scholarly journals Transcriptional and Epigenetic Regulation of Krüppel-Like Transcription Factors

2020 ◽  
Author(s):  
Morgan Salmon
Keyword(s):  
Transcription Factors ◽  
Epigenetic Regulation

scholarly journals Epigenetic regulation by the menin pathway

2017 ◽  
Vol 24 (10) ◽  
pp. T147-T159 ◽  
Author(s):  
Zijie Feng ◽  
Jian Ma ◽  
Xianxin Hua
Keyword(s):  
Transcription Factors ◽  
Cell Signaling ◽  
Signaling Pathways ◽  
Gene Transcription ◽  
Epigenetic Regulation ◽  
Posttranslational Modifications ◽  
Genetic Model ◽  
Mirna Biogenesis ◽  
Endocrine Organs

There is a trend of increasing prevalence of neuroendocrine tumors (NETs), and the inherited multiple endocrine neoplasia type 1 (MEN1) syndrome serves as a genetic model to investigate how NETs develop and the underlying mechanisms. Menin, encoded by the MEN1 gene, at least partly acts as a scaffold protein by interacting with multiple partners to regulate cellular homeostasis of various endocrine organs. Menin has multiple functions including regulation of several important signaling pathways by controlling gene transcription. Here, we focus on reviewing the recent progress in elucidating the key biochemical role of menin in epigenetic regulation of gene transcription and cell signaling, as well as posttranslational regulation of menin itself. In particular, we will review the progress in studying structural and functional interactions of menin with various histone modifiers and transcription factors such as MLL, PRMT5, SUV39H1 and other transcription factors including c-Myb and JunD. Moreover, the role of menin in regulating cell signaling pathways such as TGF-beta, Wnt and Hedgehog, as well as miRNA biogenesis and processing will be described. Further, the regulation of the MEN1 gene transcription, posttranslational modifications and stability of menin protein will be reviewed. These various modes of regulation by menin as well as regulation of menin by various biological factors broaden the view regarding how menin controls various biological processes in neuroendocrine organ homeostasis.

scholarly journals Gastrointestinal transcription factors drive lineage-specific developmental programs in organ specification and cancer

2019 ◽  
Vol 5 (12) ◽  
pp. eaax8898 ◽  
Author(s):  
Roshane Francis ◽  
Haiyang Guo ◽  
Catherine Streutker ◽  
Musaddeque Ahmed ◽  
Theodora Yung ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Epigenetic Regulation ◽  
Gastrointestinal Cancer ◽  
Chromatin Accessibility ◽  
Lineage Specification ◽  
Developmental Programs ◽  
Tissue Specific ◽  
Cancer Data ◽  
Gastrointestinal Tissue

Transcription factors (TFs) are spatially and temporally regulated during gut organ specification. Although accumulating evidence shows aberrant reactivation of developmental programs in cancer, little is known about how TFs drive lineage specification in development and cancer. We first defined gastrointestinal tissue–specific chromatin accessibility and gene expression during development, identifying the dynamic epigenetic regulation of SOX family of TFs. We revealed that Sox2 is not only essential for gastric specification, by maintaining chromatin accessibility at forestomach lineage loci, but also sufficient to promote forestomach/esophageal transformation upon Cdx2 deletion. By comparing our gastrointestinal lineage-specific transcriptome to human gastrointestinal cancer data, we found that stomach and intestinal lineage-specific programs are reactivated in Sox2high/Sox9high and Cdx2high cancers, respectively. By analyzing mice deleted for both Sox2 and Sox9, we revealed their potentially redundant roles in both gastric development and cancer, highlighting the importance of developmental lineage programs reactivated by gastrointestinal TFs in cancer.

scholarly journals Reprogramming and remodeling: transcriptional and epigenetic regulation of salicylic acid-mediated plant defense

2020 ◽  
Vol 71 (17) ◽  
pp. 5256-5268 ◽  
Author(s):  
Jian Chen ◽  
Michael Clinton ◽  
Guang Qi ◽  
Daowen Wang ◽  
Fengquan Liu ◽  
...  
Keyword(s):  
Salicylic Acid ◽  
Transcription Factors ◽  
Plant Defense ◽  
Epigenetic Regulation ◽  
Current Knowledge ◽  
Plant Immunity ◽  
Defense Responses ◽  
Transcriptional Networks ◽  
Transcriptional Reprogramming ◽  
Genomic Tools

