scholarly journals Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities

2018 ◽  
Vol 46 (11) ◽  
pp. 5455-5469 ◽  
Author(s):  
Sarah Rennie ◽  
Maria Dalby ◽  
Marta Lloret-Llinares ◽  
Stylianos Bakoulis ◽  
Christian Dalager Vaagensø ◽  
...  
Keyword(s):  
Transcription Start Site ◽  
Core Promoter ◽  
Start Site ◽  
Transcription Start ◽  
Site Analysis ◽  
Divergent Transcription

scholarly journals Maneuver at the transcription start site: Mot1p and NC2 navigate TFIID/TBP to specific core promoter elements

Epigenetics ◽  
2009 ◽  
Vol 4 (1) ◽  
pp. 1-4 ◽  
Author(s):  
Zhuo Zhou ◽  
I-Ju Lin ◽  
Russell P. Darst ◽  
Jörg Bungert
Keyword(s):  
Transcription Start Site ◽  
Core Promoter ◽  
Start Site ◽  
Transcription Start ◽  
Promoter Elements

scholarly journals Core Promoter-Dependent TFIIB Conformation and a Role for TFIIB Conformation in Transcription Start Site Selection

2002 ◽  
Vol 22 (19) ◽  
pp. 6697-6705 ◽  
Author(s):  
Jennifer A. Fairley ◽  
Rachel Evans ◽  
Nicola A. Hawkes ◽  
Stefan G. E. Roberts
Keyword(s):  
Transcription Start Site ◽  
Site Selection ◽  
Transcription Initiation ◽  
Core Promoter ◽  
Initiation Site ◽  
Start Site ◽  
Wild Type ◽  
Transcription Start ◽  
General Transcription Factor ◽  
Selection Of

ABSTRACT The general transcription factor TFIIB plays a central role in the selection of the transcription initiation site. The mechanisms involved are not clear, however. In this study, we analyze core promoter features that are responsible for the susceptibility to mutations in TFIIB and cause a shift in the transcription start site. We show that TFIIB can modulate both the 5′ and 3′ parameters of transcription start site selection in a manner dependent upon the sequence of the initiator. Mutations in TFIIB that cause aberrant transcription start site selection concentrate in a region that plays a pivotal role in modulating TFIIB conformation. Using epitope-specific antibody probes, we show that a TFIIB mutant that causes aberrant transcription start site selection assembles at the promoter in a conformation different from that for wild-type TFIIB. In addition, we uncover a core promoter-dependent effect on TFIIB conformation and provide evidence for novel sequence-specific TFIIB promoter contacts.

scholarly journals Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster

2017 ◽  
Author(s):  
Michael P. Meers ◽  
Karen Adelman ◽  
Robert J. Duronio ◽  
Brian D. Strahl ◽  
Daniel J. McKay ◽  
...  
Keyword(s):  
Transcription Start Site ◽  
Transcription Initiation ◽  
Local Density ◽  
Global Analysis ◽  
Regulatory Elements ◽  
Start Site ◽  
Transcription Start ◽  
Vast Number ◽  
Animal Development ◽  
Divergent Transcription

AbstractBackgroundHigh-resolution transcription start site (TSS) mapping in D. melanogaster embryos and cell lines has revealed a rich and detailed landscape of both cis- and trans-regulatory elements and factors. However, TSS profiling has not been investigated in an orthogonal in vivo setting. Here, we present a comprehensive dataset that links TSS dynamics with nucleosome occupancy and gene expression in the wandering third instar larva, a developmental stage characterized by large-scale shifts in transcriptional programs in preparation for metamorphosis.ResultsThe data recapitulate major regulatory classes of TSSs, based on peak width, promoter-proximal polymerase pausing, and cis-regulatory element density. We confirm the paucity of divergent transcription units in D. melanogaster, but also identify notable exceptions. Furthermore, we identify thousands of novel initiation events occurring at unannotated TSSs that can be classified into functional categories by their local density of histone modifications. Interestingly, a sub-class of these unannotated TSSs overlaps with functionally validated enhancer elements, consistent with a regulatory role for “enhancer RNAs” (eRNAs) in defining transcriptional programs that are important for animal development.ConclusionsHigh-depth TSS mapping is a powerful strategy for identifying and characterizing low-abundance and/or low-stability RNAs. Global analysis of transcription initiation patterns in a developing organism reveals a vast number of novel initiation events that identify potential eRNAs as well as other non-coding transcripts critical for animal development.

Drosophila OVO regulates ovarian tumor transcription by binding unusually near the transcription start site

Development ◽  
2001 ◽  
Vol 128 (9) ◽  
pp. 1671-1686 ◽  
Author(s):  
J. Lu ◽  
B. Oliver
Keyword(s):  
Transcription Start Site ◽  
Ovarian Tumor ◽  
Core Promoter ◽  
Regulatory Region ◽  
Start Site ◽  
Loss Of Function ◽  
Transcription Start ◽  
Germline Expression ◽  
Promoter Swapping

Evolutionarily conserved ovo loci encode developmentally regulated, sequence-specific, DNA-binding, C(2)H(2)-zinc-finger proteins required in the germline and epidermal cells of flies and mice. The direct targets of OVO activity are not known. Genetic experiments suggest that ovo acts in the same regulatory network as ovarian tumor (otu), but the relative position of these genes in the pathway is controversial. Three OVO-binding sites exist in a compact regulatory region that controls germline expression of the otu gene. Interestingly, the strongest OVO-binding site is very near the otu transcription start, where basal transcriptional complexes must function. Loss-of-function, gain-of-function and promoter swapping constructs demonstrate that OVO binding near the transcription start site is required for OVO-dependent otu transcription in vivo. These data unambiguously identify otu as a direct OVO target gene and raise the tantalizing possibility that an OVO site, at the location normally occupied by basal components, functions as part of a specialized core promoter.

