DNA and genes

see also:

• genetics
• genomics
• gene regulation
• micro RNAs (miRNAs)

• the human genome consists of over three billion nucleotide pairs which make up the 46 chromosomes in each nucleated cell
  • an average chromosome contains 130 million nucleotide pairs which if put into a line would be 4cm long!
  • to fit all of this DNA into the nucleus of a microscopic cell, the DNA must be tightly wound around proteins
  • it is also organized so that specific segments can be accessed as needed by a specific cell type
    • first level of organization, or packing, is the winding of DNA strands around histone proteins
      • histones package and order DNA into structural units called nucleosome complexes, which can control the access of proteins to the DNA regions
      • If a gene is to be transcribed, the nucleosomes surrounding that region of DNA can slide down the DNA to open that specific chromosomal region and allow access for RNA polymerase and other proteins, called transcription factors, to bind to the promoter region and initiate transcription
      • as DNA is negatively charged, changes in the charge of the histone will change how tightly wound the DNA molecule will be
        • unmodified, the histone proteins have a large positive charge;
        • by adding chemical modifications like acetyl groups, the charge becomes less positive
        • epigenetic modification of histone protein genes thus can affect DNA transcription
      • If a gene is to remain turned off, or silenced, the histone proteins and DNA have different modifications that signal a closed chromosomal configuration
      • the histone proteins movement is dependent on signals found on the histone proteins.
        • These signals are “tags” – in the form of phosphate, methyl, or acetyl groups – that open or close a chromosomal region
        • these tags are not permanent, but may be added or removed as needed
      • cohesin is a protein that forms a ring-shaped complex which wraps and alters the DNA molecule shape. It moves through the DNA and creates specific loops in the genetic material which determine the architecture of the genome and gene expression. The NIPBL protein (cohesion loading factor) protein, bound to the MAU2 protein, enables cohesion to bind to specific points on the DNA known as gene enhancers. These genomic regions are DNA sequences where binding to transcription factors, such as members of the nuclear receptor superfamily, takes place. The NIPBL protein interacts with both the MAU2 protein and the glucocorticoid receptor (GR) - This NIPBL-MAU2-GR ternary complex modulates the transcription, since it facilitates the interaction of the glucocorticoid receptor (GR) with NIPBL and MAU2, which is the cohesion-loading factor. When the GR interacts with these two proteins, it alters the structure of chromatin and affects the process of gene expression ¹⁾
• the majority of DNA is made up of non-coding regions
  • these do not result in the creation of proteins however, when mutated, do have the potential to create novel “orphan” proteins and it has been shown that a large proportion of these can have folding structures which are important for them to have a function
• over half of our genomes consists of thousands of remnants of ancient viral DNA, known as transposable elements (TE)
  • TE sequences contain cis-regulatory elements that enable recruitment of transcription factors (TFs) and chromatin remodelers, which in turn regulate and initiate transcriptional activity.
  • many of these are reactivated during the first hours and days following fertilization and become part of the EGA transcriptome
  • a hallmark of preimplantation development is embryonic genome activation (EGA), during which the embryo transitions from inherited maternal transcripts to genes transcribed from its own genome. EGA coincides with extensive reprogramming of both parental chromatins, as histone modifications are reestablished and TFs regain binding.²⁾
  • it seems each mammalian species expresses distinct types of these elements ³⁾
• ~8% of our genome comprises sequences called Human Endogenous Retroviruses (HERVs), which are products of ancient viral infections that occurred hundreds of thousands of years ago.
  • a set of specific HERVs expressed in the human brain contribute to psychiatric disorder susceptibility. In 2024, it was discovered five robust HERV expression signatures associated with psychiatric disorders, including two HERVs that are associated with risk for schizophrenia, one associated with risk for both bipolar disorder and schizophrenia, and one associated with risk for depression ⁴⁾
• 24 hr rhythmicity in gene expression is ubiquitous: it is present in all eukaryotic and some prokaryotic species and in nearly all tissues, organs, and cells of these organisms. This rhythmicity in gene expression generates variation in molecular and physiological processes in central and peripheral tissues to optimize adaptation to the organism’s temporal niche, e.g., nocturnal or diurnal. This rhythmicity is driven by a core circadian molecular mechanism but also by environmental, systemic, and behavioral factors, which may affect either the core circadian machinery or the expression of genes outside the core circadian machinery. Factors include light-dark and endocrine cycles, “sleep-wake” cycle, feeding-fasting cycles, immune challenges, alterations between the upright and supine posture.
  • microgravity (eg. 60 days of constant bed rest with head-down tilt) severely disrupts rhythmic gene expression in humans and even 10 days later, 3/4 of the transcriptome incuding core circadian genes were still affected ⁵⁾
• assessing “Identity by Descent” (IBD) segments can detect up to 6th degree relatives (second to third cousins would be, or a great great great great grand parent)
• regeneration of limbs and organs
  • this appears to be orchestrated by the Hand2 gene which in humans becomes generally inactivated after embryogenesis but which is responsible for regenerating limbs in salamanders

