Essay On Sequence Processing, Alignment, And Transcripts Assembly

In this project, C. Elegans are hermaphrodite worms that will be used since they are easy to maintain in lab, as well as have short life cycles. The gene that the project attempted to knockdown in C. Elegans with RNAi treatment is the unc-22 gene. RNAi disrupts gene expression in the presence of double stranded RNA (dsRNA) that is complementary to target gene sequence. The unc-22 gene codes for a muscle protein called twitchin in wild-type worms. The Unc-22 is required for muscle regulation and maintenance in C.Elegans. To verify that the RNAi treatment worked, would check the unc-22 mRNA levels in the worms, in addition to phenotype observation.

To develop nursing career in an environment that offers tremendous potential for professional growth and achievement; exploring opportunities offered with impactful challenges utilizing my experience, skills and passion.

Recent advantages in genome-wide analyses have revealed that roughly 90% of the human genome is transcribed, yet less than 3% of the genome consists of protein-coding genes (Wu et al., 2013). The remaining genes are transcribed as noncoding RNAs (ncRNAs), which resemble mRNA in length and splicing structures yet do not encode any proteins (Wu et al., 2013). It has been debated whether all of the ncRNA transcripts are functional due to their low expression levels and low evolutionary conservation. However, many functional ncRNA have

Structurally, miRNAs are initially transcribed from the genome as a long primary transcript that are cleaved or undergoes sequential processing by the RNAse III endonucleases Drosha and Dicer to yield the 17-23 mature nucleotide species (Kim, 2005). Mature miRNAs enters the RNA-induced silencing complex (RISC), thus a multiprotein complex that separate the mature strand from passenger strand and assists the interaction of mRNAs with miRNA that contain complementary sequences (Bader, 2012). As a result, mRNAs targeted by miRNA loads are either degraded or silenced in order not to be translated into protein. In the genome, a given miRNA can regulate several hundred transcripts whose molecules function within various cellular pathways including cell proliferation and apoptosis. To date, more than 50% of the activities of all protein-coding genes in mammals are controlled by miRNAs and greatly contributes to cell-type specific profiles of protein expression

In the second paper, “Novel RNA Modifications in the Nervous System: Form and Function,” Lee discusses the role of several novel RNA modification in the physiological setting of the nervous system. RNA editing plays a major role in many pathologies; for example, loss of normal function in an m6a demethylase, FTO, has been connected with cancer, ADHD, and Alzheimer’s. Other RNA modifications are necessary for proper development of the central nervous system. NSUN2 is an m5C RNA modification heavily implicated in embryogenesis, especially in the brain. Mutation of the NSUN2 gene is correlated with intellectual disability, developmental delay, and facial dysmorphism. The aforementioned A-to-I RNA edit is also enriched in the brain, and is necessary for the proper function of genes such as GluA2, which without modification leads to postnatal death. GluA2 is also implicated in glutamate reception by neurons, and consequently in the mechanisms of addiction. Furthermore, A-to-I RNA editing failure been linked with several chronic diseases, including

In this paper, the necessary RNA data set was generated by subcellular fractionation of the 15 cell lines considered to analyse the human transcriptome. Thus isolated RNAs were classified into two categories long (>200 nucleotides) and short (<200 nucleotides) and the long transcripts were further separated into polyadenylated and non-polyadenylated transcripts.

Long non-coding RNAs (lncRNAs) are a class of RNAs that are more than 200 nucleotides long (2) and do not encode proteins. LncRNAs regulate a spectrum of biological functions and their misregulation or differential expression contribute to tumerogenesis. Exploiting this feature of lncRNAs make them excellent candidates for cancer therapy. An important indication of cancer is metabolic reprogramming which is indicated by increase in various pathways in cells such as glycolysis, glutaminolysis, Pentose Phosphate Pathway, synthesis of nucleotide and fatty acids, and formation of citrate through TCA cycle (4). Prostate Cancer Gene expression marker 1 (PCGEM1) (3), is a lncRNA that control the reprogramming of metabolic pathways in prostate

Many work has been done to perform an integrated analysis using genetic and gene expression data.

Specifically, over 1400 positively validated tissue-specific enhancers were downloaded from the VISTA Enhancer Browser (31). These in-vivo validation was tissue-specific, thus an empirical p-value was also calculated per type of tissue and enriched for neural tube (empirical P<0.005, Fig 3D). We conclude that risk-group dependent lncRNAs are a powerful metric to indicate tissue-specific functional enhancers. A “risk-dependent enhancer” was hereafter defined from the neuro-tube-specific enhancers if its locus overlaps with any risk-dependent lncRNAs.

The development of 19 to 22-nucleotide siRNAs specifically recognizing particular mRNA sequences provides new powerful reagents to selectively down-regulate gene expression and holds great potential not only for the analysis of

1B, they used a hexagonal binding routine to show where LHP1 and RNA pol II joined which gave the authors a good dimension of differentiation of overlapping points based on count. As shown on the figure the Y axis belongs to the H3K27me3 and the X-axis belongs to RNA pol II which helped them to compare the midpoints of the gene. Based on the result they identified 8,882 genes by LHP1 but most of them are not related to RNA pol II. However, in fig C, hexagonal binning of LHP1 and H3K27me3 revealed there is a strong association between the two. Points in fig. 1C, shows the distance from the midpoints of the gene to the nearest gene. Fig. 1D. shows the average CHIP-seq enrichment profiles of H3K27me3 and LHP1 in WT which is stratified by the gene length. They also did spin algorithm over genes and flanking 2kb region for

Alternative splicing (AS) plays a fundamental role in the diversification of protein function and regulation. AS is the main contributor to cellular diversity, hence, the identification and quantification of differentially spliced transcripts in genome-wide transcript analysis are very important aspects (Conesa et al., 2016). AS is the main component in eukaryotic gene expression that increases coding capacity of the human genome (Tazi et al., 2009) being used frequently to produce tissue-specific protein isoforms (Merkin et al., 2012). The disruption of specific AS events and the use of wrong splice sites have been associated with a number of human genetic diseases (Xiong et al., 2015). To date, the 20,000 or so

1a. To select sRNA, mRNA, and lncRNA unique to Cn but not present in mammalian hosts.

troubleshooting. As the control RNA also did not yield any results through the several runs attempted, it is still unknown why long template cDNA was not reliably produced for the next step of the sequencing process. It is possible further optimisation is required for cDNA to be synthesised, but funding and time constraints limited it for this study.

About 1 % of the genome encodes for miRNA, and it is estimated that about one third of all human genes might be targeted by miRNAs. MiRNAs are transcribed from either intronic (coding and non-coding), or exonic regions of the genome. The primary transcription is typically several kilobases long with (a) hairpin structure(s) that contain(s) either one miRNA or a cluster of miRNA hairpin structures, as shown in Figure 1[31, 36, 37].