Guides RNA Folding To Populate Transiently Stable RNA Structures For Riboswitch-Based Biology : Analysis

The small ribosomal subunit, amongst other things, is initiates the engagement of the mRNA and is responsible decoding the genetic information during translation [4].

It took an additional six years for researchers to glimpse at the functions provided by SMN1. Meister et al. categorized the SMN1 protein an essential to promote correct assembly of U12 small ribonucleoproteins (snRNPs). In genetics, snRNPs are nucleic proteins responsible for the splicing of premature ribonucleic acid chains (pre-mRNA) derived from genes. Without correct splicing, mature ribonucleic acid chains (mRNAs) produce dysfunctional proteins when translated. In this case, splicing functionality of U12 - intron containing transcripts is lost, and because the transcript is wrongly coded, its translation will produce a functionless protein. Hence, loss of SMN1 results in an inability form U12 snRNPs splicing complexes, and reduced splicing functionality results in loss of U12 - intron splicing functionality (Patel and Steitz, 2003).

Dr. Tina Henkin’s seminar “Flipping the switch: How cells use RNA to regulate genes expression”, was outlined by four general questions. The first question addressed in the seminar was “Why study Microbes?”. The next, “Why study bacterial gene regulation?”. The third question, “What are the basics of gene expression?”. Finally, “What’s special about riboswitches?”. Dr. Henkin addressed these questions throughout her seminar, which eventually led into to more specific questions of gene expression and predicted hypotheses of her model. However, to understand these more specific questions and predictions it is crucial to understand the first four questions outlined in the beginning of the seminar.

Title​: Studies of Large RNAP­NusG­70S Transcription­Translation Linking Complex  Author​: Dominique Gutierrez, Cristina Gutierrez­Vargas, and Dr. Joachim Frank      Abstract    Escherichia coli (E.coli)​ is an ideal model organism. Many mechanisms found in                        E.coli are resembled in other species. S10, a protein on the 30S subunit of the                               ribosome, is highly conserved and found in pathogens, including Pseudomonas                     aeruginosa, Staphylococcus aureus, and Streptococcus pneumoniae. S10 has been                   shown to interact with NusG, a transcription elongation factor, linking the translational                         machinery to that of transcription. The coupling

RNA toxicity is based in the three-dimensional structure of mRNA and the creation of hairpin loops. Normally mRNA is completely linear but when the strand of mRNA is abnormally long it increases the likelihood of folding to occur. Long CAG repeats match C-G with an A-A Match. Figure 1 is several examples of mismatch formation that can result in RNA toxicity. As Figure 1 displays not all hairpin loop formations are singular. In some cases, multiple loops can form depending on the exaggerated length of the mutant mRNA. In a healthy individual, the ATXN1 gene has CAT (histidine) triplets imbedded between long sections of CAG. Loss of these CAT triplets leads to changes in the RNA and the protein level and is associated with disease development.13 In normal individuals, these interspersed CAT triplets destabilize the hairpin structure, which is then stabilized in patients.13

In bacteria and in eukaryotes, the continuing presence of the activator is required to keep the gene on. Scientists argue that active genes often associated with acetylated nucleosomes not because of epigenetic reasons but because of other reasons. One reason is that as genes are transcribed, their nucleosomes are removed and then replaced to make way for RNA polymerase which is involved in transcription. They argue that this nucleosome-replacement machinery works to replace one set of nucleosomes with others that are more highly acetylated. Therefore, nucleosome acetylation accompanies but does not cause transcription. (Ptashne, 2013)

With that being said, this mRNA sequence codes for six codons and six amino acids. After the creation of mRNA, proteins need to be made in order to make hameglobin, through translation. The mRNA strand exits the nucleus and attaches onto a ribosominal sub-unit, within the cytoplasm. Every three letters, which code for one amino acid is read, as the mRNA strand flows through the ribomsomes. Once the mRNA is positioned properly in the ribosomal sub uint, it triggers the approach for tRNA. Each tRNA (anti codon) brings one amino acid and complentary binds it with the mRNA codon. The tRNA will then drop off its amio acids, which will be attached onto the growing polypeptide chain. Once the polypeptide chain has gained all the needed amino acids for new protein, it will break of the ribosome and make its way to the endoplasmic reticulum. Later on these amino acids will combine and create a hemoglobin protein (McKinley, O'Loughlin & Bidle,

