Omar Bennett
CTD can refer to either Conductivity, Temperature, and Depth sensors, which are used to determine the physical properties of seawater, or Connective Tissue Disease, an autoimmune disease that affects the thyroid gland. This article will focus on the former. CTD sensors are attached to a large metal frame called a rosette, which is lowered down to the seafloor to collect data on water temperature, salinity, and density. This information is crucial for understanding how oceans affect life. The rosette may also hold water-sampling bottles and other sensors that measure chemical and physical properties, providing a detailed understanding of ocean water characteristics.
| Characteristics | Values |
|---|---|
| Full form | Conductivity, Temperature, Depth |
| Application | Determining essential physical properties of sea water |
| Function | Provides precise and comprehensive charting of the distribution and variation of water temperature, salinity, and density |
| Composition | Set of small probes attached to a large metal rosette wheel |
| Deployment | Lowered on a cable down to the seafloor |
| Data collection | Scientists observe the water properties in real time via a conducting cable connecting the CTD to a computer on the ship |
| Water sampling | Done at specific depths to learn the physical properties of the water column at that particular place and time |
| Advantages | Remote sensing, very accurate, lightweight, can be used at depths up to several thousand meters |
| Disadvantages | Complex to operate, need to calibrate individual sensors |
| Other accessories | Niskin bottles, Acoustic Doppler Current Profilers (ADCP), oxygen sensors |
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What You'll Learn
- The C-terminal domain (CTD) of RNA polymerase II (Pol II) integrates nuclear events
- CTD-binding proteins recognise a specific CTD phosphorylation pattern
- CTD phosphorylation occurs mainly at residues S2 and S5
- Transcription initiation involves the interaction of the unphosphorylated CTD with the Mediator complex
- The CTD functions to help couple transcription and processing of the nascent RNA
The C-terminal domain (CTD) of RNA polymerase II (Pol II) integrates nuclear events
The C-terminal domain (CTD) of RNA polymerase II (Pol II) is a highly disordered region that plays a crucial role in integrating nuclear events. It is responsible for transcribing all protein-coding mRNAs, as well as some small nuclear and microRNAs in eukaryotes. The CTD is subject to extensive post-translational modifications (PTMs), with phosphorylation being the most notable modification during active transcription.
Phosphorylation of the CTD occurs mainly at residues S2 and S5, resulting in four different phosphorylation states. The phosphorylation state is believed to be regulated by site-specific CTD kinases and phosphatases. This phosphorylation pattern changes during the transcription cycle, leading to the recruitment of specific RNA-processing factors. CTD-binding proteins recognize these specific phosphorylation patterns, either through direct contact with phosphorylated residues or indirectly without contact.
The CTD forms a tail-like extension from the catalytic core of Pol II and is flexibly linked to a region near the RNA exit pore of the enzyme. It consists of heptapeptide repeats of the consensus sequence Y1-S2-P3-T4-S5-P6-S7, with the number of repeats varying depending on the species. For example, there are 26 repeats in yeast and 52 in humans.
The CTD plays a crucial role in coordinating transcription and RNA processing, including mRNA co-processing. It provides a means to recruit histone modifiers and chromatin remodeling complexes, influencing transcription initiation, elongation, and termination. The CTD is also involved in transcription activation and mRNA export, interacting directly with the transcription/export factor Sus1. Additionally, the CTD is essential for the formation of a stable yeast Pol II-Mediator complex, as antibodies against the unphosphorylated CTD can displace the Mediator from Pol II.
In summary, the C-terminal domain (CTD) of RNA polymerase II (Pol II) integrates nuclear events by undergoing various post-translational modifications, primarily phosphorylation. These modifications regulate the recruitment of transcriptional proteins and influence transcription initiation, elongation, and termination. The CTD's ability to form distinct condensates and its involvement in mRNA export further contribute to its role in integrating nuclear events.
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CTD-binding proteins recognise a specific CTD phosphorylation pattern
The C-terminal domain (CTD) of RNA polymerase II (Pol II) integrates nuclear events by binding proteins involved in mRNA biogenesis. CTD-binding proteins recognise specific phosphorylation patterns on the CTD, which change during the transcription cycle due to the action of CTD-modifying enzymes. Structural and functional studies of CTD-binding and -modifying proteins have revealed some of the mechanisms underlying CTD function.
