Transcription initiation complex. Medical search. Frequent questions

TAF9 is a TATA-binding protein associated factor (TAF) conserved from yeast to humans and shared by two transcription coactivator complexes, TFIID and SAGA. (thebiogrid.org)
The protein that coordinates these activities is transcription factor IID (TFIID), which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. (antikoerper-online.de)
These constitutive promoters comprise a short nucleosome-free region (NFR) adjacent to a +1 nucleosome, which together bind the transcription-initiation factor TFIID to form a preinitiation complex. (genengnews.com)
The transcription initiation TFIID complex is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). (embl-heidelberg.de)

DNA replication occurs once and only once per cell cycle mainly regulated by DNA replication initiation factors in eukaryotic cells. (intechopen.com)
We determined subnanometer-resolution cryo-electron microscopy structures of eukaryotic ribosome-Sec61 complexes. (cipsm.de)

The structures of AMPA receptors in complex with auxiliary proteins are resolved by cryo-electron microscopy, and reveal conformational and permeation pathway changes that are associated with activation and desensitization of ionotropic glutamate receptors. (nature.com)
Recent breakthroughs have uncovered more and more DNA replication licensing machinery proteins (ORC, Cdc6, Cdt1, geminin, etc.) functioning in other cell cycle events, including centrosome replication, mitotic events, transcription and so on. (intechopen.com)
RCSB PDB is a member of the Worldwide Protein Data Bank (wwPDB) that manages the PDB archive of information about the structures of proteins, nucleic acids, and complex assemblies. (rutgers.edu)
And then Mehmet Berkman will highlight the SHuffle line of E. coli strains for producing proteins with complex disulphide bonds. (neb.com)
And finally, many proteins from higher organisms require complex disulfide bonds for stability and proper folding. (neb.com)
Fundamental differences exist between proteins when comparing one complex to another. (sdbonline.org)
In Drosophila, the majority of Notch target genes known so far is located in the Enhancer of split complex , encoding small basic helix-loop-helix (bHLH) proteins that presumably act as transcriptional repressors. (sdbonline.org)
In addition, this subunit interacts with the transcription factor CREB, which has a glutamine-rich activation domain, and binds to other proteins containing glutamine-rich regions. (antikoerper-online.de)
We identified 21 meta-assemblages consisting of roughly 400 different proteins that are related to DNA replication, centromeres, subtelomeres, transposons, and transcription by RNA polymerase (Pol) I, II, and III. (genengnews.com)
It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. (embl.de)
The heterochromatin-enriched HP1 proteins play a critical role in regulation of transcription. (cipsm.de)
The trimeric Sec61/SecY complex is a protein-conducting channel (PCC) for secretory and membrane proteins. (cipsm.de)
There are a myriad of mutations identified in genes encoding cardiac transcription factors, ion channels, gap junctions, energy metabolism regulators, lamins and other structural proteins. (medscape.com)
Some inherited arrhythmias are caused by a malfunction of proteins that are related to the initiation or propagation of electrical activity. (medscape.com)

