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SMCHD1 protein controls genes and responds to multiple diseases

Posted by star on 2018-08-29 19:31:54
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On August 20th, "Smchd1 regulates long-range chromatin interactions on the inactive X chromosome and at Hox clusters" was published in the journal Nature Structural & Molecular Biology. The researchers found that SMHHD1 is a highly strategic protein that recognizes and collects genes from different parts of the chromosome; then, SMSCHD1 aggregates genes into specific regions of the nucleus where they are effectively silenced.

The Hox gene is a type of gene that regulates biological forms in an organism. Once these genes are mutated, a part of the body is deformed. To the surprise of the researchers, they found that SMCHD1 is required for disruption of the Hox gene.SMCHD1 extracts the Hox gene from different points in the chromosome and silences it into a specific "control room." For example, a Fox with a defective Hox gene may have a leg out of the head. In addition, the Hox gene is often turned on in cancer. And promote tumor growth.

Basic knowledge about how SMHHD1 works may help researchers develop potential treatments for diseases caused by SMCHD1.Prader-Willi syndrome is a hereditary disease that, in addition to abnormal symptoms, can cause muscle weakness and persistent hunger, leading to obesity and type 2 diabetes, drugs that help inhibit SMCHD1 activity or treat the disease.The researchers further explained that Prader-Willi syndrome occurs because a specific set of genes are dormant and cannot be turned on. If a way to activate this set of genes can be found, they may be able to develop targeted therapies for this disease.



Activity of the core components of the polymerase

Posted by star on 2018-08-29 19:09:02
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The subassembly responsible for chain extension, the core polymerase (previously known as DNA polymerase Ⅲ), consists of three polypeptide subunits.

1. The α-subunit, encoded by dnaE, catalyzes 5'→3'chain growth and is essential for DNA synthesis.

2.The ∈-subunit, encoded by dnaQ (also called mutD), has 3'→5'exonuclease activity. On those rare occasions when the polymerase makes an error, the exonuclease removes the mispaired nucleotide, thereby providing a proofreading function. Consistent with this function, cells with defective ∈-subunits have high mutation rates.

3. The θ-subunit, encoded by bolE, seems to stimulate the∈-subunit. However, this is not an essential function because DNA polymerase Ⅲ holoenzyme isolated from bolE deletion mutants is fully active even though it lacks the θ-subunit. Thus,θ does not appear to have a unique function at this time.

Binding studies provide some information about the way the subunits of the core polymerase subassembly are organized. The α-and ∈-subunits form a 1:1 complex in which each subunit's activity is greater than it is in the free subunit. The θ-subunit joins this complex by binding to ∈ to form a linear α-∈-θ arrangement. Association between the subunits in the core subassembly is so tight that denaturing agents are required for dissociation. Detailed information about the structure of the subunits within the core polymerase subassembly and the nature of the association among them awaits crystallographic studies. The core polymerase subassembly does not bind tightly to DNA. We now examine the subassembly that tethers the core polymerase subassembly to DNA.



The relation between sliding clamp group and DNA

Posted by star on 2018-08-29 01:08:24
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    The sliding clamp (also known as theβ-dimer or theβ-clamp) is made of two identical polypeptides that are encoded by dnaN. X-ray crystallography studies reveal that head-to-tail interactions between the two semicircular shaped polypeptide subunits give the sliding clamp subassembly the appearance of a ring. The diameter of the hole within the ring is about 3. 5 nm and therefore big enough for a double-stranded DNA molecule to fit inside.

    Each polypeptide chain has three domains. Even though the amino acid sequences of the segments making up the three domains are different, each domain has the same folding pattern, consisting of two β-strands on the outside and two α-helices on the inside. The net effect is that the β-dimer appears to have a sixfold rotational axis of symmetry even though it only has a true twofold rotational axis of symmetry. Twelve α-helices (2 polypeptides * 3 domains/polypeptide* 2 α-helices/domain) line the inside of the sliding clamp.

