Monika Sharma, PhD’s Post

How does LINE-1 propagate in the genome? 1- First, a LINE-1 locus is de-repressed and transcribed. The mRNA is transported to the cytoplasm (polyadenylated introneless RNA). 2-In the cytoplasm, LINE-1 RNA is translated into the corresponding proteins (ORF1p & ORF2p). ORF1p amount is much more compared to ORF2p. 3-ORF1p is a chaperone that helps L1 RNA fold properly, while ORF2p has endonuclease and reverse transcriptase activities. 4-The two proteins bind to the L1 RNA in cis (the translated proteins bind to the RNA that codes for them). LINE-1 RNA and the proteins form RiboNucleoProtein (RNP) complexes. 5- RNP complexes enter the nucleus. 6- ORF2p nicks the DNA in an AT-rich region(endonuclease) and the L1 RNA poly A tail anneals to the nicked DNA. ORF2p (reverse transcriptase) makes L1 cDNA (full-length L1 or a truncated copy). This step is called Target-Primed Reverse Transcription (TPRT). 7- The cell repairs the DNA damage and a new L1 copy is integrated into the genome. Photo credit: https://lnkd.in/e63X7esr #LINE_1 #L1 #transposable_elements #retroelements #dna

How to find DNA and RNA base composition The two main types of nucleic acids are deoxyribonucleic acid \(DNA\) and ribonucleic acid \(RNA\). DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is found in the nucleus of eukaryotes and in the chloroplasts and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous envelope, but rather free-floating within the cytoplasm. The entire genetic content of a cell is known as its genome and the study of genomes is genomics. In eukaryotic cells, but not in prokaryotes, DNA forms a complex with histone proteins to form chromatin, the substance of eukaryotic chromosomes. A chromosome may contain tens of thousands of genes. Many genes contain the information to make protein products; other genes code for RNA products. DNA controls all of the cellular activities by turning the genes on or off. The other type of nucleic acid, RNA, is mostly involved in protein synthesis. In eukaryotes, the DNA molecules never leave the nucleus but instead use an intermediary to communicate with the rest of the cell. This intermediary is the messenger RNA \(mRNA\). Other types of RNA like rRNA, tRNA, and microRNA are involved in protein synthesis and its regulation. Youtube video: https://lnkd.in/ddhqkWUW \#nikolays_genetics_lessons

Researchers have discovered a molecular oddity in bacteria that could lead to customizable genome redesign. The technique exploits the natural ability of mobile genetic sequences, called jumping genes, to insert themselves into genomes. The system, guided by an #RNA molecule called "bridge" RNA or "seekRNA," 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. To find tools, the researchers screened a diverse class of enzymes that allow mobile DNA elements in bacteria to hop from one place to another. They found a family of transposable elements called IS110, which uses a complex and unusual RNA-based targeting system. By altering the sequences at either end of this bridge, the researchers were able to program IS110 enzymes to insert a cargo (up to 5kb) of their choice anywhere in the genome. The second group of researchers characterized the biochemistry of IS110 molecules and those of another family, IS1111, which use a similar mechanism and are also programmable. They call their RNA intermediaries 'seekRNA'. The IS110 and IS1111 systems require only a single protein, which is less than half the size of many of the Cas enzymes used in CRISPR genome editing systems. This size difference is important for medical applications: the viruses often used to deliver genome-editing components (#AAVs) into human cells have limited cargo capacity (4.7 kb). So far, members of the IS110 family do not appear to work well in mammalian cells, and the research team is now trying to engineer them to work better in mammalian cells. Regardless of their success, the IS110 mechanism stands out as a novel and elegant way for mobile DNA elements to hitchhike around the genome.

What is CRISPR-Cas9? CRISPR-Cas9 is a genome editing technology used to change parts of the genome by removing, adding, or altering sections of DNA. It uses a pre-designed RNA sequence to guide the Cas9 enzyme to the location where the genome needs to be altered. The Cas9 enzyme then cleaves the DNA strands, and the cell's natural repair mechanism joins the two ends together by removing, adding, or replacing certain sections.

How many ways are there to encode an amino acid sequence in messenger RNA? The number of possible sequences is enormous, thanks to the redundancy of the genetic code. Roughly, a 100 aa protein can be encoded by 3^100 RNA sequences - a huge space of potential design. A new paper out in Genome Research describes an LLM for designing optimal protein-coding RNAs that improve stability and expression. We typically just codon optimize our synthetic genes, but this fails to account for other RNA features (2ndary structure) that affect stability and expression. How much better can we do, by using AI to design our synthetic genes? I wrote about this over at This Genomic Life: https://lnkd.in/erwFaEFQ

Why Larger Fragments Are Not Good for cDNA SMARTer Library Preparation? Efficiency of Reverse Transcription and Amplification: Larger fragments are harder to reverse transcribe and amplify efficiently, which can result in incomplete or biased representation of the original RNA population. Library Complexity: The presence of larger fragments can reduce library complexity because they may amplify preferentially, leading to uneven representation of different transcript sizes. Sequencing Performance: Sequencing platforms have optimal fragment size ranges. Larger fragments can cause issues with cluster generation and sequencing fidelity.

A type of genetic element is called a retrotransposon. ⁉ 💠 Retrotransposons are sometimes called “jumping genes,” pieces of DNA that can move around the genome. To move, retrotransposons are transcribed into RNA, and then that RNA is reverse-transcribed into DNA and inserted in a new genomic location.   Retrotransposons are very common in the genomes of humans and other animals. However, our cells try to stop retrotransposons from “jumping” to other genomic locations because they can be harmful if they land in the wrong place. An important noncoding RNA called a piwi-RNA targets the DNA and RNA of retrotransposons to stop them from moving.  

https://lnkd.in/gWSXzeDf 27 June https://lnkd.in/g-9SC5wM 26 June https://lnkd.in/gawCRagn 26 June https://lnkd.in/gY69Fhqg 19 June https://lnkd.in/gye_FiFz 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.

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

#RNA structure prediction is not possible at present due to a lack of abundant high-quality reference data. GARNET (Gtdb Acquired RNa with Environmental Temperatures) is a new database linking RNA sequences derived from GTDB genomes to experimental and predicted optimal growth temperatures of GTDB reference organisms, which is used to define the minimal requirements for a sequence- and structure-aware RNA generative model. #MachineLearning deployed to make connections between RNA sequence, structure, and function. https://lnkd.in/e_sYQeEA