This bi-genomic division is accompanied by profoundly different transcription regulatory system: whereas nDNA-encoded genes are transcribed individually by RNA polymerase 2 and the general nuclear transcription machinery, mtDNA transcription is long known to be regulated mainly by a dedicated RNA polymerase (POLRMT) and mtDNA-specific transcription factors (TFAM and TFB2) ( Shutt and Shadel 2010 ). (biorxiv.org)
However, as mtDNA transcription was mostly studied in vitro, little remains known about the mode and tempo of in vivo OXPHOS genes' transcription residing on the mtDNA. (biorxiv.org)
Binding of TFIIIC to sine elements controls the relocation of activity-dependent neuronal genes to transcription factories. (nih.gov)
The phenomenon of a group of genes with the same function and location on the chromosome signifies a so-called gene complex. (sdbonline.org)
The Enhancer of split complex (E[spl]-C) includes eight genes spread over 50 kilo bases on the Drosophila third chromosome. (sdbonline.org)
Other examples of Drosophila gene complexes include the Antennapedia complex (ANTP-C), the bithorax complex (BX-C) and the achaete-scute complex (AS-C). The hallmark of all these gene complexes, including the E(spl)-C is that within any complex the genes are evolutionarily related and jointly regulated. (sdbonline.org)
Each gene in any given cluster or complex of genes will have a similar function and structure to the others in its group. (sdbonline.org)
For example, the AS-C transcription factors activate transcription of other genes, while the transcription factors of the E(spl)-C repress transcription. (sdbonline.org)
Developmental signals received by the Notch receptor cause Suppressor of Hairless (Su[H]) to mediate transcription of target genes. (sdbonline.org)
All three genes depend on Su(H) for initiation and/or maintenance of transcription. (sdbonline.org)
Yeast cells provide a simple model system with 6,000 genes, most of which are found in other organisms, including humans, making them excellent candidates for studying fundamental genetics and complex biological pathways. (genengnews.com)
However, the researchers found that "housekeeping" genes-which comprise the majority of genes in yeast-lacked a protein-DNA architecture that would allow specific transcription factors to bind, a hallmark of inducible genes. (genengnews.com)
Recurrent mutational targets in MDS are the genes involved in RNA splicing, DNA methylation, histone modification, transcription, signal transduction, cohesin complex and DNA repair. (go.jp)
Sequential acquisition of mutations in these sets of genes serves as a driver for the initiation, clonal evolution and progression of MDS. (go.jp)
D'Souza works to elucidate the structural aspects of retroviral replication, including the initiation of reverse transcription, transcription, and translation of viral genes. (harvard.edu)
Next, the importance of embryonic developmental genes such as homeobox and T-box transcription factors are highlighted in conduction system development and function. (medscape.com)

This transcription initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. (osti.gov)
Adjacent to this termination signal was a stretch of conserved nucleotides that might function as a transcription initiation signal Technical Appendix Table 1). (cdc.gov)
In this chapter, we revise a previously described quantitative reverse transcription polymerase chain reaction method, which now utilizes degenerate nucleotides at certain positions in the probe and the reverse primer to accommodate the sequence heterogeneity observed within the Nipah henipavirus species. (cdc.gov)

Here, we apply permanganate treatment and chromatin immunoprecipitation (PIP-seq) of initiation factors to identify the precise location of melted DNA separately associated with the pre-initiation complex (PIC) and the adjacent paused complex (PC). (nih.gov)
Thompson, M. (2009) Polybromo-1: the chromatin targeting subunit of the PBAF complex. (mtu.edu)

All organisms-bacteria, archaea, and eukaryotes-have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. (osti.gov)
During transcription initiation RNAP remains associated with the upstream promoter DNA via sequence-specific interactions between the σ factor and the promoter DNA while moving downstream for RNA synthesis. (umn.edu)
We report crystal structures of Mtb RNAP, alone and in complex with Rif, at 3.8-4.4 A resolution. (proteopedia.org)
We also report non-Rif-related compounds-Nalpha-aroyl-N-aryl-phenylalaninamides (AAPs)-that potently and selectively inhibit Mtb RNAP and Mtb growth, and we report crystal structures of Mtb RNAP in complex with AAPs. (proteopedia.org)

However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. (osti.gov)
In this paper, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate and define details of stepwise, RNA-extension-driven displacement of the "σ-finger" of the bacterial transcription initiation factor σ. (osti.gov)
Here we report the crystal structures of E. coli transcription initiation complexes (TICs) containing the stressresponsive σ S factor, a de novo synthesized RNA oligonucleotide, and a complete transcription bubble (σ S -TIC) at about 3.9-Å resolution. (umn.edu)
Further analysis found that the crown root proliferation from YUC overexpression lines required the transcription factor WOX11 . (isaaa.org)
These mutants exhibited crown rootless phenotype, which was partially rescued by overexpression of the transcription factor WOX11 . (isaaa.org)
Part of transcription factor TFIIIC complex. (nih.gov)
Human transcription factor IIIC box B binding subunit. (nih.gov)
Purification and characterization of two forms of human transcription factor IIIC. (nih.gov)
The activity of transcription factor IIIC1 is impaired during differentiation of F9 cells. (nih.gov)
changes in DYX1C1, one involving the translation initiation sequence and an Elk - 1 transcription factor. (wikigenes.org)
induced transactivation of the ternary complex factor Elk - 1 using a GAL4- Elk - 1 construct. (wikigenes.org)
rapidly increased( 1 min) the phosphorylation of the transcription factor Elk - 1 , and this was inhibited by pertussis toxin( PTX). (wikigenes.org)
In a paper published in Science, the Rutgers CCB scientists show how the molecular machine responsible for transcription initiation--a protein complex that consists of the enzyme RNA polymerase and the initiation factor δ- recognizes a specific site on DNA preceding a gene, binds to DNA, unwinds the DNA helix, and pre-organizes the unwound DNA to enable subsequent reactions. (rutgers.edu)
The AML1-CBFbeta transcription factor complex is essential for the definitive hematopoiesis of all lineages and is the most frequent target of chromosomal rearrangements in human leukemia. (embl-heidelberg.de)
The four-subunit negative elongation factor (NELF) complex mediates RNA polymerase II (Pol II) pausing at promoter-proximal regions. (bvsalud.org)
For example, we have applied light-activatable cMOs to interrogate transcription factor function during zebrafish notochord, pancreas, and vascular patterning. (cdc.gov)

