Serna Bio’s Post

Whole genome and whole transcriptome all in one library prep also compatible with hybrid capture :)

‘Jumping gene’ enzyme edits genomes A technique that harnesses ‘jumping genes’ — mobile genetic sequences naturally found in bacteria that can cut, copy and paste themselves into genomes — could hold the key to redesigning DNA at will. Guided by an RNA molecule called a ‘bridge’ RNA or ‘seekRNA’, the system has been shown to edit genes in a bacterium and in test-tube reactions, but it is still unclear whether it can be adapted to work in human cells. If it can, it could be revolutionary, owing to its small size and its ability to make genetic changes that are thousands of bases long — much larger than is practical with the CRISPR — without breaking DNA. https://lnkd.in/dtPStDsw

RNA (ribonucleic acid) plays a central role in the translation of DNA information into proteins. There are different types of RNA, one of which is known as messenger RNA (mRNA). Messenger RNA is a type of coding RNA and its job is to transmit the building instructions for proteins from the DNA in the cell nucleus out into the cytoplasm, where other cell components translate them into proteins.

Human cells communicate with each other through RNA: RNA facilitates cell-to-cell communication through vesicles, influencing biological processes across species. #HumanCells #CellCommunication #RNA #CellToCell #RNACommunication #BiologicalProcess #MolecularCourier #RNAInterference #RNAi #ImmuneSystem #EarthDotCom #EarthSnap #Earth

rDNA, dsDNA, mtDNA, cDNA, ssDNA explained In genetics, complementary DNA \(cDNA\) is DNA synthesized from a single stranded RNA \(e.g., messenger RNA \(mRNA\) or microRNA\) template in a reaction catalyzed by the enzyme reverse transcriptase. cDNA is often used to clone eukaryotic genes in prokaryotes. When scientists want to express a specific protein in a cell that does not normally express that protein \(i.e., heterologous expression\), they will transfer the cDNA that codes for the protein to the recipient cell. cDNA is also produced naturally by retroviruses \(such as HIV-1, HIV-2, simian immunodeficiency virus, etc.\) and then integrated into the host's genome, where it creates a provirus. The term cDNA is also used, typically in a bioinformatics context, to refer to an mRNA transcript's sequence, expressed as DNA bases \(GCAT\) rather than RNA bases \(GCAU\). cDNA is derived from mRNA, so it contains only exons, with no introns. Youtube video: https://lnkd.in/gKrzPMWC \#nikolays_genetics_lessons

A bacterial version of reverse transcriptase reads RNA as a template to make completely new genes written in DNA. It will definitively change our way to look at the genome and read the transcriptome. doi: https://lnkd.in/eCiZ2tdx

"A team at NDORMS has developed a new approach to significantly improve the accuracy of RNA sequencing. They have pinpointed the primary source of inaccurate quantification in both short and long-read RNA sequencing, and have introduced the concept of "majority vote" error correction leading to a substantial improvement in RNA molecular counting. Accurate sequencing of genetic material is crucial in modern biology, particularly for comprehending and addressing diseases linked to genetic anomalies. However, current methodologies encounter substantial constraints." #rnasequencing

🔍Fantastic Plots and How to Read Them!🔍 Ever looked at a plot and had no idea what info to extract from it? We got you! In each post of this series we will present a common plot used for presenting DNA and RNA sequencing related results. We will then give some background on the plots' purpose and how to interpret it. Have fun and stay tuned! This week: 🍣 Sashimi Plots🍣  Most human genes are built to express more than one transcript isoform of a gene depending on a variety of inner- and extracellular factors like cell-state or temperature changes. If those alternatively spliced variants are of interest while conducting a bulk RNA-seq experiment, a fitting plot type to visualise the splice variants is essential. This is where Sashimi plots come into play! 🔍How do you read a Sashimi plot? 🧬Exons are represented by blocks in a Sashimi plot. Their length is dependent on the length of the exon they represent and their height shows the abundance of sequencing reads found for specific sequences in the exon. 🧬Introns are only represented passively as space between the exons (unless there are reads present due to intron retention). 🧬Splice junctions are shown as lines connecting the exon-blocks. They carry a number that stands for the count of sequencing reads, that were spanning this junction, which is an indicator of how often this specific splice variant was abundant in the cell. 🔍What can be extracted from a Sashimi plot? Sashimi plots are usually used to compare the splice isoforms of different conditions. Every row represents such a condition. Of course, for each condition multiple splice isoforms can occur. This is also visualised by the junction-spanning lines that hold information about every junction found in the reads and therefore about the different exon-combinations that might exist in a sample. In short, a Sashimi plot effectively conveys information about which splice forms are abundant in a sample and how that varies dependent on its state. We hope this post gave you some new insights! If you want to read more about bulk RNA-sequencing and its application in research on alternative splicing, our latest blogpost is perfect for you: https://lnkd.in/dD3BdAQ2 The plots below are from a publication by Alexander Neumann et al. (2020). They used bulk RNA-seq amongst other methods to investigate temperature-dependent alternative splicing and mRNA decay in primary mouse hepatocytes. Can you interpret their shown results? #OmiqaBioinformatics #Statistics #LifeScience #NextGenerationSequencing #bulkRNAseq

Bridge RNAs direct programmable recombination of target and donor DNA:- Genomic rearrangements,encompassing mutational changes in the genome such as insertions, deletions or inversions, are essential for genetic diversity. These rearrangements are typically orchestrated by enzymes that are involved in fundamental DNA repair processes, such as homologous recombination, or in the transposition of foreign genetic material by viruses and mobile genetic elements1,2. Here we report that IS110 insertion sequences, a family of minimal and autonomous mobile genetic elements, express a structured non-coding RNA that binds specifically to their encoded recombinase. This bridge RNA contains two internal loops encoding nucleotide stretches that base-pair with the target DNA and the donor DNA, which is the IS110 element itself. We demonstrate that the target-binding and donor-binding loops can be independently reprogrammed to direct sequence-specific recombination between two DNA molecules. This modularity enables the insertion of DNA into genomic target sites, as well as programmable DNA excision and inversion. The IS110 bridge recombination system expands the diversity of nucleic-acid-guided systems beyond CRISPR and RNA interference, offering a unified mechanism for the three fundamental DNA rearrangements—insertion, excision and inversion—that are required for genome design.