scholarly journals The SAGA core module is critical during Drosophila oogenesis and is broadly recruited to promoters

PLoS Genetics ◽  
2021 ◽  
Vol 17 (11) ◽  
pp. e1009668
Author(s):  
Jelly H. M. Soffers ◽  
Sergio G-M Alcantara ◽  
Xuanying Li ◽  
Wanqing Shao ◽  
Christopher W. Seidel ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Resolution ◽  
Start Site ◽  
Drosophila Oogenesis ◽  
Core Module ◽  
Entire Complex ◽  
Biological Context ◽  
Active Genes ◽  
Coactivator Complex

The Spt/Ada-Gcn5 Acetyltransferase (SAGA) coactivator complex has multiple modules with different enzymatic and non-enzymatic functions. How each module contributes to gene expression is not well understood. During Drosophila oogenesis, the enzymatic functions are not equally required, which may indicate that different genes require different enzymatic functions. An analogy for this phenomenon is the handyman principle: while a handyman has many tools, which tool he uses depends on what requires maintenance. Here we analyzed the role of the non-enzymatic core module during Drosophila oogenesis, which interacts with TBP. We show that depletion of SAGA-specific core subunits blocked egg chamber development at earlier stages than depletion of enzymatic subunits. These results, as well as additional genetic analyses, point to an interaction with TBP and suggest a differential role of SAGA modules at different promoter types. However, SAGA subunits co-occupied all promoter types of active genes in ChIP-seq and ChIP-nexus experiments, and the complex was not specifically associated with distinct promoter types in the ovary. The high-resolution genomic binding profiles were congruent with SAGA recruitment by activators upstream of the start site, and retention on chromatin by interactions with modified histones downstream of the start site. Our data illustrate that a distinct genetic requirement for specific components may conceal the fact that the entire complex is physically present and suggests that the biological context defines which module functions are critical.

scholarly journals The SAGA core module is critical during Drosophila oogenesis and is broadly recruited to promoters

2021 ◽  
Author(s):  
Jelly HM Soffers ◽  
Sergio Garcia-Moreno Alcantara ◽  
Xuanying Li ◽  
Wanqing Shao ◽  
Chrisopher Seidel ◽  
...  
Keyword(s):  
Gene Activation ◽  
Start Site ◽  
Saga Complex ◽  
Drosophila Oogenesis ◽  
The Core ◽  
Core Module ◽  
Entire Complex ◽  
Active Genes ◽  
Coactivator Complex

The Spt/Ada-Gcn5 Acetyltransferase (SAGA) coactivator complex has multiple modules with different enzymatic and non-enzymatic functions. How each module contributes to gene activation in specific biological contexts is not well understood. Here we analyzed the role of the non-enzymatic core module during Drosophila oogenesis. We show that depletion of several SAGA-specific subunits belonging to the core module blocked egg chamber development during mid-oogenesis stages, resulting in stronger phenotypes than those obtained after depletion of SAGA’s histone acetyltransferase module or deubiquitination module. These results, as well as additional genetic analyses pointing to an interaction with TBP, suggested a differential role of SAGA modules at different promoter types. However, SAGA subunits co-occupied all promoter types of active genes in ChIP-seq and ChIP-nexus experiments. Thus, the SAGA complex appears to occupy promoters in its entirety, consistent with the strong biochemical integrity of the complex. The high-resolution genomic binding profiles are congruent with SAGA recruitment by activators upstream of the start site, and retention on chromatin by interactions with modified histones downstream of the start site. The stronger genetic requirement of the core module during oogenesis may therefore be explained through its interaction with TBP or its role in recruiting the enzymatic modules to the promoter. We propose the handyman principle, which posits that a distinct genetic requirement for specific components may conceal the fact that the entire complex is physically present.

Investigating the function of follicular subpopulations during Drosophila oogenesis through hormone-dependent enhancer-targeted cell ablation

Development ◽  
2000 ◽  
Vol 127 (3) ◽  
pp. 573-583 ◽  
Author(s):  
D.D. Han ◽  
D. Stein ◽  
L.M. Stevens
Keyword(s):  
Gene Expression ◽  
Diphtheria Toxin ◽  
Follicle Cells ◽  
Specific Gene ◽  
Border Cells ◽  
Drosophila Oogenesis ◽  
Cell Ablation ◽  
Powerful Approach ◽  
Human Estrogen Receptor

