated DNA methylation changes have been widely reported across many different tissue and cell types. Epigenetic ‘clocks’ that can predict chronological age with a surprisingly high degree of accuracy appear to do so independently of tissue and cell-type, suggesting that a component of epigenetic drift is cell-type independent. However, the relative amount of age-associated DNAm changes that are specific to a cell or tissue type versus the amount that occurs independently of cell or tissue type is unclear and a matter of debate, with a recent study concluding that most epigenetic drift is tissue-specific. Here, we perform a novel comprehensive statistical analysis, including matched multi cell-type and multi-tissue DNA methylation profiles from the same individuals and adjusting for cell-type heterogeneity, demonstrating that a substantial amount of epigenetic drift, possibly over 70%, is shared between significant numbers of different tissue/cell types. We further show that ELOVL2 is not unique and that many other CpG sites, some mapping to genes in the Wnt and glutamate receptor signaling pathways, are altered with age across at least 10 different cell/tissue types. We propose that while most age-associated DNAm changes are shared between cell-types that the putative functional effect is likely to be tissue-specific.

scholarly journals SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans

2020 ◽  
Author(s):  
Charlotte P. Choi ◽  
Rebecca J. Tay ◽  
Margaret R. Starostik ◽  
Suhua Feng ◽  
James J. Moresco ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Protein Complex ◽  
Ectopic Expression ◽  
Germline Development ◽  
Male And Female ◽  
C Elegans ◽  
The Core ◽  
Specific Manner ◽  
Specific Regulation ◽  
Male Specific

ABSTRACTPiwi-interacting RNAs (piRNAs) play essential roles in silencing repetitive elements to promote fertility in metazoans. Studies in worms, flies, and mammals reveal that piRNAs are expressed in a sex-specific manner. However, the mechanisms underlying this sex-specific regulation are unknown. Here we identify SNPC-1.3, a variant of a conserved subunit of the snRNA activating protein complex, as a male-specific piRNA transcription factor in C. elegans. Binding of SNPC-1.3 at male piRNA loci drives spermatogenic piRNA transcription and requires the core piRNA transcription factor SNPC-4. Loss of snpc-1.3 leads to depletion of male piRNAs and defects in male-dependent fertility. Furthermore, TRA-1, a master regulator of sex determination, binds to the snpc-1.3 promoter and represses its expression during oogenesis. Loss of TRA-1 targeting causes ectopic expression of snpc-1.3 and male piRNAs during oogenesis. Thus, sexual dimorphic regulation of snpc-1.3 coordinates male and female piRNA expression during germline development.

scholarly journals GRAM: A generalized model to predict the molecular effect of a non-coding variant in a cell-type specific manner

2018 ◽  
Author(s):  
Shaoke Lou ◽  
Kellie A. Cotter ◽  
Tianxiao Li ◽  
Jin Liang ◽  
Hussein Mohsen ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Cell Line ◽  
Cell Lines ◽  
K562 Cell ◽  
Cell Type ◽  
Generalized Model ◽  
Molecular Effect ◽  
Specific Manner ◽  
A Cell ◽  
Coding Variants

AbstractThere has been much effort to prioritize genomic variants with respect to their impact on “function”. However, function is often not precisely defined: Sometimes, it is the disease association of a variant; other times, it reflects a molecular effect on transcription or epigenetics. Here we coupled multiple genomic predictors to build GRAM, a generalized model, to predict a well-defined experimental target: the expression-modulating effect of a non-coding variant in a cell-specific manner. As a first step, we performed feature engineering: using a LASSO regularized linear model, we found transcription factor (TF) binding most predictive, especially for TFs that are hubs in the regulatory network; in contrast, evolutionary conservation, a popular feature in many other functional-impact predictors, has almost no contribution. Moreover, TF binding inferred from in vitro SELEX is as effective as that from in vivo ChIP-Seq. Second, we implemented GRAM integrating SELEX features and expression profiles. The program combines a universal regulatory score for a variant in a non-coding element with a modifier score reflecting the particular cell type. We benchmarked GRAM on a large-scale MPRA dataset in the GM12878 cell line, achieving a ROC score of ∼0.73; performance on the K562 cell line was similar. Finally, we evaluated the performance of GRAM on targeted regions using luciferase assays in MCF7 and K562 cell lines. We noted that changing the insertion position of the construct relative to the reporter gene gives very different results, highlighting the importance of carefully defining the functional target the model is predicting.Author SummaryNoncoding variants lie outside of protein-coding regions, and are found to have disease associations. However, knowledge on the molecular effect of these non-coding variants in a cell-specific context is very limited. Also, different output between multiple experiment platforms may introduce extra complexity in analyzing the molecular function of these variants. We developed GRAM, a generalized model to predict molecular effect of non-coding variants in multiple cell types for different experimental platforms. We first selected the most informative cell-independent SELEX transcription factor binding score on the variant locus as features and then combine cell-specific gene expression profile to build a multi-step prediction model. GRAM has been successfully tested on both MPRA and Luciferase assay, and on three different cell lines: GM12878, K562 and MCF7, shows high performance.

scholarly journals Novel Insights into the Role of Caveolin-2 in Cell- and Tissue-Specific Signaling and Function

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Grzegorz Sowa
Keyword(s):  
Tissue Type ◽  
Major Protein ◽  
Direct Role ◽  
Tissue Specific ◽  
Caveolin 1 ◽  
Cell Tissue ◽  
A Cell ◽  
Protein Components ◽  
And Function

