Académique Documents
Professionnel Documents
Culture Documents
Proposal Summary:
spliceosomal activity within the cell plays a critical role in pre-mRNA splicing by removing
non-coding introns and ligating code-carrying exons. This is done through the complex and
varied process of spliceosome assembly, ligation, and disassembly, in which various snRNPs
splicing. As mistakes in this splicing can lead to disease, it is critical to identify the processes of
spliceosome assembly and function, to understand and ensure their success. The objective as
such is to ensure the success of the splicing of introns and the ligation of exons of pre-mRNA.
To do this, proteins found in the spliceosomal catalytic core assembly will be isolated, and used
to identify where and how they interact to promote or cause pre-mRNA splicing.
Background:
which the genetic information carried by deoxyribonucleic acid, or DNA, is copied into single
stranded messenger ribonucleic acid, or mRNA. This copy of the original genetic information is
sent to the ribosome, which assembles proteins based on the template provided by DNA, and is
or transcribed RNA that contain relevant genetic information, by the removal of introns, buffer
regions of RNA that separate the relevant message regions of transcribed RNA, the
aforementioned exons. The chemistry of this reaction is not understood, but advances in the
technology used to analyze the structure and function of biochemical molecules has allowed
further study of this unknown chemical process.1 This has led to a better understanding of the
chemistry behind this molecule, and perhaps an understanding of how mistakes of the major
spliceosome can lead to problems. For example, failure of proper spliceosome activity can lead
to a variety of genetic diseases, either through long term mutation or the genetic change of
single cells. This can lead to cancers and other genetic diseases.2
One example of relatively recent and widely acknowledged feature of the nature of the
major spliceosomal catalytic core and its assembly, is the catalytically active U5 and U6 small
nuclear RNA complex. This portion of the process, a part of the spliceosomal assembly phase
of steps A and B (shown in Figure 1), is connected to the introduction of certain proteins, such
as Prp2 (also shown in Figure 1). Because of its critical part in the splicing step in major
spliceosome function, the Bact to B* step of catalytic activation has been researched in greater
The steps of the process of major spliceosome assembly, location, function and
disassembly are extremely complex; the introduction and departure of many complex
RNA-protein molecules and individual proteins necessitates a complete list of steps to the
process.5 This transition from inactive catalytically to catalytically active is known as Bact-->B*, B
being the step of the spliceosome process in which the transition from non catalytically active to
catalytically active occurs, and named for the complex B which is formed at the beginning of the
step. Additionally, the significance of biomolecules with similar function are mentioned, such as
the group II self-splicing intron, which is of note because it presumably is able to perform the
same chemical reaction to separate introns from exons and ligate important RNA that the
the Bact to B* provides more specific information about the biomolecules involved in each step of
the process. The Spliceosome: Design Principles of a Dynamic RNP Machine describes the
chemical parts of certain critical biomolecules, one example being U2 snRNA.3 The most major
named parts of spliceosome assembly, such as U2 and other U snRNAs, are composed of both
RNA and protein, but the specifics of these components are as yet unknown. Thus, it is
important to understand what chemical parts allow for the structurally and chemically dynamic
nature of these biomolecules. Additionally, the ability of these molecules themselves to change
form is addressed, such as the massive remodeling that occurs in U4/U6.U5 tri-snRNP to allow
it to become catalytically active and ligate. The U4 departs, while the U5 and U6 remain,
becoming able to perform the chemical reaction necessary. The most important implication of
spliceosome.
process by which the spliceosome forms and functions. The U2/U6 spliceosomal catalytic center
of the active spliceosome is the functional region which performs the splicing and ligation.6 For
this reason, a significant portion of current research is going toward the understanding of this
process, which is the reason the spliceosome assembles in the first place. It is also one of the
most complicated steps of the process, and requires the introduction of many proteins.