Although it is known that the establishment of polarity during Drosophila oogenesis is initiated by signalling from the oocyte to the overlying follicle cells, much less is understood about the role of specific follicular subpopulations. One powerful approach for addressing this question, toxigenic cell ablation of specific subpopulations, has not previously been applicable to studying follicular subpopulations because many of the genes and Gal4 enhancer trap insertions that are expressed in the ovary are also expressed at earlier times in development. To overcome this problem, we have utilized a fusion protein between Gal4 and the human estrogen receptor to achieve hormone-dependent, tissue-specific gene expression of UAS-linked transgenes in flies. We used this system to study the role of the polar subpopulations of follicle cells during oogenesis by expressing within them a modified form of diphtheria toxin that causes cell death. Our results confirmed previous functions ascribed to these cells, and also demonstrated a previously undescribed role for the border cells in facilitating the migration of the anterior Fasciclin III-expressing polar pair cells to the edge of the oocyte.

scholarly journals Transcription factor abundance controlled by an auto-regulatory mechanism involving a transcription start site switch

2013 ◽  
Vol 42 (4) ◽  
pp. 2171-2184 ◽  
Author(s):  
Richard Patryk Ngondo ◽  
Philippe Carbon
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Start Site ◽  
Regulatory Mechanism ◽  
Start Site ◽  
Transcription Start ◽  
Aberrant Expression ◽  
Alternative Transcription ◽  
Activating Transcription Factor

Abstract A transcriptional feedback loop is the simplest and most direct means for a transcription factor to provide an increased stability of gene expression. In this work performed in human cells, we reveal a new negative auto-regulatory mechanism involving an alternative transcription start site (TSS) usage. Using the activating transcription factor ZNF143 as a model, we show that the ZNF143 low-affinity binding sites, located downstream of its canonical TSS, play the role of protein sensors to induce the up- or down-regulation of ZNF143 gene expression. We uncovered that the TSS switch that mediates this regulation implies the differential expression of two transcripts with an opposite protein production ability due to their different 5′ untranslated regions. Moreover, our analysis of the ENCODE data suggests that this mechanism could be used by other transcription factors to rapidly respond to their own aberrant expression level.

scholarly journals High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Damien J. Downes ◽  
Robert A. Beagrie ◽  
Matthew E. Gosden ◽  
Jelena Telenius ◽  
Stephanie J. Carpenter ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Resolution ◽  
Regulatory Element ◽  
Gene Promoters ◽  
Entire Genome ◽  
Chromosome Conformation ◽  
Genome Wide ◽  
Wide Scale

AbstractChromosome conformation capture (3C) provides an adaptable tool for studying diverse biological questions. Current 3C methods generally provide either low-resolution interaction profiles across the entire genome, or high-resolution interaction profiles at limited numbers of loci. Due to technical limitations, generation of reproducible high-resolution interaction profiles has not been achieved at genome-wide scale. Here, to overcome this barrier, we systematically test each step of 3C and report two improvements over current methods. We show that up to 30% of reporter events generated using the popular in situ 3C method arise from ligations between two individual nuclei, but this noise can be almost entirely eliminated by isolating intact nuclei after ligation. Using Nuclear-Titrated Capture-C, we generate reproducible high-resolution genome-wide 3C interaction profiles by targeting 8055 gene promoters in erythroid cells. By pairing high-resolution 3C interaction calls with nascent gene expression we interrogate the role of promoter hubs and super-enhancers in gene regulation.

Role of multifunctional coactivator complex SAGA in regulation of eukaryotic gene expression

2013 ◽  
Vol 47 (6) ◽  
pp. 796-802 ◽  
Author(s):  
D. Ya. Gurskiy ◽  
E. N. Nabirochkina ◽  
D. V. Kopytova
Keyword(s):  
Gene Expression ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene ◽  
Coactivator Complex

scholarly journals A cis Repression Sequence Adjacent to the Transcription Start Site of the Human Cytomegalovirus US3 Gene Is Required To Down Regulate Gene Expression at Early and Late Times after Infection

1998 ◽  
Vol 72 (12) ◽  
pp. 9575-9584 ◽  
Author(s):  
Philip E. Lashmit ◽  
Mark F. Stinski ◽  
Eain A. Murphy ◽  
Grant C. Bullock
Keyword(s):  
Gene Expression ◽  
Viral Replication ◽  
Transcription Start Site ◽  
Human Cytomegalovirus ◽  
Maximum Level ◽  
Start Site ◽  
Wild Type ◽  
Transcription Start ◽  
Recombinant Viruses

