Oxford Nanopore Technologies
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Oxford Nanopore Technologies
Single Molecule Real Time Sequencing - Pacific Biosciences
Single molecule sequencing
Ion Torrent Semiconductor Sequencing
Semiconductor sequencing
Bioinformatics
Genomes sequencing gives large amount of data--> Need a system to gather and analyse all these data- Compare sequence - from DNA to RNA to protein Align then together Stat plays a great deal here
Lesk, 2014, Introduction to Bioinformatics 4th edn
Repeat sequences in human
But beyond these individual methods for data processing, the profound biological insights of ENCODE undoubtedly come from computational approaches that integrated multiple data types. For example, by combining data on DNA methylation, DNA accessibility and transcription-factor expression. Thurman et al. (4) provide fascinating insight into the causal role of DNA methylation in gene silencing. They find that transcription-factor binding sites are, on average, less frequently methylated in cell types that express those transcription factors, suggesting that binding-site methylation often results from a passive mechanism that methylates sites not bound by transcription factors. Despite the extensive functional information provided by ENCODE, we are still far from the ultimate goal of understanding the function of the genome in every cell of every person, and across time within the same person. Even if the throughput rate of the ENCODE profiling methods increases dramatically, it is clear that brute-force measurement of this vast space is not feasible. Rather, we must move on from descriptive and correlative computational analyses, and work towards deriving quantitative models that integrate the relevant protein, RNA and chromatin components. We must then describe how these components interact with each other, how they bind the genome and how these binding events regulate transcription. If successful, such models will be able to predict the genome’s function at times and in settings that have not been directly measured. By allowing us to determine which assumptions regarding the physical interactions of the system lead to models that better explain measured patterns, the ENCODE data provide an invaluable opportunity to address this next immense computational challenge.
Erker et al., 2012
in its 1,640 genome-wide data sets, ENCODE provides a profile of the accessibility, methylation, transcriptional status, chromatin structure and bound molecules for every base pair. Processing the project's raw data to obtain this functional information has been an immense effort.
However, despite the progress brought by the ENCODE consortium and other research groups, it remains difficult to discern with confidence which variants in putative regulatory regions will drive functional changes, and what these changes will be. We also still have an incomplete understanding of how regulatory sequences are linked to target genes. Furthermore, the ENCODE project focused mainly on the control of transcription, but many aspects of post-transcriptional regulation, which may also drive evolutionary changes, are yet to be fully explored.
Erker et al, 2012, ENCODE, Nature
However, until now there has been little information about which genomic regions have regulatory activity. The ENCODE project has provided a first draft of a 'parts list' of these regulatory elements, in a wide range of cell types, and moves us considerably closer to one of the key goals of genomics: understanding the functional roles (if any) of every position in the human genome.
It has been argued that potentially adaptive changes to protein-coding sequences may often be prevented by natural selection because, even if they are beneficial in one cell type or tissue, they may be detrimental elsewhere in the organism. By contrast, because gene-regulatory sequences are frequently associated with temporally and spatially specific gene-expression patterns, changes in these regions may modify the function of only certain cell types at specific times, making it more likely that they will confer an evolutionary advantage
Non-protein coding DNA harbour regions that bind proteins and RNA molecules, bringing these into positions from which they cooperate with each other to regulate the function and level of expression of protein-coding genes. In addition, it seems that widespread transcription from non-coding DNA potentially acts as a reservoir for the creation of new functional molecules, such as regulatory RNAs.
an encyclopaedic knowledge of chromatin organization would be needed if we were to understand how gene expression is regulated. The ENCODE project goes a long way to achieving this goal and highlights the pivotal role of transcription factors in sculpting the chromatin landscape.
A further challenge is identifying how the genomic ingredients are combined to assemble the gene networks and biochemical pathways that carry out complex functions, such as cell-to-cell communication, which enable organs and tissues to develop. An even greater challenge will be to use the rapidly growing body of data from genome-sequencing projects to understand the range of human phenotypes (traits), from normal developmental processes, such as ageing, to disorders such as Alzheimer's disease (10).
Lecture 4 SP Endocytosis
Clarthrin coated vesicle Formation Structure Adaptin - 3 main categories - adapton heterotrimers - subunits AP 1 trans-Golgi network AP2 - u2 subunit of plasma membrane adaptor complex binds to YXX(0)-receptor tails - form a molecular link AP 3 Clathrin present a the trans-Golgi Signals Examples LDL receptor and particle
Ribosomal RNA is the predominant product of transcription, constituting some 80-90% of the total mass of cellular RNA in both prokaryotes and eukaryotes.
Lewin Genes X Ch7.3