• each pair of chromosomes must “find” each other and they do this via “barcode-like” ID from non-coding “satellite DNA repeats” on the DNA and then the pair bond to each other via a protein called D1, but if part of the barcode is deleted or changes occur due to natural mutations – the D1 protein can bond two chromosomes together that do not belong together⁶⁾
  • as long as individuals of a species produce offspring with one another, the satellite DNA barcodes remain similar across the population due to the constant mixing of genetic material - individuals with recognition patterns that differ too greatly suffer from meiosis defects and are unable to reproduce
  • if a population of an animal species becomes geographically isolated – for example, due to the formation of a mountain range over millions of years – the satellite DNA in both groups evolves independently of one another. When the two groups meet again after a long period of time, the recognition patterns of the chromosomes no longer match. The result: the animals can no longer reproduce, and one species has become two.

• there is a complex process to ensure DNA is replicated accurately when cells are dividing
  • nearly all cells divide into just two cells, each with their own replication of the DNA
  • some bacteria such as Corynebacterium matruchotii undergo multiple fission dividing into multiple cells at once and this presumably is what allows colonies that form dental plaque biofilms to grow up to a half a millimeter per day ⁷⁾
• in 1 and 2 cell embryos, DNA is replicated by uniform forked slower replication and these have higher copy error rates ⁸⁾
• by 8 cells and onwards, DNA is replicated sequentially in different regions with faster fork movement
• a molecular complex called CTF18-RFC in humans and Ctf18-RFC in yeast loads a “clamp” onto DNA to keep parts of the replication machinery from falling off the DNA strand - this is the leading strand clamp loader. There is also a the lagging strand clamp loader (RFC). ⁹⁾
• unzipping DNA's ladder-like structure, resulting in two strands called the leading and lagging strands
• a molecular replication machinery including DNA polymerases then assembles the missing halves of the strands, turning a single DNA helix into two
  • DNA polymerases
• cohesin
  • one of the most important proteins involved in cell division found in all eucaryotes
  • holds together the two copies of each chromosome generated before cell division, ensuring their correct distribution into daughter cells
  • helps newly replicated DNA adopt the correct three-dimensional organization inside the nucleus - DNA molecules are several metres long when fully extended, yet they must fit inside a microscopic nucleus
  • protects genetic material during DNA replication, cohesin is rapidly recruited to sites where DNA replication is disrupted and can prevent the activation of another factor, primpol, which can restart DNA replication as an emergency response but may introduce a high number of genetic errors in the process ¹⁰⁾
• pathology:
  • at least 40 diseases, including many cancers and rare disorders, have been linked to problems with DNA replication

• cells generally have a pair of each chromosome - one from the father and one from the mother
• silencing genes from one of the chromosomes generally avoids excessive “double dosing” of DNA activation of each gene
• in women, one of their two X chromosomes is silenced during embryogenesis:¹¹⁾
  • via X-inactive specific transcript (XIST)–mediated XCI, generating an active X (Xa) and an inactive X (Xi)
  • however, ~15 to 30% of Xi genes constitutively escape XCI in humans (and 3 to 7% in mice) with variability across genes, cell types, tissues, individuals, and species
    • this is referred to as Constitutive XCI escape and enables expression from both the Xa and Xi and increasing X-linked gene dose in female cells
    • eg. KDM6A, a histone demethylase that constitutively escapes XCI and is expressed at higher levels in XX compared with XY brains of both mice and humans - in humans, increased neural expression of KDM6A, through a genetic variant, is associated with cognitive resilience in Alzheimer’s disease - these protective effects extend to males, which highlights that understanding mechanisms of XCI can benefit both sexes
  • reactivation of the Xi chromosome “X chromosome reactivation (XCR)” has emerged as a dynamic, lifespan-dependent process and a source of sex differences that may contribute to aging and disease

