scholarly journals Genome-Wide Profiling of the Core Clock Protein BMAL1 Targets Reveals a Strict Relationship with Metabolism

2010 ◽  
Vol 30 (24) ◽  
pp. 5636-5648 ◽  
Author(s):  
Fumiyuki Hatanaka ◽  
Chiaki Matsubara ◽  
Jihwan Myung ◽  
Takashi Yoritaka ◽  
Naoko Kamimura ◽  
...  
Keyword(s):  
Dna Microarrays ◽  
Target Genes ◽  
Clock Genes ◽  
Significant Proportion ◽  
Circadian Gene ◽  
Circadian Expression ◽  
Genome Wide ◽  
E Boxes ◽  
Circadian Transcription ◽  
Clock Protein

ABSTRACT Circadian rhythms are common to most organisms and govern much of homeostasis and physiology. Since a significant fraction of the mammalian genome is controlled by the clock machinery, understanding the genome-wide signaling and epigenetic basis of circadian gene expression is essential. BMAL1 is a critical circadian transcription factor that regulates genes via E-box elements in their promoters. We used multiple high-throughput approaches, including chromatin immunoprecipitation-based systematic analyses and DNA microarrays combined with bioinformatics, to generate genome-wide profiles of BMAL1 target genes. We reveal that, in addition to E-boxes, the CCAATG element contributes to elicit robust circadian expression. BMAL1 occupancy is found in more than 150 sites, including all known clock genes. Importantly, a significant proportion of BMAL1 targets include genes that encode central regulators of metabolic processes. The database generated in this study constitutes a useful resource to decipher the network of circadian gene control and its intimate links with several fundamental physiological functions.

scholarly journals Oxidative Stress-Activated Zinc Cluster Protein Stb5 Has Dual Activator/Repressor Functions Required for Pentose Phosphate Pathway Regulation and NADPH Production

2006 ◽  
Vol 26 (17) ◽  
pp. 6690-6701 ◽  
Author(s):  
Marc Larochelle ◽  
Simon Drouin ◽  
François Robert ◽  
Bernard Turcotte
Keyword(s):  
Oxidative Stress ◽  
Pentose Phosphate Pathway ◽  
Chromatin Immunoprecipitation ◽  
Dna Microarrays ◽  
Target Genes ◽  
Pentose Phosphate ◽  
Zinc Cluster ◽  
Genome Wide ◽  
Pathway Regulation ◽  
Insight Into

ABSTRACT In Saccharomyces cerevisiae, zinc cluster protein Pdr1 can form homodimers as well as heterodimers with Pdr3 and Stb5, suggesting that different combinations of these proteins may regulate the expression of different genes. To gain insight into the interplay among these regulators, we performed genome-wide location analysis (chromatin immunoprecipitation with hybridization to DNA microarrays) and gene expression profiling. Unexpectedly, we observed that Stb5 shares only a few target genes with Pdr1 or Pdr3 in rich medium. Interestingly, upon oxidative stress, Stb5 binds and regulates the expression of most genes of the pentose phosphate pathway as well as of genes involved in the production of NADPH, a metabolite required for oxidative stress resistance. Importantly, deletion of STB5 results in sensitivity to diamide and hydrogen peroxide. Our data suggest that Stb5 acts both as an activator and as a repressor in the presence of oxidative stress. Furthermore, we show that Stb5 activation is not mediated by known regulators of the oxidative stress response. Integrity of the pentose phosphate pathway is required for the activation of Stb5 target genes but is not necessary for the increased DNA binding of Stb5 in the presence of diamide. These data suggest that Stb5 is a key player in the control of NADPH production for resistance to oxidative stress.

scholarly journals CRISPR/Cas9 screen for functional MYC binding sites reveals MYC-dependent vulnerabilities in K562 cells

2021 ◽  
Author(s):  
Marta Kazimierska ◽  
Marta Podralska ◽  
Magdalena Zurawek ◽  
Tomasz Wozniak ◽  
Marta Elzbieta Kasprzyk ◽  
...  
Keyword(s):  
Binding Sites ◽  
Target Genes ◽  
K562 Cells ◽  
Myelogenous Leukemia ◽  
Cancer Type ◽  
Genome Wide ◽  
A Genome ◽  
E Box ◽  
A Cell ◽  
E Boxes

The transcription factor MYC is a proto-oncogene with a well-documented essential role in the pathogenesis and maintenance of several types of cancer. MYC binds to specific E-box sequences in the genome to regulate expression of adjacent genes in a cell type- and developmental stage-specific manner. To date, a comprehensive analysis of direct MYC targets with essential roles in different types of cancer is missing. To enable identification of functional MYC binding sites and corresponding target genes, we designed a CRISPR/Cas9 library to destroy E-box sequences in a genome-wide fashion. As a proof of principle, using this library we identified several known and novel MYC targets critical for K562 chronic myelogenous leukemia cells and uncovered specific features of essential E-boxes. Our unique, well-validated tool opens new possibilities to gain novel insights into MYC-dependent vulnerabilities in any cancer type.

scholarly journals Circadian gene PER1 senses progesterone signal during human endometrial decidualization

2019 ◽  
Vol 243 (3) ◽  
pp. 229-242 ◽  
Author(s):  
Ying Zhang ◽  
Nan Meng ◽  
Haili Bao ◽  
Yufei Jiang ◽  
Ningjie Yang ◽  
...  
Keyword(s):  
Target Genes ◽  
Clock Genes ◽  
Circadian System ◽  
Homeostatic Regulation ◽  
Female Reproductive System ◽  
Circadian Gene ◽  
Female Reproduction ◽  
Reproductive Process ◽  
Reproductive Processes

