scholarly journals Top2a promotes the development of social behavior via PRC2 and H3K27me3

2021 ◽  
Author(s):  
Yijie Geng ◽  
Tejia Zhang ◽  
Sean C. Godar ◽  
Brock R. Pluimer ◽  
Devin L. Harrison ◽  
...  
Keyword(s):  
Social Behavior ◽  
Binding Sites ◽  
Social Deficits ◽  
Topoisomerase Iiα ◽  
Human Infants ◽  
Polycomb Repressive Complex 2 ◽  
Gene Sets ◽  
Evolutionarily Conserved ◽  
Regulatory Complex ◽  
Core Symptoms

Human infants exhibit innate social behaviors at birth, yet little is understood about the embryonic development of sociality. We screened 1120 known drugs and found that embryonic inhibition of topoisomerase IIα (Top2a) resulted in lasting social deficits in zebrafish. In mice, prenatal Top2 inhibition caused behavioral defects related to core symptoms of autism, including impairments in social interaction and communication. Mutation of Top2a in zebrafish caused downregulation of a set of genes highly enriched for genes associated with autism in humans. Both the Top2a-regulated and autism-associated gene sets possess binding sites for polycomb repressive complex 2 (PRC2), a regulatory complex responsible for H3K27 trimethylation. Moreover, both gene sets are highly enriched for H3K27me3. Inhibition of PRC2 component Ezh2 rescued social deficits caused by Top2 inhibition. Therefore, Top2a is a key component of an evolutionarily conserved pathway that promotes the development of social behavior through PRC2 and H3K27me3.

scholarly journals Nuclear Import of TFIIB Is Mediated by Kap114p, a Karyopherin with Multiple Cargo-binding Domains

2005 ◽  
Vol 16 (7) ◽  
pp. 3200-3210 ◽  
Author(s):  
Jennifer L. Hodges ◽  
Jennifer H. Leslie ◽  
Nima Mosammaparast ◽  
Yurong Guo ◽  
Jeffrey Shabanowitz ◽  
...  
Keyword(s):  
Nuclear Import ◽  
Binding Sites ◽  
Binding Domains ◽  
Transcription Factor Iib ◽  
General Transcription Factor ◽  
Proteomic Approach ◽  
Evolutionarily Conserved ◽  
Import And Export ◽  
Transport Factors

Nuclear import and export is mediated by an evolutionarily conserved family of soluble transport factors, the karyopherins (referred to as importins and exportins). The yeast karyopherin Kap114p has previously been shown to import histones H2A and H2B, Nap1p, and a component of the preinitiation complex (PIC), TBP. Using a proteomic approach, we have identified several potentially new cargoes for Kap114p. These cargoes include another PIC component, the general transcription factor IIB or Sua7p, which interacted directly with Kap114p. Consistent with its role as a Sua7p import factor, deletion of KAP114 led to specific mislocalization of Sua7p to the cytoplasm. An interaction between Sua7p and TBP was also detected in cytosol, raising the possibility that both Sua7p and TBP can be coimported by Kap114p. We have also shown that Kap114p possesses multiple overlapping binding sites for its partners, Sua7p, Nap1p, and H2A and H2B, as well as RanGTP and nucleoporins. In addition, we have assembled an in vitro complex containing Sua7p, Nap1p, and histones H2A and H2B, suggesting that this Kap may import several proteins simultaneously. The import of more than one cargo at a time would increase the efficiency of each import cycle and may allow the regulation of coimported cargoes.

scholarly journals Identification of a mouse protein whose homolog in Saccharomyces cerevisiae is a component of the CCR4 transcriptional regulatory complex.

1995 ◽  
Vol 15 (7) ◽  
pp. 3487-3495 ◽  
Author(s):  
M P Draper ◽  
C Salvadore ◽  
C L Denis
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Yeast Cells ◽  
Significant Similarity ◽  
Eukaryotic Transcription ◽  
C Elegans ◽  
Mouse Protein ◽  
Transcriptional Regulatory ◽  
Evolutionarily Conserved ◽  
Regulatory Complex

The CCR4 protein from Saccharomyces cerevisiae is a component of a multisubunit complex that is required for the regulation of a number of genes in yeast cells. We report here the identification of a mouse protein (mCAF1 [mouse CCR4-associated factor 1]) which is capable of interacting with and binding to the yeast CCR4 protein. The mCAF1 protein was shown to have significant similarity to proteins from humans, Caenorhabditis elegans, Arabidopsis thaliana, and S. cerevisiae. The yeast gene (yCAF1) had been previously cloned as the POP2 gene, which is required for expression of several genes. Both yCAF1 (POP2) and the C. elegans homolog of CAF1 were shown to genetically interact with CCR4 in vivo, and yCAF1 (POP2) physically associated with CCR4. Disruption of the CAF1 (POP2) gene in yeast cells gave phenotypes and defects in transcription similar to those observed with disruptions of CCR4, including the ability to suppress spt10-enhanced ADH2 expression. In addition, yCAF1 (POP2) when fused to LexA was capable of activating transcription. mCAF1 could also activate transcription when fused to LexA and could functionally substitute for yCAF1 in allowing ADH2 expression in an spt10 mutant background. These data imply that CAF1 is a component of the CCR4 protein complex and that this complex has retained evolutionarily conserved functions important to eukaryotic transcription.