• chromatin regulation
  • all eucaryotic cells including humans have the same molecular mechanism to activate genes - namely via small tags attached to histone proteins tell the cell which stretches of DNA to read and which to ignore
  • this is what allows the same genome to produce a liver cell or a neuron, and a leaf or a root
  • faults in the regulation of chromatin underpin many diseases, including cancers
  • the chemical tags are ancient, dating back roughly two billion years to a single-celled organism known as the Last Eukaryotic Common Ancestor, or LECA, the founder of all complex cellular life, from which every plant, animal, fungus and protist on Earth descends and the enzymes that add and remove the tags are also broadly shared across plants, animals, fungi and microbial eukaryotes.
  • the signature of an active gene, marked by the pattern of histone modifications clustered around its start and along its body, was nearly identical in every species the team examined¹²⁾
  • in contrast, evolution has created many ways to turn off these genes via diverse configurations of repressive heterochromatin states associated with silenced genes and transposable elements

• RNA is usually a single-stranded molecule (ssRNA) and unlike DNA, its sugar backbone is ribose, not deoyxribose, and whereas the complementary base to adenine in DNA is thymine, in RNA, it is uracil
• the enzyme RNA polymerase generates RNA from the DNA base pairs
  • it has also been shown it can do this with at least 4 different synthetic DNA bases
• several types of RNA are synthesized within the cell by RNA polymerases based upon the base sequences in DNA which is likely to have major implications in future new diagnostics, therapeutics and engineered biological systems¹³⁾
  • messenger RNA (mRNA)
    • to convey genetic information (using the bases of guanine, uracil, adenine, and cytosine, denoted by the letters G, U, A, and C) that directs synthesis of specific proteins
  • non-coding RNA
    • performs the function itself rather than synthezing protein to do it
    • ribosomal RNA (rRNA)
      • the structures which read the base sequences on mRNA and then synthesizes protein
    • transfer RNA (tRNA)
      • delivers amino acids to the ribosome for incorporation into protein strands
      • precursor tRNAs (pre-tRNAs) require nucleolytic removal by endoribonuclease RNase P of 5′-leader and 3′-trailer sequences for maturation, which is essential for proper tRNA function
        • HARP protein forms a star-shaped complex of 12 protein molecules, making it capable of cutting both the 5' and 3' ends of tRNA ¹⁴⁾
    • small nuclear RNA (snRNAs)
      • found within the splicing speckles and Cajal bodies of the cell nucleus in eukaryotic cells - spliceosomes catalyse splicing, an integral step in eukaryotic precursor messenger RNA maturation
      • primary function is in the processing of pre-messenger RNA (hnRNA) in the nucleus
      • they also aid in the regulation of transcription factors (7SK RNA) or RNA polymerase II (B2 RNA), and maintaining the telomeres
      • are always associated with a set of specific proteins, and the complexes are referred to as small nuclear ribonucleoproteins (snRNP, often pronounced “snurps”)
      • eg. U1 spliceosomal RNA, U2 spliceosomal RNA, U4 spliceosomal RNA, U5 spliceosomal RNA, and U6 spliceosomal RNA
      • mutations in these may result in diseases such as spinal muscular atrophy, dyskeratosis congenita, Prader–Willi syndrome, and medulloblastoma
    • small nucleolar RNAs (snoRNAs)
      • a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs.
    • small interfering RNAs (siRNAs)
      • part of the RNA interference (RNAi) pathway
    • microRNA (miRNA)
      • see also micro RNAs (miRNAs)
      • small, single-stranded, non-coding RNA molecules containing 21 to 23 nucleotides
      • base-pair to complementary sequences in mRNA molecules
      • are involved in RNA silencing and post-transcriptional regulation of gene expression
      • 90 families of miRNAs have been conserved since at least the common ancestor of mammals and fish, and most of these conserved miRNAs have important functions
      • at least 40% of miRNA genes may lie in the introns or even exons of other genes
      • 6% of human miRNAs show RNA editing which increases the diversity and scope of miRNA action beyond that implicated from the genome alone
    • guide RNA (gRNA)
      • a short sequence of RNA that functions as a guide for the Cas9-endonuclease or other Cas-proteins that cut the double-stranded DNA and thereby can be used for CRISPR gene editing
    • PIWI-interacting RNA (piRNA)
      • can silence jumping genes (aka transposons or transposable elements (TEs) ) and can do so variably so that new transposon mutations can all so be silenced ¹⁵⁾
      • piRNA malfunctions have been linked to conditions such as human male infertility
• alternative splicing
  • a genetic process where different segments of genes are removed, and the remaining pieces are joined together during transcription to messenger RNA (mRNA)
  • this allows the evolutionary creation new protein isoforms but also, perhaps more importantly, has a role in regulating gene expression levels
• chimeric proteins
  • DNA instructions from different genes - even those on different chromosomes - can combine to create chimeric mRNAs that produce previously unknown, functional proteins
  • there are potentially thousands of chimeric proteins and at least some of these play important roles throughout the body ¹⁶⁾
• post-transcriptional modification of RNA / RNA editing
  • adenosine deaminases acting on RNA (ADARs) to produce different proteins
    • a widespread post-transcriptional modification that converts adenosine to inosine (A to I) a mimic for guanosine during translation (especially in squid which have been shown to edit almost 8000 sites in 2,091 squid proteins)¹⁷⁾
    • ADARs can thus alter protein-coding sequences, splice sites, microRNA (miRNA) interactions, and innate immune sensing of endogenous RNA
    • in most animals, editing is limited and acts as a highly specialized regulatory buffer that fine-tunes RNA function on top of DNA-encoded sequences
    • only a small number of RNA editing events in mammals are known to exert physiological effects, such as the Q/R recoding of the AMPA receptor subunit GluA2, I/V recoding of Kv1.1, and R/R recoding of NEIL1
• post-translational modifications of proteins (PTMs)
  • further tune protein function through residue-specific chemical changes
  • include phosphorylation, ubiquitylation, and acetylation