Predicted to be involved in 5S class rRNA transcription by RNA polymerase III and transcription initiation from RNA polymerase III promoter. (nih.gov)
as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. (embl.de)
They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. (embl.de)

The coordinated transcription of the genome is the fundamental mechanism in molecular biology. (mdpi.com)
Transcription of protein-coding and noncoding DNA occurs pervasively throughout the mammalian genome. (nih.gov)
These finding reveal a common core to pervasive Pol II initiation throughout the human genome. (nih.gov)

Transcription initiation protein SPT3 homolog is a protein that in humans is encoded by the SUPT3H gene. (wikipedia.org)
The traditional model of gene regulation involves transcription factors, which bind to specific DNA sequences to control the expression of a nearby gene. (genengnews.com)
The computational methods that we've developed to analyze this data could serve as a jumping-off point for further development for gene regulatory studies in more complex organisms. (genengnews.com)
This gene encodes a protein that is a component of the PCAF histone acetylase complex and structurally similar to one of the histone-like TAFs, TAF6. (abnova.com)
In principle, development of small molecule inhibitors of interactions of specific transcriptional activators (or repressors) with DNA or with the basal transcription machinery could provide highly selective regulators of gene expression and thus highly selective therapeutic agents (e.g., antiviral agents based on disabling essential viral gene expression). (mtu.edu)
gene that contains a sequence that hybridizes with an oligonucleotide probe specific for M. tuberculosis complex bacteria. (cdc.gov)

MMDB and VAST+: tracking structural similarities between macromolecular complexes. (nih.gov)
Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition. (proteopedia.org)
The work on these projects has been informed by our research and studies in structural biology, in particular protein-nucleic acid interactions, collagen, binary and ternary complexes with catabolite activating protein (CAP), and nucleic acids. (rutgers.edu)
Here, we review the structural elements required for designing mRNA vaccine constructs for effective in vitro synthetic transcription reactions. (mdpi.com)
Structural basis of transcription initiation , Science 338, 1076-1080. (rutgers.edu)
During the process of airway inflammation, complex interactions of innate and adaptive immune cells as well as structural cells and their cytokines have many important roles. (cdc.gov)

NGL viewer: web-based molecular graphics for large complexes. (icr.ac.uk)
Our multi-disciplinary research program aims to understand the molecular architecture and recognition features of the early events in transcription initiation, and to use these insights to develop inhibitors of transcriptional assembly. (mtu.edu)
A growing number of studies are finding diverse and essential roles for molecular recognition events in mediating information transfer and complex assembly in biology. (mtu.edu)

In this chapter, we mainly discuss the coordination regulations between DNA replication initiation and other cell cycle events that ensure genomic integrity. (intechopen.com)
The pre-replication complex (pre-RC) assembly or the DNA replication licensing is the first step in DNA replication initiation, characterized by the sequential recruitment of ORCs, Cdc6, Cdt1 and MCMs to the DNA replication origins to form the pre-RC at the end of mitosis ( Bell and Dutta 2002 ). (intechopen.com)
Surprisingly, accurate detection of human mtDNA transcription initiation sites (TIS) in the heavy and light strands revealed a novel conserved transcription pausing site near the light strand TIS, upstream to the transcription-replication transition region. (biorxiv.org)

