38 Matching Annotations
  1. Nov 2017
    1. accession Nos

      An accession number in BLAST is the specific identification number of a sequence. AT

    2. homology

      Homology in protein sequences means that the sequences are similar enough that we can assume they developed from the same ancestral gene. AT

    3. marine biotoxin okadaic acid

      This marine biotoxin is incredibly common in aquatic environments because of pollution and other factors. Thus it was important to investigate how it affects the DNA/chromatin of mussels. Researchers mapped out the specific effects of the biotoxin and compiled it in a database.

    4. (Talbert and Henikoff 2014; Santoro and Dulac 2015; Suárez-Ulloa et al. 2015).

      The way that organisms respond to their environment is ultimately through gene expression. For example, growth is caused by production of growth hormones, among other factors, which are turned on and off. Eukaryotic organisms use histone regulation as one way to respond to environmental changes. It has been found that exchange of histones can occur due to changes in temperature and season, during conflict, movement, learning, and more. AT

    5. Indeed, bivalve molluscs constitute emerging models in epigenetics, as illustrated by recent studies examining the role of DNA methylation in the Pacific oyster

      Earlier in the year, researchers were using mollusks to derive a non addicting painkiller in the hopes of solving the U.S. opioid epidemic. Read more at salon: https://www.salon.com/2017/03/04/a-little-mollusk-may-lead-to-a-big-discovery-in-helping-solve-the-u-s-opioid-epidemic/ EM

    6. models

      A model organism is a species with a fast regeneration time and a relatively simple genome. We try to find similarities between model organisms and complex ones in order to make a clinical use of the research. AT

    7. (González-Romero et al. 2012)

      H2A.Z.1 is a well documented histone variant. It plays a role in keeping genome integrity, They are highly conserved, even more than H2A.X. AT

    8. (Gavery and Roberts 2010, 2012; Suárez-Ulloa et al. 2015).

      Recent research on mollusc DNA has found that they do use methylation systems to regulate their expression. This was determined by using bisulfate PCR. The bisulfate creates a tag on a methylated amino acid in the protein sequence, and PCR is a way to generate many different copies of a single strand of DNA. Using different mapping techniques the locations of methyl group were determined. A methyl group added to a DNA structure serves to wrap the DNA tighter around the histone in order to block transcription. AT

    9. sessile

      fixed in one place; immobile. EM

    10. (Talbert and Henikoff 2014).

      The histone variant H2A.Z Is the most important regarding environmental epigenetic responses. environmental epigenetic are everyday factors in an organism’s life that affect how their genes are expressed that does not create a change in their DNA. AM

    11. (Simonet et al. 2013) and at least 3 different H2A.Z variants in plants (Yi et al. 2006).

      H2A.Z was found to have four different subtypes in the Cyprinus carpio, due to the organisms high sense of acclimatization (an individual organisms ability to adjust to a change in its environment such a s a change in altitude, temperature, and humidity). The four subtype variants aid in the thermoregulation (process that allows the body to maintain a core internal temperature) and stability of the organism. KM

    12. alternative splicing

      A regulated process during gene expression that results in a single gene coding for multiple proteins. EM

    13. Bönisch et al. 2012

      H2A.Z.2.2 is found in all human (and some primate species) cell lines but it is found mostly in the brain. It is achieved through alternative splicing of the H2AZ variant. Through biochemical fractionation, the paper results suggest that Z.2.2 causes major structural changes and significantly destabilizes nucleosomes. The findings add to the list of known variants of the H2A.Z family. EM

    14. (Dryhurst et al. 2009; Horikoshi et al. 2013; Nishibuchi et al. 2014).

      The papers research clear differences in the structure of the two H2A variants: one in amino acid 38 and one in the structures of the L1 loop. Through mutational analysis, the paper concluded that the amino acid difference at position 38 is partially responsible for the unique functional specializations of H2AZ.1 and H2AZ.2. EM

    15. nonallelic

      Alleles are different possible expressions of a single gene. When one is expressed the other is silenced. For nonallelic genes, both can be expressed at the same time. AT

    16. (Eirín-López et al. 2009b)

      H2AZ has experienced multiple rounds of specialization which gave rise to new variants. Most vertebrates exhibit the H2AZ.1 and H2AZ.2 variants encoded by independent genes. While their protein products are similar, their promoter regions are very different, suggesting they are each tasked with different roles. The research utilized phylogenetic analysis of the promoter regions to conclude that they evolved separately during vertebrate evolution. EM

    17. (Matsuda et al. 2010), the differences in their mRNA expression levels in human tissues (Dryhurst et al. 2009), the presence of embryonic lethality in mice lacking H2A.Z.1 (Faast et al. 2001), and the specific role of H2A.Z.2 in metastatic melanomas (Vardabasso et al. 2015).