• LINE-1
  • a mobile genetic element capable of producing the molecular machinery to copy RNA into DNA and insert it into a genome

• mitochondria have their own DNA (in early evolution this was derived from a bacterium and in humans is 37 genes but each mitochondrion may have hundreds of copies of these) and is inherited only from the maternal DNA
• see mitochondria
• mtDNA is a circular DNA molecule composed of 16,568 base pairs, divided into heavy and light strands¹⁸⁾
  • it primarily encodes 13 protein subunits of the electron transport chain, two rRNAs (16S and 12S), and 22 tRNAs
  • unlike diploid nuclear DNA, mtDNA is polyploid, with tens to thousands of copies per cell, and healthy cells exhibit relatively low levels of mtDNA mutations
  • due to the lack of protective histones and limited error correction mechanisms, the mtDNA mutation rate is 100 times higher than that of nuclear DNA
• all eukaryotes contain either bacteria-like mitochondria with bacterial DNA or, in exceptional cases, remnants of it
• each cell has a “mitochondrial pool”: most somatic cells contain 300-400 mitochondria, female ova contain 100,000 perhaps “fresh unused mitochondria” (in female embryos some are stored away in the developing ovaries in their pristine state) whereas sperm only contains a few dozen as it needs to be small and fast and mitochondria in human spermatozoa are devoid of intact mtDNA and lack mitochondrial transcription factor A (TFAM) — the major nucleoid protein required to protect, maintain and transcribe mtDNA¹⁹⁾
• sexual reproduction involves passing on not only genes but also all the rest of the fertilized egg, including live mitochondria from the maternal ovum
• this DNA creates the mitochondria and its processes which primarily are involved in producing energy for the cell in the form of ATP via oxidative phosphorylation and the Krebs cycle but this requires acetyl-CoA (from pyruvate which is from glucose), oxygen and co-factors such as NADH, FAD, ADP; and the waste products are CO2, water and potentially damaging free radicals which need to be neutralized by anti-oxidants they make or are provided to them
  • mitochondria act as both regulators and mediators of Reactive Oxygen Species (ROS), balancing cellular survival and apoptosis and are the primary producers of ROS
  • the brain is a major user of mitochondria consuming 25% of body energy, a resting cortical neuron consumes 4.7 billion ATP molecules per second and a resting human brain uses nearly 6 kilograms of ATP per day
• mitochondrial repair:
  • pairs of malfunctioning mitochondria fuse together and come apart again; in the process, the best components of each pair are left in one mitochondrion and the other is targeted for destruction, but if too many dysfunctional ones are present the cell may undergo apoptosis (via release of cytochrome c from leaky mitochondria)
• there are many other roles of mitochondria:
  • mitochondria are involved in regulating cellular metabolism, health and longevity, cell death, tumour microenvironment, autophagy, and cell fate²⁰⁾
  • Mitochondrial stress responses:
    • retrograde signaling to the cell's nuclear DNA to alter the cell's gene expression:
      • when mitochondria experience stress, they send signals back to the cell nucleus (and outward to other cells) to alter gene expression, regulate the Mitochondrial Unfolded Protein Response (UPRmt), and influence systemic resilience
    • inter-tissue communication:
      • mitochondria appear to act as social organelles that send stress and signaling molecules to distant tissues - when mitochondrial function is disrupted in one part of the body, it can trigger adaptive or damaging responses throughout the entire organism ²¹⁾
    • trigger systemic inflammatory response:
      • inflammaging and immune activation:
        • damaged mitochondria leak mitochondrial DNA (mtDNA) and reactive oxygen species (ROS) into the cell and bloodstream. These act as danger signals that activate inflammatory pathways (like the cGAS-STING and NLRP3 inflammasomes), driving chronic, low-grade systemic inflammation known as inflammaging
    • cellular aging:
      • stem cell exhaustion:
        • mitochondrial decay in stem cells reduces their capacity to regenerate tissues, accelerating functional aging across organs
  • role in control of cell cycles, body clock, etc
  • NUMTs
    • the transfer of mitochondrial DNA into the nuclear genomes of somatic cells
  • potential interaction with the earth's magnetosphere
  • potential hybrid quantum effects
    • an anomalous 71.0-THz oscillation mode (=4222nm infrared light) only in living cells and tissues was found and it seems to arise from a quantum superposition state of functional mitochondrion forms by the coupling of light and lipid CH2 bonds in functional cristae, and induces a splitting of the intrinsic CH2 vibration mode of 87 THz to two levels at 71 THz and 103 THz²²⁾