Project Description:
within the process of spliceosome assembly. Specifically, there will be two goals to the project:
determining the mechanism by which the transition to catalytically active state (in the Bact to B*
transition) occurs and the dynamics of the resulting shift in catalytic core functionality by way of
certain proteins identified in the process. This portion, the catalytic core of U2-U6 snRNA is
naturally dormant, unable to splice even when assembled. Only when certain proteins, such as
the currently being studied Cwc 27 and p147 parts, are added to the system does the catalytic
center become active. As such, the project will focus on determining how this selected proteins
chemistry allows it to perform its function. The result will not necessarily be a complete
understanding of the molecules chemistry, but rather an understanding of the part important to
such that is so critical to the activation of the spliceosomal catalytic center. This protein will be
chosen on a combination of three factors: its accessibility within the process (i.e. the required
effort to isolate and test the sample), the importance of its role in said process, determined by its
location within the process and other details of its role, and its complexity, as more simple
protein components will require less time to create structural analysis through X-Ray
crystallography.
Research Strategy:
RNA and/or protein components of yeast spliceosomes will be site-specifically marked with
fluorescent dyes or gold nanoparticles. Determining which proteins to use require nondenaturing
gel electrophoresis. Samples of a mixture of U2 snRNA and specific proteins identified in the
process or U6 snRNA in a similar mixture will be ran using gel electrophoresis. The mixture
denaturing polyacrylamide gel. Figure 2 displays a polyacrylamide gel, which separates bonded
and nonbonded RNAs and proteins through an electric charge from electrodes on opposite ends
of the gel. These electrodes attract them differently due to their different charges, separating
them (nucleic acids have a negative charge and proteins have a significantly weaker negative
charge).
The gel will be stained with two dyes, one that darkens when bonded to RNA, and another
which darkens when bonded to proteins. Each sample will be loaded in a separate lane, with
more than one sample being typically loaded in the same gel. If the areas of each lane which
darken in each color overlap significantly, the protein will clearly have bonded to the specific
snRNA component of the Bact spliceosomal catalytic core. When this protein(s) has been
determined, the protein will be ran in non-denaturing gel electrophoresis, to determine the
peptide count of the protein. This protein will be tested in conjunction with other elements of the
Bact stage spliceosome (not yet chosen), which will be mixed in small samples with the selected
protein(s). These samples will be run in a final gel. The proteins which are found to have
bonded in greatest numbers, determined by the size and boldness of the line when
the bonded parts of the spliceosome, providing information on their structure after the B* step
2
Zhou, J., & Chng, W.-J. (2017). Aberrant RNA splicing and mutations in spliceosome complex
in acute myeloid leukemia. Stem Cell Investigation, 4, 6.
http://doi.org/10.21037/sci.2017.01.06
3
Wahl, M. C., Will, C. L., & Lhrmann, R. (2009). The Spliceosome: Design Principles of a
Dynamic RNP Machine. Cell, 136(4), 701-718. doi:10.1016/j.cell.2009.02.009
4
Spliceosome [Digital image]. (2003). Retrieved January 8, 2017, from 2017, from
http://www.mpibpc.mpg.de/luehrmann
5
Ruby, S. W., Chang, T. H., & Abelson, J. (1993). Four yeast spliceosomal proteins (PRP5,
PRP9, PRP11, and PRP21) interact to promote U2 snRNP binding to pre-mRNA. Genes
& Development, 7(10), 1909-1925. doi:10.1101/gad.7.10.1909
6
Schmitzov, J., & Pena, V. (2012). Emerging views about the molecular structure of the
spliceosomal catalytic center. RNA Biology, 9(11), 1311-1318. doi:10.4161/rna.22359
7
Schmitzov, J., Rasche, N., Dybkov, O., Kramer, K., Fabrizio, P., Urlaub, H., . . . Pena, V.
(2012). Crystal structure of Cwc2 reveals a novel architecture of a multipartite
RNA-binding protein. The EMBO Journal, 31(9), 2222-2234. doi:10.1038/emboj.2012.58
8
Perea, W., Schroeder, K. T., Bryant, A. N., & Greenbaum, N. L. (2016). Interaction between the
Spliceosomal Pre-mRNA Branch Site and U2 snRNP Protein p14. Biochemistry, 55(4),
629-632. doi:10.1021/acs.biochem.5b01036
9
APA MLA Chicago Protein Electrophoresis [Jpg]. (2017). Bio Rad.