scholarly journals Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Michael P. Meers ◽  
Karen Adelman ◽  
Robert J. Duronio ◽  
Brian D. Strahl ◽  
Daniel J. McKay ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Transcription Start Site ◽  
Start Site ◽  
Transcription Start ◽  
Divergent Transcription

Role of the Sulfolobus shibatae viral T6 initiator in conferring promoter strength and in influencing transcription start site selection

2006 ◽  
Vol 52 (11) ◽  
pp. 1136-1140 ◽  
Author(s):  
Sohail A Qureshi
Keyword(s):  
Transcription Start Site ◽  
Dna Sequences ◽  
Site Selection ◽  
Core Promoter ◽  
Promoter Strength ◽  
Start Site ◽  
Transcription Start ◽  
Recognition Element ◽  
Sulfolobus Shibatae

Archaeal promoters contain a TATA-box, an adjacent upstream TFB-recognition element (BRE), and a downstream initiator (INR) region from which transcription originates. While the contribution of A-box and BRE to promoter strength is well established, the role of DNA sequences within the INR region and its vicinity on transcription efficiency and start site selection remains unclear. Here, I demonstrate using the strong Sulfolobus shibatae viral T6 promoter that either substitution of its natural sequence from –17 and beyond with plasmid DNA or introduction of point transversion mutations at +3, –2, –4, and –5 positions reduce promoter strength dramatically, whereas +1, –1, and –2 mutations influence the transcription start site. These data therefore reveal that the INR region plays a role as important as the BRE and the A-box in T6 gene transcription. Key words: Archaea, transcription, initiator (INR), Sulfolobus shibatae, core promoter.

The Wsh, W57, and Ph Kit Expression Mutations Define Tissue-Specific Control Elements Located Between −23 and −154 kb Upstream of Kit

Blood ◽  
1999 ◽  
Vol 94 (8) ◽  
pp. 2658-2666 ◽  
Author(s):  
Georgina Berrozpe ◽  
Inna Timokhina ◽  
Steven Yukl ◽  
Youichi Tajima ◽  
Masao Ono ◽  
...  
Keyword(s):  
Mast Cells ◽  
Transcription Start Site ◽  
Tyrosine Kinases ◽  
Cell Types ◽  
Start Site ◽  
Transcription Start ◽  
Hematopoietic Stem ◽  
Site Analysis ◽  
Positive Elements ◽  
Hypersensitive Sites

The Kit and PDGFRa receptor tyrosine kinases are encoded in close proximity at the murine white spotting (W) and patch (Ph) loci. Whereas W mutations affect hematopoiesis, melanogenesis, and gametogenesis, the Ph mutation affects melanogenesis and causes early lethality in homozygotes. TheWsh, W57, and Phmutations diminish Kit expression in certain cell types such as mast cells and enhance it in others. The Wsh,W57, and Ph mutations arose from deletions and inversions affecting sequences in between the Kit andPDGFRa genes. We have determined the precise location of the breakpoint of the Wshinversion and the endpoints of the W57deletion upstream of the Kittranscription start site and examined the effect of these mutations on Kit expression in mast cells and hematopoietic stem cells and lineage progenitors. Our results indicate that positive elements controlling Kit expression in mast cells mapping in between −23 and −154 kb from the transcription start site can be dissociated from negative elements controlling Kit misexpression during embryonic development in the vicinity of the PDGFRa gene. In addition, we have identified two clusters of hypersensitive sites in mast cells at −23 −28 kb and −147 −154 kb from the Kit gene transcription start site. Analysis of these hypersensitive sites in mutant mast cells indicates a role for HS4-6 in Kit expression in mast cells. These findings provide a molecular basis for the phenotype of these Kit expression mutations and they provide insight into the complex mechanisms governing the regulation ofKit expression.

scholarly journals Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions

2018 ◽  
Author(s):  
Christoph S. Börlin ◽  
Nevena Cvetesic ◽  
Petter Holland ◽  
David Bergenholm ◽  
Verena Siewers ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Start Site ◽  
Environmental Conditions ◽  
Transcription Initiation ◽  
Core Promoter ◽  
Regulatory Region ◽  
Laboratory Strain ◽  
Start Site ◽  
Transcription Start ◽  
Strong Negative Correlation

ABSTRACTOne of the fundamental processes that determine cellular fate is regulation of gene transcription. Understanding these regulatory processes is therefore essential for understanding cellular responses to changes in environmental conditions. At the core promoter, the regulatory region containing the transcription start site (TSS), all inputs regulating transcription are integrated. Here, we used Cap Analysis of Gene Expression (CAGE) to analyze the pattern of transcription start sites at four different environmental conditions (limited in ethanol, limited in nitrogen, limited in glucose and limited in glucose under anaerobic conditions) using the Saccharomyces cerevisiae strain CEN.PK113-7D. With this experimental setup we were able to show that the TSS landscape in yeast is stable at different metabolic states of the cell. We also show that the shape index, a characteristic feature of each TSS describing the spatial distribution of transcription initiation events, has a surprisingly strong negative correlation with the measured expression levels. Our analysis supplies a set of high quality TSS annotations useful for metabolic engineering and synthetic biology approaches in the industrially relevant laboratory strain CEN.PK113-7D, and provides novel insights into yeast TSS dynamics and gene regulation.

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