• DNA epigenetics organises the available genes and RNA epigenetics dynamically adjusts their use and offers incredibly precise regulation of gene activity, essential to the development of organisms and the harmonious functioning of cells ²³⁾
• this mechanism is particularly important in key stages like cells' development or their specialisation into different types
• these modifications also occur in response to the exposome
• see also gene regulation

• DNA-protein cross-links (DPCs)
  • these are highly toxic lesions in which proteins become covalently attached to DNA, blocking essential processes such as replication and transcription and thus these need to be removed to ensure the cell's genomic stability and ability to divide
  • DPCs can result from:
    • natural cellular activities:
      • Reactive Oxygen Species (ROS)
      • reactive aldehydes:
        • endogenous aldehydes (e.g., formaldehyde, malondialdehyde) act as bridges, cross-linking protein amino groups to DNA bases
      • topoisomerase trapping:
        • during DNA replication or transcription, TOP1 or TOP2 enzymes can become covalently trapped on DNA when trying to relieve tension, forming Top-DPCs
    • exogenous issues:
      • UV radiation
      • excessive alcohol drinking increasing aldehydes
      • cytotoxic drugs
      • toxins
        • exposure to chromium (Cr), nickel (Ni), and formaldehyde
  • the protease SPRTN was the first enzyme identified to resolve these lesions by cleaving the protein component from DNA - SPRTN repairs DPCs not only during replication (S phase) but also mitosis (M phase)
  • inherited inactivating mutations in SPRTN cause Ruijs-Aalfs progeria syndrome (RJALS), a rare disorder marked by premature aging and early-onset liver cancer
  • if this repair process is inadequate, DPCs can leak into the cytoplasm which activates the cGAS-STING innate immune pathway through recognition of cytosolic DNA and micronuclei and this activation can result in cell death ²⁴⁾

• template-independent DNA synthesis / DeNovo DNA
  • discovered in 2026, DRT3 and DRT7 utilize entirely distinct chemical mechanisms to synthesize DNA from scratch
  • DRT3 binds specific raw nucleotides through a highly conserved geometric cavity, DRT7 relies on an open catalytic cleft that allows for a highly flexible, unguided polymerization sequence
  • the lack of structural overlap strongly suggests that the capacity to generate genetic data from scratch may have evolved independently multiple times across different biological lineages