Caveolin-2 is one of the major protein components of cholesterol- and glycosphingolipid-rich flask-shaped invaginations of plasma membrane caveolae. A new body of evidence suggests that caveolin-2 plays an important, and often more direct, role than caveolin-1 in regulating signaling and function in a cell- and tissue type-specific manner. The purpose of this paper is to primarily focus on discussing how these recent discoveries may help better understand the specific contribution of caveolin-2 to lipid raft- and caveolae-regulated cell/tissue-specific signaling and functions.

scholarly journals Sialylation of Glycosylphosphatidylinositol (GPI) Anchors of Mammalian Prions Is Regulated in a Host-, Tissue-, and Cell-specific Manner

2016 ◽  
Vol 291 (33) ◽  
pp. 17009-17019 ◽  
Author(s):  
Elizaveta Katorcha ◽  
Saurabh Srivastava ◽  
Nina Klimova ◽  
Ilia V. Baskakov
Keyword(s):  
Cultured Cells ◽  
Host Tissue ◽  
Prion Strain ◽  
Cell Tissue ◽  
Specific Manner ◽  
A Cell ◽  
Conformational Conversion ◽  
The Brain ◽  
C2c12 Myotube ◽  
Mammalian Prions

Prions or PrPSc are proteinaceous infectious agents that consist of misfolded, self-replicating states of the prion protein or PrPC. PrPC is posttranslationally modified with N-linked glycans and a sialylated glycosylphosphatidylinositol (GPI) anchor. Conformational conversion of PrPC gives rise to glycosylated and GPI-anchored PrPSc. The question of the sialylation status of GPIs within PrPSc has been controversial. Previous studies that examined scrapie brains reported that both sialo- and asialo-GPIs were present in PrPSc, with the majority being asialo-GPIs. In contrast, recent work that employed cultured cells claimed that only PrPC with sialylo-GPIs could be recruited into PrPSc, whereas PrPC with asialo-GPIs inhibited conversion. To resolve this controversy, we analyzed the sialylation status of GPIs within PrPSc generated in the brain, spleen, or cultured N2a or C2C12 myotube cells. We found that recruiting PrPC with both sialo- and asialo-GPIs is a common feature of PrPSc. The mixtures of sialo- and asialo-GPIs were observed in PrPSc universally regardless of prion strain as well as host, tissue, or type of cells that produced PrPSc. Remarkably, the proportion of sialo- versus asialo-GPIs was found to be controlled by host, tissue, and cell type but not prion strain. In summary, this study found no strain-specific preferences for selecting PrPC with sialo- versus asialo-GPIs. Instead, this work suggests that the sialylation status of GPIs within PrPSc is regulated in a cell-, tissue-, or host-specific manner and is likely to be determined by the specifics of GPI biosynthesis.

TheDrosophila daughterlessgene autoregulates and is controlled by both positive and negativecisregulation

Development ◽  
2001 ◽  
Vol 128 (23) ◽  
pp. 4705-4714 ◽  
Author(s):  
John E. Smith ◽  
Claire Cronmiller
Keyword(s):  
Negative Regulation ◽  
Fourth Chromosome ◽  
Developmentally Regulated ◽  
Tissue Specific ◽  
Binding Partner ◽  
Helix Loop Helix ◽  
Specific Manner ◽  
Specific Allele ◽  
A Cell ◽  
Bhlh Transcription Factors

As the only class I helix-loop-helix transcription factor in Drosophila, Daughterless (Da) has generally been regarded as a ubiquitously expressed binding partner for other developmentally regulated bHLH transcription factors. From analysis of a novel tissue-specific allele, dalyh, we show that da expression is not constitutive, but is dynamically regulated. This transcriptional regulation includes somatic ovary-specific activation, autoregulation and negative regulation. Unexpectedly, the diverse functions of da may require that expression levels be tightly controlled in a cell and/or tissue-specific manner. Our analysis of dalyh identifies it as the first springer insertion that functions as an insulating element, with its disruptive activity mediated by the product of a fourth chromosome gene, Suppressor of lyh [Su(lyh)].

scholarly journals Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor

Blood ◽  
2010 ◽  
Vol 115 (26) ◽  
pp. 5376-5384 ◽  
Author(s):  
Yair Benita ◽  
Zhifang Cao ◽  
Cosmas Giallourakis ◽  
Chun Li ◽  
Agnès Gardet ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Transcription Factor ◽  
T Cell ◽  
T Cell Development ◽  
Gene Enrichment ◽  
Cell Tissue ◽  
Development And Differentiation ◽  
A Cell ◽  
And Function

Abstract The identification of transcriptional regulatory networks, which control tissue-specific development and function, is of central importance to the understanding of lymphocyte biology. To decipher transcriptional networks in T-cell development and differentiation we developed a browsable expression atlas and applied a novel quantitative method to define gene sets most specific to each of the represented cell subsets and tissues. Using this system, body atlas size datasets can be used to examine gene enrichment profiles from a cell/tissue perspective rather than gene perspective, thereby identifying highly enriched genes within a cell type, which are often key to cellular differentiation and function. A systems analysis of transcriptional regulators within T cells during different phases of development and differentiation resulted in the identification of known key regulators and uncharacterized coexpressed regulators. ZBTB25, a BTB-POZ family transcription factor, was identified as a highly T cell–enriched transcription factor. We provide evidence that ZBTB25 functions as a negative regulator of nuclear factor of activated T cells (NF-AT) activation, such that RNA interference mediated knockdown resulted in enhanced activation of target genes. Together, these findings suggest a novel mechanism for NF-AT mediated gene expression and the compendium of expression data provides a quantitative platform to drive exploration of gene expression across a wide range of cell/tissue types.

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