    If we make the reasonable assumption that DNA is perpendicular to the plane of the sliding clamp, then the axis of each α-helix will be perpendicular to the major and minor grooves, blocking the protein from gaining access to either DNA groove and allowing the clamp to slide along the long axis of DNA. There is sufficient space for one or two water layers between the DNA and the sliding clamp, suggesting that the clamp may "ice skate" along the double stranded DNA. Twelve α-helices line the center of the sliding clamp. The arrangement of the α-helices in the sliding clamp is in marked contrast to their arrangement in DNA-binding proteins, which usually have their α-helices parallel to the grooves so that the helices can fit into the major groove. The carboxyl ends of the two polypeptides project from the same face of the sliding clamp and serve as points of association for the r......

SIRT6 —A Key Gene Related to Primates' Growth, Lifespan

Posted by star on 2018-08-28 19:43:26
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SIRT6 gene, a homologue of Sir2, is involved in the regulation of aging and longevity in rodents. Deficiency of SIRT6 from mice leads to features of accelerated aging. Recently,Chinese scientists have discovered that the gene is also involved in the development of primate embryos.

On August 22, Nature published an article entitled SIRT6 deficiency results in developmental retardation in cynomolgus monkeys. By using CRISPR-Cas9-based gene editing technology, the researchers were able to knock out the SIRT6 gene in a cynomolgus monkey model.SIRT6-

-deficient monkeys die hours after birth and exhibit severe prenatal developmental retardation. This was not previously found in rodent research based on this longevity protein.

SIRT6 loss delays neuronal differentiation by transcriptionally activating the long non-coding RNA H19 (a developmental repressor). SIRT6 deficiency results in histone hyperacetylation at the imprinting control region of H19, CTCF recruitment and upregulation of H19.

Chinese scientists conducted in vitro experiments to generate SIRT6-null human embryonic stem cells. The results showed that the differentiation of such mutant cells to neurons was delayed compared to wild-type cells. Moreover, the cells overexpress the H19 gene. This suggests that human cells lacking SIRT6 can resolve their neural differentiation defects by reducing the expression of H19.Thus, SIRT6 regulates nerve development in human cells by inhibiting the expression of H19, just like in monkeys.

In the evolutionary ladder from mice to monkeys to humans, some of the features caused by the absence of SIRT6 are becoming more and more serious – SIRT6-deficient mice die within weeks to months of birth, and defective monkeys can be within a few hours. Death, and humans can't even live until they are born.

This new discovery reveals that SIRT6 acts as an epigenetic factor that regulates prenatal development of primates and provides i......

Bacterial replication tool Ⅲ DNA polymerase holoenzyme

Posted by star on 2018-08-28 19:39:28
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A polymerase with a low processivity value dissociates from its template after only a few nucleotides are added, catalyzing nonprocessive or distributive replication. Distributive replication is inefficient because the polymerase requires considerable time to associate with its template after each dissociation event.

There is a simple laboratory method for determining whether a polymerase has a high or low processivity value. A reaction is begun by adding all the necessary components and then diluting the reaction mixture. If the polymerase has a high processivity value, it will remain associated with DNA and the rate of new polynucleotide synthesis will remain about the same as before dilution. However if the polymerase has a low processivity value, it will dissociate from DNA and the rate of new polynucleotide synthesis will decrease.

One possible explanation for DNA polymerase Ⅲ's Iow activity is that additional proteins are needed to increase its processivity. Kornberg and coworkers thought that they might be able to detect these additional proteins by using a different DNA template. Their choice of template was influenced by the knowledge that the circular single-stranded DNA molecules in bacteriophage such as M13 andΦX174 are so small (5-6kb long) that they lack sufficient genetic information to code for most of the enzymes needed for DNA replication. Therefore, the bacteriophage use bacterial enzymes to catalyze the first stage of DNA re plication, the conversion of circular. Single stranded DNA to the double-stranded replication form. Hence, it seemed reasonable to expect that bacterial extracts would be able to extend a primer annealed to circular single stranded bacteriophage DNA completely around the template.

This primer extension is exactly what Kornberg and coworkers observed. Taking advantage of this assay, Kornberg's laboratory used standard protein fractionation procedures to purify the fully active replicase, DNA poly......

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