• CRISPR = “clustered regularly interspaced short palindromic repeats” found in bacteria as part of their adaptive immunity system
• in 2010, the basic function and mechanism of CRISPR-cas system has become clear.
• this system is comprised of a genetic locus with non-repetitive, spacer sequences and adjacent 6–20 genes that encode CRISPR-associated (cas) proteins.
• use in genome editing²⁵⁾
  • cas-9 in particular is being used to by scientists to selectively edit an organism's DNA as it allows genetic material to be added, removed, or altered at particular locations in the genome
  • They create a small piece of RNA with a short “guide” sequence that attaches (binds) to a specific target sequence in a cell's DNA, much like the RNA segments bacteria produce from the CRISPR array.
  • This guide RNA also attaches to the Cas9 enzyme. When introduced into cells, the guide RNA recognizes the intended DNA sequence, and the Cas9 enzyme cuts the DNA at the targeted location, mirroring the process in bacteria.
  • Once the DNA is cut, they use the cell's own DNA repair machinery to add or delete pieces of genetic material, or to make changes to the DNA by replacing an existing segment with a customized DNA sequence.
  • VERVE-101 permanently deactivates the PCSK9 gene in the liver by using CRISPR to change just one letter in its DNA thereby seemingly permanently halving the production of LDL cholesterol in patients with heterozygous familial hypercholesterolemia (HeFH) after one dose but with some safety concerns that will need to be addressed - this was the 1st trial of such technology in humans ²⁶⁾
  • a Jan 2024 paper demonstrated a new CRISPR technique that restored sight in blind mice by editing 20% of their retinal cells using a re-engineered eVLP (engineered virus-like particle to deliver the gene editing tools) and made tweaks to two parts of their prime editor: the Cas9 protein - the prime editor cargo(protein-RNA complexes) must be efficiently packaged into eVLPs when the particles form but must also be efficiently released from the particles after target cell entry, they also tested their new system in the brains of mice and found that it edited nearly 50% of the cells in the target region without making any unwanted edits - compared to a standard prime editor packed into the original eVLP, the new combo was 170 times more efficient at editing human cells and could be used to correct almost 90% of genetic conditions ²⁷⁾
• bacterial roles:
  • adaptive immune role:
    • it is an adaptive immune system of bacteria and archaea, which protects the bacteria from invaders, including bacteriophages or phages and mobile genetic elements (MGEs).
    • it degrades foreign genetic elements in three steps²⁸⁾:
      • spacer sequence after recognition is integrated into the CRISPR array
      • expression of CRISPR RNA (crRNA), in which pre-CRISPR RNA (pre-crRNA) are transcribed by RNA polymerase (RNAP) and then cleaved into the small crRNA (aka “guide RNAs”) by specific endoribonucleases
      • crRNAs then recognize and form base pair specific to foreign RNA or DNA with almost perfect complementarity leading to the cleavage of the crRNA-foreign nucleic acid complex
        • if there is any mutation in proto-spacer adjacent motif (PAM) or mismatch between spacer and invader’s DNA, the cleavage does not occur and the host is susceptible to infection
  • bacterial pathogenicity role:
    • the system also controls endogenous transcription and is involved in the regulation of bacterial pathogenicity
    • for example, it may repress bacterial lipoproteins and hence improve the ability of the bacteria to escape activation of Toll-like receptor 2 (TLR2) complement inflammatory response mechanism in host phagocytic cells
    • N. meningitides use cas9 for attachment to host cell surface and intracellular replication
    • // Campylobacter jejuni// uses cas9 for attachment as well as for invasion in epithelial cells
  • antimicrobial resistance role
    • regulation of BLP can promote envelope integrity and resistance to certain antibiotics
  • role in promoting genetic heterogeneity and new bacteria species
• it is divided into three subtypes, all having cas1 and cas2 proteins, since these two proteins play a key role in spacer:
  • CRISPR-cas system type I
    • has cas3 gene
    • present in most bacteria and archaea
  • CRISPR-cas system type II
    • has cas9 gene
    • present only in bacteria and is the simplest type
  • CRISPR-cas system type III
    • has cas10 gene
    • most commonly present in archaea
• in 2023, a new search algorithm has identified 188 kinds of new rare CRISPR systems in bacterial genomes ²⁹⁾
  • they found several new variants of known Type I CRISPR systems, which use a guide RNA that is 32 base pairs long rather than the 20-nucleotide guide of Cas9. Because of their longer guide RNAs, these Type I systems could potentially be used to develop more precise gene-editing technology that is less prone to off-target editing.
  • the new systems could potentially be harnessed to edit mammalian cells with fewer off-target effects than current Cas9 systems.
  • they could also one day be used as diagnostics or serve as molecular records of activity inside cells