Kernicterus in Rats with an Inherited Deficiency of Glucuronyal Transferase

PEDIATRICS ◽  
1959 ◽  
Vol 24 (1) ◽  
pp. 73-73
Keyword(s):  
Binding Sites ◽  
Renal Excretion ◽  
Practical Importance ◽  
Human Beings ◽  
Human Infants ◽  
Toxic Agent ◽  
History Of ◽  
The Central Nervous System ◽  
The Brain ◽  
Comprehensive Study

Aside from the great theoretic interest, the experiments described in this paper have considerable practical importance in providing a means of studying the efficacy of treatments designed to prevent kernicterus. A comprehensive study of a strain of rats (the Gunn strain) which have a hereditary deficiency of the enzyme required to conjugate bilirubin, and thus develope jaundice due to increased concentration of unconjugated bilirubin in the blood and tissues. The rats developed kernicterus which was apparently identical with that seen in human beings and is the only example of kernicterus in animals that fulfills rigid criteria outlined by the authors. Extensive data on the natural history of the bilirubinemia and development of kernicterus in the rats, as determined by chemical and pathologic techniques, are provided. Bilirubin itself is incriminated as the toxic agent producing the characteristic changes in the brain in kernicterus. Sulfonamides were found to augment the toxic effects of bilirubin, apparently because of competition between bilirubin and sulfonamides for binding sites on serum albumin. Neither infection nor hypoxia appeared to aggravate the effects of bilirubin. Administration of sodium glucuronate to jaundiced rats was followed by a decrease in bilirubin in the serum which at times exceeded 50%. This was not accompanied by any postponement of the onset of signs of damage to the central nervous system and did not prevent development of kernicterus. It appeared that the decrease in bilirubin in the serum may have resulted from an increased transferral to tissues rather than elimination through renal excretion. On the basis of the knowledge of this strain of rats, it should be possible to explore the usefulness of proposed therapeutic regimens in the experimental animal without jeopardizing the course of human infants who might be successfully treated with exchange transfusion pending the discovery of a more satisfactory therapy.

scholarly journals The Roles of the Histone Protein Modifier EZH2 in the Uterus and Placenta

Epigenomes ◽  
2020 ◽  
Vol 4 (3) ◽  
pp. 20
Author(s):  
Ana M. Mesa ◽  
Cheryl S. Rosenfeld ◽  
Geetu Tuteja ◽  
Theresa I. Medrano ◽  
Paul S. Cooke
Keyword(s):  
Critical Role ◽  
Histone H3 ◽  
Gene Promoter ◽  
Epigenetic Changes ◽  
Promoter Regions ◽  
Polycomb Repressive Complex 2 ◽  
Gene Sets ◽  
Ezh2 Expression ◽  
And Function ◽  
Transcription Enhancer

Epigenetic modifications regulate normal physiological, as well as pathological processes in various organs, including the uterus and placenta. Both organs undergo dramatic and rapid restructuring that depends upon precise orchestration of events. Epigenetic changes that alter transcription and translation of gene-sets regulate such responses. Histone modifications alter the chromatin structure, thereby affecting transcription factor access to gene promoter regions. Binding of histones to DNA is regulated by addition or removal of subunit methyl and other groups, which can inhibit or stimulate transcription. Enhancer of zeste homolog 2 (EZH2) is the catalytic subunit of polycomb repressive complex 2 (PRC2) that catalyzes tri-methylation of histone H3 at Lys 27 (H3K27me3) and subsequently suppresses transcription of genes bound by such histones. Uterine EZH2 expression exerts a critical role in development and function of this organ with deletion of this gene resulting in uterine hyperplasia and expression of cancer-associated transcripts. Elucidating the roles of EZH2 in uterus and placenta is essential as EZH2 dysregulation is associated with several uterine and placental pathologies. Herein, we discuss EZH2 functions in uterus and placenta, emphasizing its physiological and pathological importance.

scholarly journals In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites

2016 ◽  
Vol 2016 ◽  
pp. 1-27 ◽  
Author(s):  
Kristopher J. L. Irizarry ◽  
Randall L. Bryden
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Binding Sites ◽  
Coat Color ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Color Variation ◽  
Factor Binding ◽  
Conserved Sequence ◽  
Evolutionarily Conserved

Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1) that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus. Our results provide insight into pigment phenotypes in pythons.

