scholarly journals Genome-wide chromatin binding of transcriptional corepressor Topless-related 1 in Arabidopsis

2020 ◽  
Author(s):  
Thomas Griebel ◽  
Dmitry Lapin ◽  
Barbara Kracher ◽  
Lorenzo Concia ◽  
Moussa Benhamed ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Plant Responses ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Genome Wide ◽  
Gene Expression Control ◽  
Specific Regulation ◽  
Transcriptional Corepressors ◽  
And Function

AbstractTimely and specific regulation of gene expression is critical for plant responses to environmental and developmental cues. Transcriptional coregulators have emerged as important factors in gene expression control, although they lack DNA-binding domains and the mechanisms by which they are recruited to and function at the chromatin are poorly understood. Plant Topless-related 1 (TPR1), belonging to a family of transcriptional corepressors found across eukaryotes, contributes to immunity signaling in Arabidopsis thaliana and wild tobacco. We performed chromatin immunoprecipitation and sequencing (ChIP-seq) on an Arabidopsis TPR1-GFP expressing transgenic line to characterize genome-wide TPR1-chromatin associations. The analysis revealed ∼1400 genes bound by TPR1, with the majority of binding sites located at gene upstream regions. Among the TPR1 bound genes, we find not only regulators of immunity but also genes controlling growth and development. To support further analysis of TPR1-chromatin complexes and other transcriptional corepressors in plants, we provide two ways to access the processed ChIP-seq data and enable their broader use by the research community.

scholarly journals The nucleosome acidic patch and H2A ubiquitination underlie mSWI/SNF recruitment in synovial sarcoma

2020 ◽  
Vol 27 (9) ◽  
pp. 836-845 ◽  
Author(s):  
Matthew J. McBride ◽  
Nazar Mashtalir ◽  
Evan B. Winter ◽  
Hai T. Dao ◽  
Martin Filipovski ◽  
...  
Keyword(s):  
Gene Expression ◽  
Synovial Sarcoma ◽  
Direct Interaction ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Selective Targeting ◽  
Associated Proteins ◽  
And Function ◽  
Genomic Regions ◽  
Nucleosome Binding

AbstractInteractions between chromatin-associated proteins and the histone landscape play major roles in dictating genome topology and gene expression. Cancer-specific fusion oncoproteins, which display unique chromatin localization patterns, often lack classical DNA-binding domains, presenting challenges in identifying mechanisms governing their site-specific chromatin targeting and function. Here we identify a minimal region of the human SS18-SSX fusion oncoprotein (the hallmark driver of synovial sarcoma) that mediates a direct interaction between the mSWI/SNF complex and the nucleosome acidic patch. This binding results in altered mSWI/SNF composition and nucleosome engagement, driving cancer-specific mSWI/SNF complex targeting and gene expression. Furthermore, the C-terminal region of SSX confers preferential affinity to repressed, H2AK119Ub-marked nucleosomes, underlying the selective targeting to polycomb-marked genomic regions and synovial sarcoma–specific dependency on PRC1 function. Together, our results describe a functional interplay between a key nucleosome binding hub and a histone modification that underlies the disease-specific recruitment of a major chromatin remodeling complex.

scholarly journals Gene Expression Is Differentially Regulated in the Epididymis after Orchidectomy

Endocrinology ◽  
2003 ◽  
Vol 144 (3) ◽  
pp. 975-988 ◽  
Author(s):  
Nadine Ezer ◽  
Bernard Robaire
Keyword(s):  
Gene Expression ◽  
Calcium Binding ◽  
Regulation Of Gene Expression ◽  
Brown Norway ◽  
Norway Rat ◽  
Associated Proteins ◽  
Specific Regulation ◽  
Cauda Epididymidis ◽  
Shock Proteins ◽  
And Function

The epididymis is the site for the transport, maturation, and storage of spermatozoa. Regulation of epididymal structure and function is highly dependent on the ipsilateral testis. At the molecular level, however, few studies have been undertaken to determine which genes are expressed in the epididymis under testicular regulation. The goal of this study was to identify genes for which expression is regulated after orchidectomy, both throughout the epididymis and in a segment-specific manner. Microarrays spotted with 474 rat cDNAs were used to examine gene expression changes over the first 7 d post orchidectomy in the initial segment, caput, corpus, and cauda epididymidis of the adult Brown Norway rat. Using k-means cluster analysis, we show that four patterns of gene expression are activated in each epididymal segment over the first week following orchidectomy. Transient up-regulation of gene expression in the epididymis after orchidectomy is described for the first time. Potential androgen-repressed genes, including Gpx-1, show increased expression in the epididymis after orchidectomy. Several glutathione-S-transferases and calcium-binding proteins decline throughout the epididymis after orchidectomy, indicating that these may be novel androgen-regulated epididymal genes. Other genes coding for metabolism-associated proteins, transporters, and α-1 acid glycoprotein show segment-specific regulation in the epididymis after orchidectomy. Finally, we describe the expression of the previously uncharacterized heat shock proteins, and apoptosis-associated genes in the epididymis after orchidectomy. Thus, gene expression in the epididymis is differentially affected over time after orchidectomy. These results provide novel insight into androgen-dependent and segment-specific epididymal function.

