The Discovery Of The Small Rna Lin 4 Essay

lncRNAs are noncoding RNAs that are longer than 200 nucleotides and were identified as a result of large-scale sequencing analyses of transcriptomes and genomes. An increasing number of functional studies indicate that lncRNAs act as regulators in almost every stage of gene expression, from epigenetic modifications in the nucleus to mRNA stability and translation in the cytoplasm. This regulatory potential, along with the abundance of lncRNAs, implies that lncRNAs may be part of a broad epigenetic network. Despite these functional insights, only a small number of lncRNAs have been studied in the nervous system and their contribution to consolidation and extinction of memories is entirely unknown. Because of the transcriptional and translational regulatory roles lncRNAs, elucidating their function in the brain areas implicated in emotional learning and memory may help identify novel therapeutic targets for PTSD. The central hypothesis of this proposal based on our own preliminary studies is that specific lncRNAs mediate consolidation of fear memories and their extinction. To test this hypothesis, we will employ mouse model for fear memories to identify and manipulate specific lncRNAs in vivo with the goal of

Deciphering MECP2-associated disorders: disrupted circuits and the hope for repair). Recently, Mellios and collaborators identified novel MECP2-regulated miRNAs during the human prenatal neurodevelopment. Utilizing human patient- and MeCP2 knockdown-derived monolayer neuronal culture and organoids models, they found an upregulation of the expression levels of miR-199 and miR-214 and their downstream targets (PAK4 and PTEN, respectively), that differentially regulate extracellular signal regulated kinase (ERK) and mitogen-activated kinase and protein kinase B (PKB/AKT) signalling pathways upstream of neurogenesis. The miR199/214 overexpression was correlated with aberrant neurogenesis and neuronal migration, whereas the inhibition of their expression rescues these effects, suggesting that the neurogenesis may be impacted in RTT via MeCP2-regulated miRNAs that acts as important effectors of neuronal development modulating molecular pathways involved in proliferation and differentiation (Mellios N et al, MeCP2-regulated miRNAs control early human neurogenesis through differential effects on ERK and AKT signaling. Molecular Psychiatry (2017) 00,

There are three types of RNA: mRNA, tRNA, and rRNA. Messenger RNA (mRNA) is synthesized from a gene segment of DNA which ultimately contains the information on the primary sequence of amino acids in a protein to be synthesized. The genetic codes is translated is for mRNA, not DNA. The messenger RNA carries the code from the nucleus to the ribosome in the cytoplasm where protein synthesis occurs. It also carries the genetic information copied from the DNA in the form of a series of three-base code “words”, also known as triplets, each of which specifies a particular amino acid. Each nucleotide triplet, called a codon, can be “read” from the mRNA and translated into an amino acid to be incorporated into a protein being synthesized. Messenger RNA is a

There is no mentioning alternative and more sensitive test (Reviewer 2). The reviewer commented that we might miss mild effects of lncRNAs in plasticity and memory storage. Mild effects of lncRNA expression changes will be difficult to dissect in vivo. Given that lncRNAs are critical mediators of transcription and translation, the two key processes that regulate long-term synaptic plasticity, we are confident that we will be able to identify lncRNAs that are critical for synaptic plasticity and memory. We are certainly interested in the mild effects of lncRNAs, but during the two-year funding of this project, we sought to identify and characterize lncRNAs that are necessary for synaptic plasticity and memory

Hypothesis: 5’ untranslated region (5’ UTR) have significant role in regulating mRNA translation. If variant #2 is causative factor, translational regulation of Gene B would be the main cause of affecting phenotype. Transcription begins with 5’ UTR and translation begins with start codon AUG. Although a SNP in 5’UTR would not affect transcription, still there are possibilities that transcription could be altered because of mRNA decay (mRNA stability). The major effect of SNP in 5’UTR would be alteration of translational efficiency. 5’UTR encode translation initiation motif and secondary structures which is related to miRNA-mediated regulation. For example, miRNA can bind to 5’UTR and usually decay and degrade mRNA. When SNP happens in 5’UTR region, it is possible that miRNA could not bind to site and change the translational efficiency.

In Archetype II lncRNA works to titrate proteins and protein factors away from chromatins, yet titrating them into nuclear subdomains while serving as decoys. This is common in miRNA sites where lncRNA appears as decoys. Acting as guides in Archetype III, lncRNA functions in either cis or trans regions to assist in the recruitment of chromatin enzymes for target genes. In cis, lncRNA occurs in co-transcriptionally. This suggests that lncRNAs acts as tethers. However, lncRNA are known to also act in trans when searching for target sites. This determines the importance chromosomal looping plays in cis effects (Rinn and Chang, 2012). During Archetype IV lncRNA forms ribonucleoproteins by acting as scaffolds (Kung, Colognori and Lee, 2013). Additionally, lncRNA in the regulation of gene expression was recent discovered in Xist, a regulatory transcript found in the X chromosome that mediates the silencing of gene expression (Malecová and Morris, 2010). According to Nagano and Fraser (2011), lncRNA is critical in genomic reprogramming. For instance, somatic cells that are reconditioned to induced pluripotent stem cells. LncRNA can also act as a post-transcriptional regulation in Mrna. A lncRNA known as Gomafu/MIAT hinders the formation of spliceosome and inhibits the splicing of one of the subsets involved in mRNA (Kung, Colognori and Lee, 2013).