      They determined that the H2A.Z.1 and H2A.Z.2 are functionally different by individually turning them off and on by knocking out/deleting the gene that codes for the protein. By doing this they discovered that each gene codes for a different protein. Then they discovered that the knockout of each protein resulted in the loss of a distinct function. This work was done in several different studies using different types of cells, such as chicken and human. AT

    18. (Dryhurst and Ausió 2014).

      Highly dynamic chromatin state means that the chromatin is quickly unraveling and raveling to allow transcription, this happens because the histones are rapidly being exchanged from a core to a variant. The variants each give different functions and change the rate of transcription. AM

    19. (González-Romero et al. 2008; Eirín-López et al. 2009a)

      H2A.Z was derived from H2A through a series of mutations that resulted in it being 60% different from the core H2A. This was determined using a system called GWLA methodology which synthesizes two protein structure determining methods. It breaks the protein into fragments and then sequences it. The H2A.Z is highly conserved throughout eukaryotes meaning that the sequence is the same. Because there are few or no mutations this means that the function is very important and a mutation would be lethal. AT

    20. Among histones, the H2A family stands out because of the high number of specialized variants it displays (González-Romero et al. 2008), including some of the most studied histones so far such as H2A.X (involved in DNA repair; Li et al. 2005) and H2A.Z (essential for the survival of most eukaryotic organisms; Eirín-López and Ausió 2007; Talbert and Henikoff 2010).

      The family of H2A histone proteins are essential in understanding the biochemistry of chromatin-associated proteins in Mollusca. H2AZ is a variant form of the histone protein that regulates a mediated thermosensory response. The H2A.X variant form contributes to the formation of the nucleosome and its structural integrity.


    21. (Ausió 2006; Talbert and Henikoff 2010; Henikoff and Smith 2015)

      The papers discuss several structural studies on core histones and linker histone variants. The papers focused on the roles of nucleosome stability, with data showing that histone variability plays an important role in regulation of chromatin metabolism. EM

    22. (Luger et al. 1997; van Holde 1988)

      They determined the structure of histone proteins through crystallography which uses a computer modeling system to determine the atomic structure and how it assembles to form a superhelix model. KM

    23. canonical

      A core protein as opposed to a variant. AT

    24. However, the role of these proteins goes beyond structure, participating in the dynamic regulation of chromatin during transcription, replication, and repair, among other DNA metabolic processes

      Histone functions can go as far as being key gene silencers in normal embryo development. Read more in ScienceDaily: https://www.sciencedaily.com/releases/2017/08/170830202141.htm EM

    25. upregulation

      Upregulation stimulates transcription and makes it go faster. Downregulation would make transcription go slower. AT

    26. gonadal

      pertaining to the sex or reproductive glands of an organism that produces gametes (sex cells) and sex hormones.

    27. promoter

      The promoter is a region in DNA that tells the RNA polymerase protein where to begin transcription. AT

    28. sequence divergence

      The H2A.Z.1 and H2A.Z.2 came from a common ancestor and developed mutations in their amino acid sequences that eventually gave them their own separate functions. AT

    29. chromatin

      A complex of nucleic acids and proteins, which condense to form chromosomes during cell division, is highly consisted of DNA, RNA and proteins.

    30. H2A.Z.2

      Similar to H2A.Z.1 in structure. Mediates cell proliferation, which is defined by the balance between cell divisions and cell loss through cell death or differentiation. EM

    31. H2A.Z.1

      H2A.Z.1 differs from H2A.Z.2 by three amino acids. Functions range from transcriptional regulation, chromosome transmission and DNA damage repair. EM

    32. H2A.Z

      H2A.Z is another variant in the H2A family. It replaces the core H2A protein and is involved in gene silencing. It wraps the DNA tighter than a normal H2A protein would. It is also involved in sensing heat which can damage the DNA or proteins. AT

    33. H2A.B

      H2A.B histone is present in actively transcribing DNA and helps during the elongation stage of transcription. AT

    34. macroH2A

      macroH2A is a variant that represses transcription (the transfer of genetic information from DNA to messenger RNA). It also works to inactivate the expression of alleles on one of the X chromosomes. AT

    35. variants

      A variant histone is a substitute protein that acts in place of a real histone protein. They have mutations that result in a functional group. A functional group is an additional group on a protein that carries out a particular job (ie. signal, attachment point, etc). AT

    36. Histones

      A protein structure that DNA winds around to compact the DNA into tight structures instead of being loose in the nucleus. The protein amino acid sequence has two tail ends, the N-terminal at the beginning and C-terminal at the end. For histones these ends act as receptors to a signal that tells them to either open up to allow transcription or close to inhibit transcription. AT

    37. chromosomes

      A threadlike structure of nucleic acids tightly wounded by histone proteins that carry complex genetic information in the form of genes.


    38. H2A

      There are five main families of histone proteins in eukaryotic cells. The family consists of several closely related histones. AT