scholarly journals Co-localization of Conditional eQTL and GWAS Signatures in Schizophrenia

2017 ◽  
Author(s):  
Amanda Dobbyn ◽  
Laura M. Huckins ◽  
James Boocock ◽  
Laura G. Sloofman ◽  
Benjamin S. Glicksberg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Wide Association Study ◽  
Regulation Of Gene Expression ◽  
Developmental Time ◽  
Tissue Cell ◽  
Genome Wide ◽  
Causal Genes ◽  
Specific Regulation ◽  
Context Specific ◽  
Eqtl Data

ABSTRACTCausal genes and variants within genome-wide association study (GWAS) loci can be identified by integrating GWAS statistics with expression quantitative trait loci (eQTL) and determining which SNPs underlie both GWAS and eQTL signals. Most analyses, however, consider only the marginal eQTL signal, rather than dissecting this signal into multiple independent eQTL for each gene. Here we show that analyzing conditional eQTL signatures, which could be important under specific cellular or temporal contexts, leads to improved fine mapping of GWAS associations. Using genotypes and gene expression levels from post-mortem human brain samples (N=467) reported by the CommonMind Consortium (CMC), we find that conditional eQTL are widespread; 63% of genes with primary eQTL also have conditional eQTL. In addition, genomic features associated with conditional eQTL are consistent with context specific (i.e. tissue, cell type, or developmental time point specific) regulation of gene expression. Integrating the Psychiatric Genomics Consortium schizophrenia (SCZ) GWAS and CMC conditional eQTL data reveals forty loci with strong evidence for co-localization (posterior probability >0.8), including six loci with co-localization of conditional eQTL. Our co-localization analyses support previously reported genes and identify novel genes for schizophrenia risk, and provide specific hypotheses for their functional follow-up.

scholarly journals Ctcf Haploinsufficiency Mediates Intron Retention in A Tissue-specific Manner

2019 ◽  
Author(s):  
Adel B Alharbi ◽  
Ulf Schmitz ◽  
Amy D Marshall ◽  
Darya Vanichkina ◽  
Rajini Nagarajah ◽  
...  
Keyword(s):  
Gene Expression ◽  
Intron Retention ◽  
Regulation Of Gene Expression ◽  
Splicing Factors ◽  
Tissue Specific ◽  
Genome Wide ◽  
Liver And Kidney ◽  
Specific Regulation ◽  
Dose Dependent

AbstractCTCF is a master regulator of gene transcription and chromatin organization with occupancy at thousands of DNA target sites. CTCF is essential for embryonic development and somatic cell viability and has been characterized as a haploinsufficient tumor suppressor. Increasing evidence demonstrates CTCF as a key player in several alternative splicing (AS) regulatory mechanisms, including transcription elongation, regulation of splicing factors, and epigenetic regulation. However, the genome-wide impact of Ctcf dosage on AS has not been investigated. We examined the effect of Ctcf haploinsufficiency on gene expression and AS in multiple tissues from Ctcf hemizygous (Ctcf+/-) mice. Distinct tissue-specific differences in gene expression and AS were observed in Ctcf+/- mice compared to wildtype mice. We observed a surprisingly large number of increased intron retention (IR) events in Ctcf+/- liver and kidney, specifically in genes associated with cytoskeletal organization, splicing and metabolism. This study provides further evidence for Ctcf dose-dependent and tissue-specific regulation of gene expression and AS. Our data provide a strong foundation for elucidating the mechanistic role of CTCF in AS regulation and its biological consequences.

scholarly journals Differential Gene Regulation by Selective Association of Transcriptional Coactivators and bZIP DNA-Binding Domains

2006 ◽  
Vol 26 (16) ◽  
pp. 5969-5982 ◽  
Author(s):  
Benoit Miotto ◽  
Kevin Struhl
Keyword(s):  
Dna Binding ◽  
Regulation Of Gene Expression ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Transcriptional Coactivators ◽  
Differential Gene Regulation ◽  
Arginine Residues ◽  
Contact Dna ◽  
Bzip Proteins ◽  
Basic Region

ABSTRACT bZIP DNA-binding domains are targets for viral and cellular proteins that function as transcriptional coactivators. Here, we show that MBF1 and the related Chameau and HBO1 histone acetylases interact with distinct subgroups of bZIP proteins, whereas pX does not discriminate. Selectivity of Chameau and MBF1 for bZIP proteins is mediated by residues in the basic region that lie on the opposite surface from residues that contact DNA. Chameau functions as a specific coactivator for the AP-1 class of bZIP proteins via two arginine residues. A conserved glutamic acid/glutamine in the linker region underlies MBF1 specificity for a subgroup of bZIP factors. Chameau and MBF1 cannot synergistically coactivate transcription due to competitive interactions with the basic region, but either protein can synergistically coactivate with pX. Analysis of Jun derivatives that selectively interact with these coactivators reveals that MBF1 is crucial for the response to oxidative stress, whereas Chameau is important for the response to chemical and osmotic stress. Thus, the bZIP domain mediates selective interactions with coactivators and hence differential regulation of gene expression.