Progesterone is an important hormone for female reproduction; however, how the fluctuation of progesterone acts upon reproductive processes remains largely unknown. Mounting evidence indicates a pivotal role of the circadian clock in sensing hormone dynamics for homeostatic regulation of physiological functions. Therefore, we sought to determine whether clock genes respond to progesterone signaling in female reproductive system. In this study, we tested the hypothesis that the circadian system could respond to progesterone signaling during human endometrial decidual transformation. The expression of the circadian gene PER1 increased immediately and remained elevated during human endometrial decidualization. The progesterone receptor activated PER1 transcription by directly binding to its promoter from the onset of the stromal proliferation-differentiation transition. PER1 knockout significantly downregulated the expression of some PGR target genes, and attenuated human endometrial decidual transformation by expediting FOXO1 protein degradation. In conclusion, progesterone could control the female reproductive process through sustained feedback from the circadian gene PER1, which is probably involved to P4-PR signaling responsiveness in the initiation and maintenance of decidualization.

scholarly journals The mutL Gene as a Genome-Wide Taxonomic Marker for High Resolution Discrimination of Lactiplantibacillus plantarum and Its Closely Related Taxa

2021 ◽  
Vol 9 (8) ◽  
pp. 1570
Author(s):  
Chien-Hsun Huang ◽  
Chih-Chieh Chen ◽  
Yu-Chun Lin ◽  
Chia-Hsuan Chen ◽  
Ai-Yun Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Target Genes ◽  
Marker Genes ◽  
Rrna Gene ◽  
Accurate Identification ◽  
Discrimination Power ◽  
Sequence Identity ◽  
Genome Wide ◽  
A Genome

The current taxonomy of the Lactiplantibacillus plantarum group comprises of 17 closely related species that are indistinguishable from each other by using commonly used 16S rRNA gene sequencing. In this study, a whole-genome-based analysis was carried out for exploring the highly distinguished target genes whose interspecific sequence identity is significantly less than those of 16S rRNA or conventional housekeeping genes. In silico analyses of 774 core genes by the cano-wgMLST_BacCompare analytics platform indicated that csbB, morA, murI, mutL, ntpJ, rutB, trmK, ydaF, and yhhX genes were the most promising candidates. Subsequently, the mutL gene was selected, and the discrimination power was further evaluated using Sanger sequencing. Among the type strains, mutL exhibited a clearly superior sequence identity (61.6–85.6%; average: 66.6%) to the 16S rRNA gene (96.7–100%; average: 98.4%) and the conventional phylogenetic marker genes (e.g., dnaJ, dnaK, pheS, recA, and rpoA), respectively, which could be used to separat tested strains into various species clusters. Consequently, species-specific primers were developed for fast and accurate identification of L. pentosus, L. argentoratensis, L. plantarum, and L. paraplantarum. During this study, one strain (BCRC 06B0048, L. pentosus) exhibited not only relatively low mutL sequence identities (97.0%) but also a low digital DNA–DNA hybridization value (78.1%) with the type strain DSM 20314T, signifying that it exhibits potential for reclassification as a novel subspecies. Our data demonstrate that mutL can be a genome-wide target for identifying and classifying the L. plantarum group species and for differentiating novel taxa from known species.

scholarly journals Genome-wide transcriptome profiling uncovers differential miRNAs and lncRNAs in ovaries of Hu sheep at different developmental stages

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Samina Shabbir ◽  
Prerona Boruah ◽  
Lingli Xie ◽  
Muhammad Fakhar-e-Alam Kulyar ◽  
Mohsin Nawaz ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Profiles ◽  
Ovarian Follicle ◽  
Follicular Development ◽  
Differentially Expressed ◽  
Ovary Development ◽  
Estrogen Metabolism ◽  
Genome Wide ◽  
Micro Rnas ◽  
Hu Sheep

AbstractOvary development is an important determinant of the procreative capacity of female animals. Here, we performed genome-wide sequencing of long non-coding RNAs (lncRNAs) and mRNAs on ovaries of 1, 3 and 8 months old Hu sheep to assess their expression profiles and roles in ovarian development. We identified 37,309 lncRNAs, 45,404 messenger RNAs (mRNAs) and 330 novel micro RNAs (miRNAs) from the transcriptomic analysis. Six thousand, seven hundred and sixteen (6716) mRNAs and 1972 lncRNAs were significantly and differentially expressed in ovaries of 1 month and 3 months old Hu sheep (H1 vs H3). These mRNAs and target genes of lncRNAs were primarily enriched in the TGF-β and PI3K-Akt signalling pathways which are closely associated with ovarian follicular development and steroid hormone biosynthesis regulation. We identified MSTRG.162061.1, MSTRG.222844.7, MSTRG.335777.1, MSTRG.334059.16, MSTRG.188947.6 and MSTRG.24344.3 as vital genes in ovary development by regulating CTNNB1, CCNA2, CDK2, CDC20, CDK1 and EGFR expressions. A total of 2903 mRNAs and 636 lncRNAs were differentially expressed in 3 and 8 months old ovaries of Hu sheep (H3 vs H8); and were predominantly enriched in PI3K-Akt, progesterone-mediated oocyte maturation, estrogen metabolism, ovulation from the ovarian follicle and oogenesis pathways. These lncRNAs were also found to regulate FGF7, PRLR, PTK2, AMH and INHBA expressions during follicular development. Our result indicates the identified genes participate in the development of the final stages of follicles and ovary development in Hu sheep.

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