The CTD consists of heptapeptide repeats of the consensus sequence Y1-S2-P3-T4-S5-P6-S7. There are five potential phosphorylation sites in a CTD consensus repeat (Y1, S2, T4, S5, and S7), but phosphorylation occurs primarily at residues S2 and S5, resulting in four different phosphorylation states of a CTD repeat. The phosphorylation state of the CTD is generally believed to be the result of the balanced action of site-specific CTD kinases and phosphatases.
CTD-binding proteins recognise CTD phosphorylation patterns either directly, by contacting phosphorylated residues, or indirectly, without contacting the phosphate. The catalytic mechanisms of CTD kinases and phosphatases are known, but the basis for CTD specificity of these enzymes remains to be fully understood. For example, it is not clear whether CTDP itself is a phosphatase or if it activates a cryptic phosphatase activity intrinsic to RNA pol II.
The phosphorylation pattern changes during the transcription cycle, resulting in the recruitment of specific RNA-processing factors. Some proteins remain bound as RNAPII changes position on the gene, and the repeats to which they are bound are assumed not to change phosphorylation state. For example, the CTD of "initiating RNAPII" is proposed to comprise two types of repeat: nonP and Ser5P. Phosphorylation patterns on the CTD ultimately depend on the combined action of CTD kinases and phosphatases, and several labs have investigated the specificity of these enzymes.
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CTD phosphorylation occurs mainly at residues S2 and S5
The C-terminal domain (CTD) of RNA polymerase II (Pol II) integrates nuclear events by binding proteins involved in mRNA biogenesis. CTD phosphorylation occurs mainly at residues S2 and S5. The CTD consists of heptapeptide repeats of the consensus sequence Y1-S2-P3-T4-S5-P6-S7, with the number of repeats depending on the species. For example, there are 26 repeats in yeast and 52 in humans.
Phosphorylation at S2 and S5 gives rise to four different phosphorylation states of a CTD repeat: unphosphorylated, phosphorylated at S2, phosphorylated at S5, and phosphorylated at both S2 and S5. The phosphorylation state of the CTD is generally believed to be the result of the balanced action of site-specific CTD kinases and phosphatases. The phosphorylation pattern changes during the transcription cycle, resulting in the recruitment of specific RNA-processing factors.
The CTD is subject to extensive post-translational modification, most notably phosphorylation, during the transcription cycle, which modulates its activities in these processes. Therefore, understanding the nature of CTD modifications, including phosphorylation, is essential to understanding the mechanisms that control gene expression. While the significance of phosphorylation of Ser2 and Ser5 residues has been studied and appreciated for some time, several additional modifications have more recently been added to the CTD repertoire, and insight into their function has begun to emerge.
The main function of the CTD is to serve as a flexible binding scaffold for a variety of nuclear factors, and binding of a factor links the process it represents to RNAPII. The CTD sequences of fission and budding yeast, zebrafish, and humans are aligned to display the context of the heptad repeats. All-consensus YSPTSPS repeats heptads are in red, and the numbers next to the parentheses indicate the repeat number. The CTD of fission yeast contains 29 heptads, while the CTD of budding yeast consists of 26 heptads.
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Transcription initiation involves the interaction of the unphosphorylated CTD with the Mediator complex
Transcription initiation is a complex process involving the interaction of the unphosphorylated CTD with the Mediator complex. The C-terminal domain (CTD) of RNA polymerase II (Pol II) plays a crucial role in gene expression and the transcription cycle. The unphosphorylated form of RNA polymerase II, known as RNA polymerase IIA, is essential for the assembly of the preinitiation complex (PIC) on the promoter. This complex includes general transcription factors (GTFs) such as TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH, as well as the Mediator complex and RNAP II with an unphosphorylated CTD.
The CTD, through its phosphorylation patterns, mediates multiple protein-protein interactions that are vital for the assembly of the preinitiation complex. The phosphorylation state of the CTD is believed to result from the balanced actions of site-specific CTD kinases and phosphatases. During the transcription cycle, the phosphorylation pattern changes, leading to the recruitment of specific RNA-processing factors. Notably, CTD phosphorylation by cdk7 within the preinitiation complex may promote the transition from the initiation to the elongation phase. This occurs by destabilizing certain intermolecular protein-protein interactions, such as TFIID/CTD binding, which facilitates the escape of RNA pol II from the initiation complex.