Abstract As a plant hormone, salicylic acid (SA) plays essential roles in plant defense against biotrophic and hemibiotrophic pathogens. Significant progress has been made in understanding the SA biosynthesis pathways and SA-mediated defense signaling networks in the past two decades. Plant defense responses involve rapid and massive transcriptional reprogramming upon the recognition of pathogens. Plant transcription factors and their co-regulators are critical players in establishing a transcription regulatory network and boosting plant immunity. A multitude of transcription factors and epigenetic regulators have been discovered, and their roles in SA-mediated defense responses have been reported. However, our understanding of plant transcriptional networks is still limited. As such, novel genomic tools and bioinformatic techniques will be necessary if we are to fully understand the mechanisms behind plant immunity. Here, we discuss current knowledge, provide an update on the SA biosynthesis pathway, and describe the transcriptional and epigenetic regulation of SA-mediated plant immune responses.

scholarly journals Genome-wide identification and characterisation of HOT regions in the human genome

2016 ◽  
Author(s):  
Hao Li ◽  
Feng Liu ◽  
Chao Ren ◽  
Xiaochen Bo ◽  
Wenjie Shu
Keyword(s):  
Stem Cells ◽  
Transcription Factors ◽  
Embryonic Stem Cells ◽  
Epigenetic Regulation ◽  
Human Cell ◽  
Embryonic Stem ◽  
Cell Types ◽  
Genome Wide ◽  
Development And Differentiation ◽  
Epigenetic Analysis

AbstractHOT (high-occupancy target) regions, which are bound by a surprisingly large number of transcription factors, are considered to be among the most intriguing findings of recent years. An improved understanding of the roles that HOT regions play in biology would be afforded by knowing the constellation of factors that constitute these domains and by identifying HOT regions across the spectrum of human cell types. We characterised and validated HOT regions in embryonic stem cells (ESCs) and produced a catalogue of HOT regions in a broad range of human cell types. We found that HOT regions are associated with genes that control and define the developmental processes of the respective cell and tissue types. We also showed evidence of the developmental persistence of HOT regions at primitive enhancers and demonstrate unique signatures of HOT regions that distinguish them from typical enhancers and super-enhancers. Finally, we performed an epigenetic analysis to reveal the dynamic epigenetic regulation of HOT regions upon H1 differentiation. Taken together, our results provide a resource for the functional exploration of HOT regions and extend our understanding of the key roles of HOT regions in development and differentiation.

Dysregulation of Principal Cell miRNAs Facilitates Epigenetic Regulation of AQP2 and Results in Nephrogenic Diabetes Insipidus

2021 ◽  
pp. ASN.2020010031
Author(s):  
Federica Petrillo ◽  
Anna Iervolino ◽  
Tiziana Angrisano ◽  
Sabina Jelen ◽  
Vincenzo Costanzo ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Diabetes Insipidus ◽  
Epigenetic Regulation ◽  
Nephrogenic Diabetes Insipidus ◽  
Cell Function ◽  
Collecting Duct ◽  
Direct Interaction ◽  
Bioinformatic Analysis ◽  
Small Rna Sequencing ◽  
Sodium Reabsorption

BackgroundMicroRNAs (miRNAs), formed by cleavage of pre-microRNA by the endoribonuclease Dicer, are critical modulators of cell function by post-transcriptionally regulating gene expression.MethodsSelective ablation of Dicer in AQP2-expressing cells (DicerAQP2Cre+ mice) was used to investigate the role of miRNAs in the kidney collecting duct of mice.ResultsThe mice had severe polyuria and nephrogenic diabetes insipidus, potentially due to greatly reduced AQP2 and AQP4 levels. Although epithelial sodium channel levels were decreased in cortex and increased in inner medulla, amiloride-sensitive sodium reabsorption was equivalent in DicerAQP2Cre+ mice and controls. Small-RNA sequencing and proteomic analysis revealed 31 and 178 significantly regulated miRNAs and proteins, respectively. Integrated bioinformatic analysis of the miRNAome and proteome suggested alterations in the epigenetic machinery and various transcription factors regulating AQP2 expression in DicerAQP2Cre+ mice. The expression profile and function of three miRNAs (miR-7688-5p, miR-8114, and miR-409-3p) whose predicted targets were involved in epigenetic control (Phf2, Kdm5c, and Kdm4a) or transcriptional regulation (GATA3, GATA2, and ELF3) of AQP2 were validated. Luciferase assays could not demonstrate direct interaction of AQP2 or the three potential transcription factors with miR-7688-5p, miR-8114, and miR-409–3p. However, transfection of respective miRNA mimics reduced AQP2 expression. Chromatin immunoprecipitation assays demonstrated decreased Phf2 and significantly increased Kdm5c interactions at the Aqp2 gene promoter in DicerAQP2Cre+ mice, resulting in decreased RNA Pol II association.ConclusionsNovel evidence indicates miRNA-mediated epigenetic regulation of AQP2 expression.

scholarly journals Dynamic epigenetic regulation of glioblastoma tumorigenicity through LSD1 modulation of MYC expression