Ablation of individual NELF subunits destabilizes the NELF complex and causes cell lethality, leading to the prevailing concept that NELF-mediated Pol II pausing is essential for cell proliferation. (bvsalud.org)

TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. (antikoerper-online.de)

In addition, σ S -TIC structures display a highly stressed pretranslocated initiation complex that traps a pyrophosphate at the active site that remains closed. (umn.edu)
Liu, B , Zuo, Y & Steitz, TA 2016, ' Structures of E. coli σ S -transcription initiation complexes provide new insights into polymerase mechanism ', Proceedings of the National Academy of Sciences of the United States of America , vol. 113, no. 15, pp. 4051-4056. (umn.edu)
Developing catalysts of this sort can impact both energy conversion strategies for renewable energy and the chemical industry by streamlining the generation of complex chemical structures with minimal waste generation. (harvard.edu)

The PCAF histone acetylase complex, which is composed of more than 20 polypeptides some of which are TAFs, is required for myogenic transcription and differentiation. (abnova.com)
genetics of a complex differentiation process. (lu.se)

Structure of the human Mediator-bound transcription preinitiation complex. (expasy.org)

This pausing site correlated with the presence of a bacterial pausing sequence motif, yet the transcription pausing index varied quantitatively among the cell lines. (biorxiv.org)
The structure provides a foundation for understanding bacterial transcription initiation and transcriptional regulation and provides a starting point for developing new antibacterial agents that function by inhibiting bacterial transcription. (rutgers.edu)

Despite previous observations of OIRs generally leading to restored progress after one single-repair initiation, data from a multiperson conversational corpus of Norwegian Sign Language (NTS) show that 68% of 112 individual repair initiations occur in multiple OIR sequences. (degruyter.com)
This article identifies three different trajectories of multiple OIR sequences in the NTS data, which are as follows: (1) a trouble source being targeted by more than one repair initiation, (2) the self-repair becomes a new trouble source, or (3) the repair initiation becomes a new trouble source. (degruyter.com)
The high frequency of multiple OIR sequences provides an opportunity to quantitatively investigate how the various formats of repair initiation are distributed in single- and multiple-OIR sequences, how they occur as first or subsequent, and whether they restore the progress of the conversation or are followed by another repair initiation. (degruyter.com)
The other question is how different formats of repair initiation are distributed in different sequential positions of single and multiple OIR sequences, employing categories such as first and subsequent cases (Rossi 2015 ) and "closing" and "nonclosing" cases. (degruyter.com)
Since many of today's expression vectors encode Shine-Dalgarno sequences it is easy to overlook problems with translation initiation. (neb.com)
However, intergenic regions between all major ORFs contained relatively conserved motifs that could be transcription termination/polyadenylation sequences (A/U) CU 7 , similar to other rhabdoviruses ( 5 ). (cdc.gov)

The transcription of COX-1 yields a 2.7-kilobase (kb) messenger ribonucleic acid (mRNA) that encodes a 576-residue, 65-kd protein. (medscape.com)
Conversely, the transcription of COX-2 yields a 4.5-kb mRNA that encodes a 70-kd protein with roughly 70-75% homology to the COX-1 protein. (medscape.com)

[3] [ SIGA_MYCTU ] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. (proteopedia.org)
Currently, we are working in new classification schemes for transcription factors with a focus on understanding the details of the protein-nucleic acid interface. (rutgers.edu)
All are basic helix-loop-helix transcription factors. (sdbonline.org)
How TCF1 partners with other transcription factors to regulate transcription remains unclear. (bvsalud.org)

However, in contrast to prevailing views they co-occurred within the same promoter region: initiation originating from a focused PIC, and broad nucleosome-linked initiation. (nih.gov)

Because the transcription machineries in bacteria and higher organisms are structurally and mechanistically related, the structure also provides a framework for understanding transcription and transcriptional regulation in higher organisms, including humans. (rutgers.edu)

It can readily be embedded in extended models of the complete HIV-1 reverse transcription process, or analogous processes in other viruses and help to guide drug development and improve our understanding of the mechanisms of resistance development during treatment. (plos.org)