The Mediator complex is a central multiprotein coactivator that transmits signals from activators and repressors to Pol II. In yeast, the CTD is essential for the formation of a stable yeast Pol II-Mediator complex. Antibodies against the unphosphorylated CTD can displace the Mediator from Pol II, highlighting the critical nature of this interaction. The CTD-Mediator interaction is required for the Mediator's function, as yeast Mediator cannot stimulate transcription by a CTD-less Pol II.
While the unphosphorylated CTD is crucial for transcription initiation, phosphorylation of the CTD occurs concurrently with the initiation of transcription. The phosphorylated form of RNA polymerase II, designated RNA polymerase IIO, plays a role in catalyzing elongation. The CTD becomes highly phosphorylated during the transcription cycle, with Ser2 and Ser5 positions being important sites of modification. CDK7, a kinase associated with TFIIH, phosphorylates Ser5 at the beginning of genes, while CDK9 or p-TEFb increasingly phosphorylates Ser2 as RNAP II elongates.
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The CTD functions to help couple transcription and processing of the nascent RNA
The C-terminal domain (CTD) of RNA polymerase II (Pol II) plays a crucial role in integrating nuclear events and coordinating transcription and RNA processing. The CTD is composed of multiple heptad repeats, with a consensus sequence of Tyr1–Ser2–Pro3–Thr4–Ser5–Pro6–Ser7. The number of repeats varies, with 26 in yeast and 52 in vertebrates, and the repeats are subject to extensive post-translational modifications, particularly phosphorylation.
The phosphorylation state of the CTD changes during the transcription cycle due to the action of CTD-modifying enzymes, such as kinases and phosphatases. This dynamic phosphorylation pattern is essential for the recruitment of specific RNA-processing factors and the regulation of gene expression. Phosphorylation occurs primarily at residues Ser2 and Ser5, resulting in four possible phosphorylation states for each CTD repeat.
During transcription initiation, the unphosphorylated CTD interacts with the Mediator complex, which is essential for the function of the Mediator and the transition to elongation. As transcription proceeds, the CTD is phosphorylated on Ser2, while Ser5 is dephosphorylated by enzymes such as Ssu72 and Pin1. This phosphorylation pattern is crucial for recruiting splicing factors and defining splice sites, facilitating the assembly of the spliceosome.
The CTD also plays a role in capping and 3' processing of both polyadenylated and non-polyadenylated RNAs. For example, the Capping Enzyme (CE) is recruited to the vicinity of nascent mRNA by the CTD phosphorylated on Ser5. Additionally, the CTD facilitates different termination mechanisms for protein-coding and non-coding genes, such as the poly(A)-dependent termination pathway and the Nrd1c-dependent termination pathway.
In summary, the CTD functions to help couple transcription and processing of nascent RNA by undergoing dynamic phosphorylation changes that recruit specific RNA-processing factors and regulate gene expression. Understanding the nature of these CTD modifications and their regulation is crucial for comprehending the mechanisms that control gene expression.
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Frequently asked questions
Connective Tissue Disease.
AVISE CTD is an advanced diagnostic test for SLE and autoimmune diseases. It helps rheumatologists more accurately diagnose lupus and other connective tissue diseases.
The AVISE CTD test uses biomarkers and a proprietary algorithm to provide improved disease information compared to traditional lab tests. It combines AVISE Lupus, a 10-marker diagnostic test, with an expanded connective tissue disease panel.
The AVISE CTD test helps improve diagnostic accuracy, reduce uncertainty, and aid in earlier diagnosis. It can identify significantly more lupus patients who would otherwise appear negative with conventional markers.
Conductivity, Temperature, and Depth.
The CTD sensor is the primary tool for determining the essential physical properties of seawater. It provides scientists with precise and comprehensive data on the distribution and variation of water temperature, salinity, and density, helping them understand how oceans affect life.
The CTD sensor is usually attached to a large metal rosette wheel, which is lowered on a cable down to the seafloor. Scientists observe water properties in real time via a conducting cable connecting the CTD to a computer on the ship. Water bottles can be closed selectively as the instrument ascends, allowing for water sampling at specific depths.
The CTD sensor provides a more detailed understanding of ocean water characteristics through the entire water column, which is crucial for comprehending the underlying physics. This knowledge enables biologists to understand why certain biology is present or absent at different depths and why the chemical composition of the water varies with depth.