This discrepancy can be explained by another feature of 22Rv1 cells. In these cells, Tet caused significant and rapid increase in phosphorylation of the initially very low p-eIF2α. It is well known that phosphorylation of eIF2α at Ser51 serves as a switch, which effectively suppresses translation initiation by preventing the functioning of eIF2B, a guanine nucleotide exchange factor [50]. eIF2B facilitates the exchange of GDP for GTP on eIF2 to restore active eIF2·GTP complex, which binds the initiator methionyl-tRNA and recruits it to the 40S ribosomal subunit. When phosphorylated, the alpha subunit of eIF2 sequesters eIF2B in an inactive complex and prevents another round of translation initiation to occur. Thus, our study showed that in

Eukaryotic cells respond to cellular stress by controlling the translation, stability and subcellular localization of mRNA (Buchan, Yoon, & Parker, 2011). This occurs through the remodeling of translating mRNAs into non-translating mRNPs which accumulate in cytoplasmic RNA- protein granules, known as P-bodies (mainly contain mRNA decay machinery) and stress granules (mainly contain translation initiation factors). (Buchan, Yoon, & Parker, 2011). Several studies reveal that both granules share specific mRNA and many protein components. Stress granules and P-bodies are likely to interact and exchange mRNP between them. In yeast, stress granules are usually initiated in conjunction with P-bodies, and it is partially overlapping P-bodies

Gene expression is the ability of a gene to produce a biologically active protein. This process is regulated by the cells of an organism, it is very important to the survival of organisms at all levels. This is much more complex in eukaryotes than in prokaryotes. A major difference is the presence in eukaryotes of a nuclear membrane, which prevents the simultaneous transcription and translation that occurs in prokaryotes. Initiation of protein transcription is started by RNA polymerase. The activity of RNA polymerase is regulated by interaction with regulatory proteins; these proteins can act both positively, as activators, and negatively as repressors. An example of gene regulation in cells is the activity of the trp operon. The trp

Rational and Hypothesis: My hypothesis in this aim is that mutations in UPF1 inhibit NMD thereby stabilizing premature transcripts that are translated to produce truncated proteins which promote pancreatic ASC. Previous studies have demonstrated that a subset of transcripts inhibited upon UPF1 knockdown are stabilized and translated. My objectives in this aim are: a) To determine global occupancy of mutant UPF1 on RNA b) To analyze if the mutant UPF1 bound RNA fragments are translated c) To determine which of the targets are essential to promote tumorigenesis.

After the 1960 numerous discovers made a huge impact in the modern science, one of these is the study on the rRNA which lead to the conclusion that the nucleolus is the site of ribosomal RNA synthesis and nascent ribosome assembly.1

Aside from that, transcription of RNA III also encodes the translation of delta toxin (hld) by antisense base pairing with 5’ untranslated regions (5’UTRs), forming the RNA duplexes.

In amber suppression, release factors (RFs) encoded by essential gene, prfA, often result in premature truncation in native prokaryotic translation systems. Therefore, through supplementation in trans with recoded essential amber-dependent genes and RF engineering, prfA can be eliminated. Moreover, amber-dependent genes were engineered to terminate with ochre stop codon (TAA). Additionally, quadruplet suppression has been used for multi-site nsAA incorporation, which uses unusual quadruplet codons to encode nsAAs.

Gene regulation plays important roles in retinal development and function. So far, studies on gene regulation in the retina mostly focus on the transcription level, although post-transcriptional mechanisms may also be critical. Little is now how post-transcriptional regulation of gene expression is involved in the development and maintenance of the neural retina and retinal diseases. In this project, we will address this issue by studying two related RNA-binding proteins, ZFP36l1 and ZFP36l2, two members of the TTP RNA binding protein family. This family of proteins are highly conserved through evolution and are involved in diverse biological processes thought regulating the stability of target mRNA species. Our preliminary