Both CarD and RbpA bind near the upstream edge of the −10 element where they likely facilitate DNA bending and impede transcription bubble collapse. (regenerativemedicine.net)

Analysis of non-human organisms enabled de novo mtDNA sequence assembly, as well as detection of previously unknown mtDNA TIS, pausing, and transcription termination sites with unprecedented accuracy. (biorxiv.org)
Our approach paves the path towards in vivo, quantitative, reference sequence-free analysis of mtDNA transcription in all eukaryotes. (biorxiv.org)
These obstacles interfered with comparative in-vivo investigation of mtDNA transcription in diverse conditions, and hampered expanding the study of mtDNA nascent transcripts to organisms lacking an mtDNA reference sequence. (biorxiv.org)
DNA sequence and shape analysis of initiation complex sites suggest that both sequence and shape contribute to specificity, but in a context-restricted manner. (nih.gov)
That is, initiation sites have the locally "best" initiator (INR) sequence and/or shape. (nih.gov)

Not all other-initiations of repair (OIR) are instantly followed by a functional self-repair that restores the progress of the conversation. (degruyter.com)
Determining the structure of a functional, specific transcription initiation complex has been a goal of researchers for three decades," said Ebright, a professor in Rutgers CCB and a laboratory director at the Waksman Institute of Microbiology at Rutgers. (rutgers.edu)

How these two modes of initiation relate is unclear. (nih.gov)

Transcription in eukaryotes is carried out by three main RNA polymerases: Pol I, II, and III. (mdpi.com)

A team of Rutgers CCB researchers led by Richard H. Ebright and Eddy Arnold has determined the three-dimensional structure of the transcription initiation complex, the key intermediate in the process by which cells read out genetic information in DNA. (rutgers.edu)

The structure defines the interactions that RNA polymerase and δ make with the DNA site for transcription initiation, known as the "promoter. (rutgers.edu)

RbpA and CarD are essential transcription regulators in mycobacteria. (regenerativemedicine.net)

Finally, mtDNA transcription termination sites have been either mapped in-vitro, or were associated with MTERF binding sites ( Christianson and Clayton 1986 ), thus, again, limiting the capability to in-vivo map transcription terminations sites in diverse organisms. (biorxiv.org)
The unprecedently speedy development of mRNA vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was enabled with previous innovations in nucleoside modifications during in vitro transcription and lipid nanoparticle delivery materials of mRNA. (mdpi.com)
In vivo studies demonstrate the essential role of RbpA, show the effects of RbpA truncations on transcription and cell physiology, and indicate additional functions for RbpA not evident in vitro. (regenerativemedicine.net)

Whereas mammals (chimpanzee, rhesus macaque, rat, and mouse) showed a human-like mtDNA transcription pattern, the invertebrate pattern (Drosophila and C. elegans) profoundly diverged. (biorxiv.org)

Pathophysiologically, asthma exert different effects at different concentrations, can is characterized by constriction of airway smooth synergize or antagonize the effects of other cytokines muscle, hyper secretion of mucus, edema and airway and regulated in a complex manner and function via hyper responsiveness (AHR),[3] mucus secretion and cytokine cascade. (cdc.gov)

The heart achieves the coordinated contraction of the atrial and ventricular chambers due to the precise timing of the cardiac conduction system (CCS), a specialized complex and heterogeneous network of cells that initiate and allow propagation of action potentials through the heart. (medscape.com)

Anatomy16

Organisms8

Diseases2

Chemicals and Drugs125

Analytical, Diagnostic and Therapeutic Techniques and Equipment27

Phenomena and Processes83

Information Science3

Health Care1

TFIID4

Eukaryotic2

Proteins14

Genes16

Nucleotides3

Chromatin2

RNAP4

Factor16

RRNA3

Genome3

Gene6

Structural6

Molecular3

Replication3

Subunits1

Promoter recognition1

Structures3

Differentiation2

Preinitiation complex1

Bacterial2

Sequences6

Encodes2

Factors4

Nucleosome1

Transcriptional1

Reverse transcription1

Bubble1

Sequence5

Functional2

Unclear1

Eukaryotes1

Ebright1

Interactions1

Regulators1

Vitro3

Drosophila1

Function1

Precise1