2015 ◽  
Vol 112 (30) ◽  
pp. E4055-E4064 ◽  
Author(s):  
David Kozono ◽  
Jie Li ◽  
Masayuki Nitta ◽  
Oltea Sampetrean ◽  
David Gonda ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Epigenetic Regulation ◽  
Low Frequencies ◽  
Primary Glioblastoma ◽  
Tumor Sphere ◽  
Histone 3 ◽  
Lysine Specific Demethylase ◽  
Core Set ◽  
Therapeutic Development ◽  
Viral Oncogene Homolog

The available evidence suggests that the lethality of glioblastoma is driven by small subpopulations of cells that self-renew and exhibit tumorigenicity. It remains unclear whether tumorigenicity exists as a static property of a few cells or as a dynamically acquired property. We used tumor-sphere and xenograft formation as assays for tumorigenicity and examined subclones isolated from established and primary glioblastoma lines. Our results indicate that glioblastoma tumorigenicity is largely deterministic, yet the property can be acquired spontaneously at low frequencies. Further, these dynamic transitions are governed by epigenetic reprogramming through the lysine-specific demethylase 1 (LSD1). LSD depletion increases trimethylation of histone 3 lysine 4 at the avian myelocytomatosis viral oncogene homolog (MYC) locus, which elevates MYC expression. MYC, in turn, regulates oligodendrocyte lineage transcription factor 2 (OLIG2), SRY (sex determining region Y)-box 2 (SOX2), and POU class 3 homeobox 2 (POU3F2), a core set of transcription factors required for reprogramming glioblastoma cells into stem-like states. Our model suggests epigenetic regulation of key transcription factors governs transitions between tumorigenic states and provides a framework for glioblastoma therapeutic development.

scholarly journals Epigenetic Regulation of Mouse Sex Determination by the Histone Demethylase Jmjd1a

Science ◽  
2013 ◽  
Vol 341 (6150) ◽  
pp. 1106-1109 ◽  
Author(s):  
Shunsuke Kuroki ◽  
Shogo Matoba ◽  
Mika Akiyoshi ◽  
Yasuko Matsumura ◽  
Hitoshi Miyachi ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Sex Determination ◽  
Epigenetic Regulation ◽  
Sex Reversal ◽  
Histone Demethylase ◽  
Developmental Gene ◽  
Histone Demethylation ◽  
Developmental Gene Expression ◽  
Male To Female

Developmental gene expression is defined through cross-talk between the function of transcription factors and epigenetic status, including histone modification. Although several transcription factors play crucial roles in mammalian sex determination, how epigenetic regulation contributes to this process remains unknown. We observed male-to-female sex reversal in mice lacking the H3K9 demethylase Jmjd1a and found that Jmjd1a regulates expression of the mammalian Y chromosome sex-determining gene Sry. Jmjd1a directly and positively controls Sry expression by regulating H3K9me2 marks. These studies reveal a pivotal role of histone demethylation in mammalian sex determination.

scholarly journals Epigenetic regulation of specific transcription factors in osteogenicdifferentiation of mesenchymal stem cells

2016 ◽  
Vol 40 ◽  
pp. 1040-1049 ◽  
Author(s):  
Milad ZADI HEYDARABAD ◽  
Mousa VATANMAKANIAN ◽  
Mina NIKASA ◽  
Majid FARSHDOUSTI HAGH
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Transcription Factors ◽  
Epigenetic Regulation

scholarly journals Epigenetic Regulation of Glycosylation in Cancer and Other Diseases

2021 ◽  
Vol 22 (6) ◽  
pp. 2980
Author(s):  
Rossella Indellicato ◽  
Marco Trinchera
Keyword(s):  
Dna Methylation ◽  
Inflammatory Bowel Disease ◽  
Transcription Factors ◽  
Epigenetic Regulation ◽  
Bowel Disease ◽  
Noncoding Rnas ◽  
Fine Tuning ◽  
Epigenetic Mechanisms ◽  
Complex Process ◽  
Inflammatory Bowel

In the last few decades, the newly emerging field of epigenetic regulation of glycosylation acquired more importance because it is unraveling physiological and pathological mechanisms related to glycan functions. Glycosylation is a complex process in which proteins and lipids are modified by the attachment of monosaccharides. The main actors in this kind of modification are the glycoenzymes, which are translated from glycosylation-related genes (or glycogenes). The expression of glycogenes is regulated by transcription factors and epigenetic mechanisms (mainly DNA methylation, histone acetylation and noncoding RNAs). This review focuses only on these last ones, in relation to cancer and other diseases, such as inflammatory bowel disease and IgA1 nephropathy. In fact, it is clear that a deeper knowledge in the fine-tuning of glycogenes is essential for acquiring new insights in the glycan field, especially if this could be useful for finding novel and personalized therapeutics.

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