scholarly journals TEM1 combinatorially binds to FLOWERING LOCUS T and recruits a Polycomb factor to repress the floral transition in Arabidopsis

2021 ◽  
Vol 118 (35) ◽  
pp. e2103895118
Author(s):  
Hongmiao Hu ◽  
Shu Tian ◽  
Guohui Xie ◽  
Rui Liu ◽  
Nana Wang ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Molecular Basis ◽  
Floral Transition ◽  
Flowering Locus T ◽  
Dna Binding Domains ◽  
Adult Transition ◽  
Binding Domains ◽  
Flowering Locus ◽  
Specific Regulation

Arabidopsis TEMPRANILLO 1 (TEM1) is a transcriptional repressor that participates in multiple flowering pathways and negatively regulates the juvenile-to-adult transition and the flowering transition. To understand the molecular basis for the site-specific regulation of FLOWERING LOCUS T (FT) by TEM1, we determined the structures of the two plant-specific DNA-binding domains in TEM1, AP2 and B3, in complex with their target DNA sequences from the FT gene 5′-untranslated region (5′-UTR), revealing the molecular basis for TEM1 specificity for its DNA targets. In vitro binding assays revealed that the combination of the AP2 and B3 binding sites greatly enhanced the overall binding of TEM1 to the FT 5′-UTR, indicating TEM1 combinatorically recognizes the FT gene 5′-UTR. We further showed that TEM1 recruits the Polycomb repressive complex 2 (PRC2) to the FT 5′-UTR. The simultaneous binding of the TEM1 AP2 and B3 domains to FT is necessary for deposition of H3K27me3 at the FT 5′-UTR and for the flowering repressor function of TEM1. Overall, our data suggest that the combinatorial recognition of FT 5′-UTR by TEM1 ensures H3K27me3 deposition to precisely regulate the floral transition.

scholarly journals Genome-wide H3K9 Acetylation Level Increases with Age-Dependent Senescence of Flag Leaf in Rice (Oryza sativa)

2021 ◽  
Author(s):  
Yu Zhang ◽  
Yanyun Li ◽  
Yuanyuan Zhang ◽  
Zeyu Zhang ◽  
Deyu Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Oryza Sativa ◽  
Leaf Senescence ◽  
Epigenetic Modification ◽  
Flag Leaf ◽  
Regulation Of Gene Expression ◽  
Leaf Aging ◽  
Genome Wide ◽  
Age Dependent ◽  
H3k9 Acetylation

Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and epigenetic modification, but the precise mechanism is as of yet unclear. Here, we analyzed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq) and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac and gene expression and transcript elongation. A set of 1,249 up-regulated, differentially expressed genes (DEGs) and 996 down-regulated DEGs showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac was observed during rice flag leaf aging. We produced a landscape of H3K9 acetylation- modified gene expression targets that includes known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis- related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac and also elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice.

scholarly journals Functional Comparison of the Tup11 and Tup12 Transcriptional Corepressors in Fission Yeast

2005 ◽  
Vol 25 (2) ◽  
pp. 716-727 ◽  
Author(s):  
Fredrik Fagerström-Billai ◽  
Anthony P. H. Wright
Keyword(s):  
Gene Expression ◽  
Gene Duplication ◽  
Fission Yeast ◽  
Budding Yeast ◽  
Functional Difference ◽  
Evolutionary Mechanism ◽  
Genome Wide ◽  
Number Of Genes ◽  
Transcriptional Corepressors ◽  
Genome Wide Gene Expression

ABSTRACT Gene duplication is considered an important evolutionary mechanism. Unlike many characterized species, the fission yeast Schizosaccharomyces pombe contains two paralogous genes, tup11 + and tup12 + , that encode transcriptional corepressors similar to the well-characterized budding yeast Tup1 protein. Previous reports have suggested that Tup11 and Tup12 proteins play redundant roles. Consistently, we show that the two Tup proteins can interact together when expressed at normal levels and that each can independently interact with the Ssn6 protein, as seen for Tup1 in budding yeast. However, tup11 − and tup12 − mutants have different phenotypes on media containing KCl and CaCl2. Consistent with the functional difference between tup11 − and tup12 − mutants, we identified a number of genes in genome-wide gene expression experiments that are differentially affected by mutations in the tup11 + and tup12 + genes. Many of these genes are differentially derepressed in tup11 − mutants and are over-represented in genes that have previously been shown to respond to a range of different stress conditions. Genes specifically derepressed in tup12 − mutants require the Ssn6 protein for their repression. As for Tup12, Ssn6 is also required for efficient adaptation to KCl- and CaCl2-mediated stress. We conclude that Tup11 and Tup12 are at least partly functionally diverged and suggest that the Tup12 and Ssn6 proteins have adopted a specific role in regulation of the stress response.

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