ABSTRACT Human cytomegalovirus has two enhancer-containing immediate-early (IE) promoters with a cis repression sequence (CRS) positioned immediately upstream of the transcription start site, designated the major IE (MIE) promoter and the US3 promoter. The role of the CRS upstream of the US3 transcription start site in the context of the viral genome was determined by comparing the levels of transcription from these two enhancer-containing promoters in recombinant viruses with a wild-type or mutant CRS. Upstream of the CRS of the US3 promoter was either the endogenous enhancer (R2) or silencer (R1). The downstream US3 gene was replaced with the indicator gene chloramphenicol acetyltransferase (CAT). Infected permissive human fibroblast cells or nonpermissive, undifferentiated monocytic THP-1 cells were analyzed for expression from the US3 promoter containing either the wild-type or mutant CRS. With the wild-type CRS, the maximum level of transcription in permissive cells was detected within 4 to 6 h after infection and then declined. With the mutant CRS and the R2 enhancer upstream, expression from the US3 promoter continued to increase throughout the viral replication cycle to levels 20- to 40-fold higher than for the wild type. In nonpermissive or permissive monocytic THP-1 cells, expression from the US3 promoter was also significantly higher when the CRS was mutated. Less expression was obtained when only the R1 element was present, but expression was higher when the CRS was mutated. Thus, the CRS in the enhancer-containing US3 promoter appears to allow for a short burst of US3 gene expression followed by repression at early and late times after infection. Overexpression of US3 may be detrimental to viral replication, and its level of expression must be stringently controlled. The role of the CRS and the viral IE86 protein in controlling enhancer-containing promoters is discussed.

Role of small nuclear RNAs in eukaryotic gene expression

2013 ◽  
Vol 54 ◽  
pp. 79-90 ◽  
Author(s):  
Saba Valadkhan ◽  
Lalith S. Gunawardane
Keyword(s):  
Gene Expression ◽  
Protein Interactions ◽  
Rna Stability ◽  
Splice Sites ◽  
Branch Site ◽  
Small Nuclear Rnas ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene ◽  
Rna Biogenesis

Eukaryotic cells contain small, highly abundant, nuclear-localized non-coding RNAs [snRNAs (small nuclear RNAs)] which play important roles in splicing of introns from primary genomic transcripts. Through a combination of RNA–RNA and RNA–protein interactions, two of the snRNPs, U1 and U2, recognize the splice sites and the branch site of introns. A complex remodelling of RNA–RNA and protein-based interactions follows, resulting in the assembly of catalytically competent spliceosomes, in which the snRNAs and their bound proteins play central roles. This process involves formation of extensive base-pairing interactions between U2 and U6, U6 and the 5′ splice site, and U5 and the exonic sequences immediately adjacent to the 5′ and 3′ splice sites. Thus RNA–RNA interactions involving U2, U5 and U6 help position the reacting groups of the first and second steps of splicing. In addition, U6 is also thought to participate in formation of the spliceosomal active site. Furthermore, emerging evidence suggests additional roles for snRNAs in regulation of various aspects of RNA biogenesis, from transcription to polyadenylation and RNA stability. These snRNP-mediated regulatory roles probably serve to ensure the co-ordination of the different processes involved in biogenesis of RNAs and point to the central importance of snRNAs in eukaryotic gene expression.

Quantitative accuracy of serotonergic neurotrans-mission imaging with high-resolution 123I SPECT

2004 ◽  
Vol 43 (06) ◽  
pp. 185-189 ◽  
Author(s):  
J. T. Kuikka
Keyword(s):  
High Resolution ◽  
Scatter Correction ◽  
Region Of Interest ◽  
Binding Potential ◽  
Partial Volume ◽  
Therapeutic Drugs ◽  
Quantitative Accuracy ◽  
Critical Error ◽  
Statistical Noise

Summary Aim: Serotonin transporter (SERT) imaging can be used to study the role of regional abnormalities of neurotransmitter release in various mental disorders and to study the mechanism of action of therapeutic drugs or drugs’ abuse. We examine the quantitative accuracy and reproducibility that can be achieved with high-resolution SPECT of serotonergic neurotransmission. Method: Binding potential (BP) of 123I labeled tracer specific for midbrain SERT was assessed in 20 healthy persons. The effects of scatter, attenuation, partial volume, mis-registration and statistical noise were estimated using phantom and human studies. Results: Without any correction, BP was underestimated by 73%. The partial volume error was the major component in this underestimation whereas the most critical error for the reproducibility was misplacement of region of interest (ROI). Conclusion: The proper ROI registration, the use of the multiple head gamma camera with transmission based scatter correction introduce more relevant results. However, due to the small dimensions of the midbrain SERT structures and poor spatial resolution of SPECT, the improvement without the partial volume correction is not great enough to restore the estimate of BP to that of the true one.

Which is the role of dynamic high-resolution ultrasound (D-HRUS) in the assessment of plantar plate tears?

2008 ◽  
Vol 29 (S 1) ◽  
Author(s):  
LM Sconfienza ◽  
F Lacelli ◽  
G Grillo ◽  
G Serafini ◽  
G Garlaschi ◽  
...  
Keyword(s):  
High Resolution ◽  
Plantar Plate
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