Complex regulation of the lactase-phlorizin hydrolase promoter by GATA-4

2004 ◽  
Vol 287 (4) ◽  
pp. G899-G909 ◽  
Author(s):  
Herbert M. van Wering ◽  
Tjalling Bosse ◽  
Anna Musters ◽  
Evelien de Jong ◽  
Naomi de Jong ◽  
...  
Keyword(s):  
Binding Sites ◽  
Intestinal Epithelial ◽  
Gata Factor ◽  
Evolutionarily Conserved ◽  
Complex Regulation ◽  
The Difference ◽  
Highly Correlated ◽  
Specific Pathway ◽  
Absorptive Enterocytes

Lactase-phlorizin hydrolase (LPH), a marker of intestinal differentiation, is expressed in absorptive enterocytes on small intestinal villi in a tightly regulated pattern along the proximal-distal axis. The LPH promoter contains binding sites that mediate activation by members of the GATA-4, -5, and -6 subfamily, but little is known about their individual contribution to LPH regulation in vivo. Here, we show that GATA-4 is the principal GATA factor from adult mouse intestinal epithelial cells that binds to the mouse LPH promoter, and its expression is highly correlated with that of LPH mRNA in jejunum and ileum. GATA-4 cooperates with hepatocyte nuclear factor (HNF)-1α to synergistically activate the LPH promoter by a mechanism identical to that previously characterized for GATA-5/HNF-1α, requiring physical association between GATA-4 and HNF-1α and intact HNF-1 binding sites on the LPH promoter. GATA-4 also activates the LPH promoter independently of HNF-1α, in contrast to GATA-5, which is unable to activate the LPH promoter in the absence of HNF-1α. GATA-4-specific activation requires intact GATA binding sites on the LPH promoter and was mapped by domain-swapping experiments to the zinc finger and basic regions. However, the difference in the capacity between GATA-4 and GATA-5 to activate the LPH promoter was not due to a difference in affinity for binding to GATA binding sites on the LPH promoter. These data indicate that GATA-4 is a key regulator of LPH gene expression that may function through an evolutionarily conserved mechanism involving cooperativity with an HNF-1α and/or a GATA-specific pathway independent of HNF-1α.

scholarly journals Evolutionarily Conserved TCR Binding Sites, Identification of T Cells in Primary Lymphoid Tissues, and Surprising Trans-Rearrangements in Nurse Shark

2010 ◽  
Vol 184 (12) ◽  
pp. 6950-6960 ◽  
Author(s):  
Michael F. Criscitiello ◽  
Yuko Ohta ◽  
Mark Saltis ◽  
E. Churchill McKinney ◽  
Martin F. Flajnik
Keyword(s):  
T Cells ◽  
Binding Sites ◽  
Lymphoid Tissues ◽  
Nurse Shark ◽  
Evolutionarily Conserved

scholarly journals Inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data

2019 ◽  
Author(s):  
Qian Qin ◽  
Jingyu Fan ◽  
Rongbin Zheng ◽  
Changxin Wan ◽  
Shenglin Mei ◽  
...  
Keyword(s):  
Binding Sites ◽  
In Silico ◽  
Transcriptional Regulators ◽  
Chromatin Accessibility ◽  
Histone Mark ◽  
Differentially Expressed ◽  
Alternative Methods ◽  
Input Gene ◽  
Integrative Modeling ◽  
Gene Sets

AbstractWe developed Lisa (http://lisa.cistrome.org) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input gene sets, Lisa first uses compendia of public histone mark ChIP-seq and chromatin accessibility profiles to construct a chromatin model related to the regulation of these genes. Then using TR ChIP-seq peaks or imputed TR binding sites, Lisa probes the chromatin models using in silico deletion to find the most relevant TRs. Applied to gene sets derived from targeted TF perturbation experiments, Lisa boosted the performance of imputed TR cistromes, and outperformed alternative methods in identifying the perturbed TRs.

scholarly journals RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins

2021 ◽  
Vol 119 (1) ◽  
pp. e2116222119
Author(s):  
Alexey A. Gavrilov ◽  
Rinat I. Sultanov ◽  
Mikhail D. Magnitov ◽  
Aleksandra A. Galitsyna ◽  
Erdem B. Dashinimaev ◽  
...  
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Wide Spectrum ◽  
Noncoding Rnas ◽  
Ctcf Binding ◽  
Polycomb Repressive Complex 2 ◽  
Proximity Ligation ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Architectural Protein

Nuclear noncoding RNAs (ncRNAs) are key regulators of gene expression and chromatin organization. The progress in studying nuclear ncRNAs depends on the ability to identify the genome-wide spectrum of contacts of ncRNAs with chromatin. To address this question, a panel of RNA–DNA proximity ligation techniques has been developed. However, neither of these techniques examines proteins involved in RNA–chromatin interactions. Here, we introduce RedChIP, a technique combining RNA–DNA proximity ligation and chromatin immunoprecipitation for identifying RNA–chromatin interactions mediated by a particular protein. Using antibodies against architectural protein CTCF and the EZH2 subunit of the Polycomb repressive complex 2, we identify a spectrum of cis- and trans-acting ncRNAs enriched at Polycomb- and CTCF-binding sites in human cells, which may be involved in Polycomb-mediated gene repression and CTCF-dependent chromatin looping. By providing a protein-centric view of RNA–DNA interactions, RedChIP represents an important tool for studies of nuclear ncRNAs.

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