However, the mechanism regulating the migration of mature ecRNAs into the cytoplasm remains unclear. The linear counterparts of circRNAs, such as mRNAs or lncRNAs, can penetrate the nuclear membrane through the nuclear pore complex. Therefore, some researchers put forward the hypothesis that ecRNA export may be regulated by a mechanism similar to the regulatory mechanism of linear RNA migration [18]. The degradation pathway of circRNAs is another unanswered question. The expression level of circRNA is dynamically modulated by the balance between biogenesis and degradation of circRNAs. CircRNAs may be degraded by short interfering RNAs [13]. A recent study found that circRNAs may be cleared by extracellular vesicles or microvesicle release in mammalian cells [43]. However, this conclusion is based on an in vitro study. Whether circRNAs are degraded in vivo by a similar mechanism still needs further

c. The results were analyzed by 3 steps. First of all, specific regions of the genes were PCR amplified and visualized on the gel. Secondy, T7EN1 cleavage assay were used to detect sgRNA:Cas9 mediated on target cleavage of specific genes. Finally, PCR amplified regions were cloned and sequenced to determine the deletions or insertions.

Since miR-193a-5p exerts its regulative functions through specifically targeting certain target genes, we here collected the possible targets of miR-193a-5p and further uncover the underlying regulatory pathways. We found that the top enriched items in BP, CC and MF were regulation of neuron apoptosis; organelle outer membrane and tubulin-tyrosine ligase activity, respectively. Mitochondria is the basic and important organelle in most of the eukaryocyte. Mitochondria outer membrane permeabilization has been reported to be involved in cancer and be a promising therapeutic target. [26-27] Thereby, miR-193a-5p might be also involved in lung cancer through similar approach. Recently, Tubulin tyrosine ligase widespread loss has been found during the tumor growth, which suggests tubulin tyrosine ligase activity may be involved in the regulation of tumor cells [28]. As a result, tubulin tyrosine ligase activity might be related miR-193a-5p, which might exert effects in lung cancer. Nevertheless, more studies are needed in the future. In KEGG

The remaining clean reads were aligned to miRBase database (www.mirbase.org/) using BLAST to identify 393 and 362 known miRNAs from FGSC9543 and CDC8219, respectively (Suppl. F1). In addition, the reads that were mapped to antisense exon, intron, or intergenic region of the genome, but not to any other RNAs, lead to the identification of 167 and 164 novel miRNAs, respectively, from these two strains (Suppl. F1).

LncRNAs can arise from several different processes; for example, it is possible for local tandem repeat sequences and retro-transposition of non-coding RNA to create lncRNAs (Lee 2012; Clark and Blackshaw 2014). Disruption of coding proteins gene frames can also result in lncRNAs, such as Lnx3 from the Xist gene (Zhu et al. 2013). The formation of new lncRNAs can also arise from the decay of protein coding genes, duplication of other lncRNAs or de novo evolution from previous noncoding sequences, the last of which is the most common (Kapusta and Feschotte 2014). A large proportion of lncRNAs, around 60% in human and murine ES cells, are synthesised from bidirectional transcription at protein coding promoter sites (Kapusta and Feschotte 2014). Other factors that result in the synthesis of lncRNA include transposable elements (TE); in fact, 2 out of 3 lncRNAs transcripts in humans and mice contain at least one TE sequence, which can be found in 20-40% of all lncRNA exonic nucleotides (Kapusta and Feschotte 2014).

Analysis of adipose derived induced pluripotent stem cells (iPSC’s) microRNA (miRNA) expression profile over multiple passages and pancreatic β-cell miRNA expression profile post differentiation from iPSC’s.

For mRNAs, functional annotation with respect to diverse protein databases, including GO, COG, KEGG, Swiss Prot, and InterPro, will be performed. lncRNAs analysis, including classification, miRNA precursor and target prediction, will also be performed. BGI has provided initial annotation of both mRNA and lncRNA that will be served as reference. One of the main focuses is expression validation that we plan to focus on. We will primarily employ the qRT-PCR approach but will also employ digital PCR to increase sensitivity and reproducibility.

Long non-coding RNA (lncRNA) genes have been defined as an important population of ncRNAs which have key roles in normal development, including dosage compensation, genomic imprinting, cell differentiation and organogenesis

The hallmarks of a stem cell are its ability to self-renew as well as its ability to differentiate and assume almost any cell fate if given the appropriate cues known as pluripotency (ref). The differentiation of stem cells requires large and rapid changes in gene expression. miRNAs are well suited to carry out this task through their ability to simultaneously inhibit the translation of several target genes allowing for coordinated control of cellular processes{Bartel:2009fh}. Furthermore, miRNAs have been shown to regulate embryonic development in addition to their role in regulating stem cell fate{Stefani:2008bw}. Evidence for this comes from experimental studies where the overall function of the miRNA biogenesis pathway was evaluated through genetic deletion of the miRNA processing enzymes DICER, DGCR8, Drosha, and AGO2. DICER knockout mice die at early stages of embryogenesis and fail to express the stem cell marker Oct4 and primitive streak marker T (brachyury), which respectively indicate a loss of stem cells and arrested development during gastrulation{Bernstein:2003dp}. Furthermore, DICER-deficient mouse ES cells are viable but incapable of differentiation, showing severe proliferation defects{Kanellopoulou:2005kf, Murchison:2005fa}. Similarly, DGCR8 knockout mice arrest early in development{Wang:2007gb}. DGCR8-deficient mouse ES cells also exhibit a proliferation defect and cannot efficiently silence the ES cell program, although these defects are not as