Molecular Development - Genetics

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Human idiogram

Genetics (Greek, genetikos = “origin”) and embryology have merged to such an extent that the two cannot now be separated from each other. The strong evolutionary conservation of developmental mechanisms has been astounding. Currently, much of modern medicine is a search for a disease gene and having found it, embryology is usually employed in understanding its mechanism. Embryological development begins with meiosis and is after all the opportunity for a specific genome to be expressed, regulated and utilized as it will never be again in the adult animal.

In combination with our statistical understanding of congenital abnormalities there now exist a large number of clinical tests for inherited abnormalities. This particular section of the notes is a link to bind our understanding of genetics with its relevance to development. There are several pages on DNA and links from the computer activities below to relevant sections. You can jump right in and look through the DNA database for a gene of interest using a keyword, or browse through the human genome by chromosome or by genetic diseases that have been identified. Or you can work through an exercise in using genetic databases for diseases.

See also the list of mouse gene knockouts which has made the geneticists not only use embryological tools, but also go back and learn some embryology. Recent research has also focussed on the new science of Epigenetics, the inheritance mechanisms that lie outside the actual DNA sequence of our genes.

Human female karyotype

Molecular Links: Introduction | Genetics | Epigenetics | Mitosis | Meiosis | X Inactivation | Signaling | Factors | Mouse Knockout | microRNA | Mechanisms | Developmental Enhancers | Protein | Genetic Abnormal | Category:Molecular

Genetic Links: Introduction | Genetic risk maternal age | Trisomy 21 | Trisomy 18 | Trisomy 13 | Trisomy X | Monosomy | Fragile X | Williams | Alagille | Philadelphia chromosome | Hydatidiform Mole | Prenatal Diagnosis | Neonatal Diagnosis | International Classification of Diseases | Molecular Development - Genetics

Some Recent Findings

Diploid Chromosome Number

Species Chromosome Number
Human (Homo sapiens) 46
Mouse (Mus musculus) 40
Fruit fly (Drosophila melanogaster) 8
Worm (Caenorhabditis elegans) 12
Frog (Xenopus laevis) 36
Dog (Canis familiaris) 78
Chicken (Gallus gallus) 78
Echidna (Tachyglossus) 63 male 64 female
Cow (Bos primigenius) 60

Chromatin Structure

Cells not undergoing cell division have their DNA dispersed throughout the nucleus in what are know as "chromosomal domains". There is also a peripheral nuclear rim area that does not contain gene-rich regions of DNA, which tend to be located in the core of the nucleus. Nucleus structure cartoon 01.jpgAdult female fibroblast nuclear DNA 01.jpg

Adult G0 fibroblast DNA and gene localization.[2]

Cells undergoing division have their DNA compacted into chromosomes with a short arm (p), a long arm (q), and a mid-section (centromere). The duplicated chromosomes are also joined together as pairs at the centromere. These chromosomal arms are only seen when the chromosome is folded for cell division.
  • p used to identify the chromosome short arm (possibly French, petit).
  • q used to identify the chromosome long arm (possibly French, tall), the next letter in alphabet after p

These letters prefixed by the chromosome number and followed by the chromosome band number, indicate gene location.

Chromosome- structure.jpg

Chromosome pair structure

Chromatin Structure.png
The folding of DNA and associated protein to form a chromosome.

Chromosome Banding

Trisomy 21 Female Karyotype G-banding stain.

The term refers to the light and dark pattern, seen after staining with a dye, of individual chromosomes identified in metaphase. It is only in meiosis and mitosis during metaphase that chromosomes can be easily identified, during the normal cell life (interphase) the chromosomes are unravelled and distributed within the nucleus in chromosome territories. A band is that part of a chromosome which is clearly distinguishable from nearby regions by appearing darker or brighter with one or more banding techniques.

Depending on the type of stain used a number of different banding patterns can be seen:

  • G-banding - banding pattern seen by treating with trypsin and then staining with the dye giemsa.
  • R-banding - banding pattern seen as a of reverse giemsa chromosome banding, producing bands complementary to G-bands often used to determine whether there are deletions. Can be fluorescent using the dye acridine orange.
  • Q-banding - banding pattern seen by treating with a fluorochrome or the fluorescent dye quinacrin.
  • C-banding - banding pattern seen for centromeric or constitutive heterochromatin, the centromere appears as a stained band compared to other regions.

Metaphase is a cell division term referring to the third mitotic stage, mitotic spindle kinetochore microtubules align chromosomes in one midpoint plane. Metaphase ends when sister kinetochores separate. Originally based on light microscopy of living cells and electron microscopy of fixed and stained cells. A light microscope analysis called a "metaphase spread" was originally used to detect chromosomal abnormalities in cells.

Links: Histology Stains

Human Genome

Human Genome Length 3,101,788,170 bp. Mitochondrial Genome 16,568 bp.

Links: Human Genome Project (HGP) | NCBI Human Genome Resources | History of the Human Genome Project | Project Timeline

Nuclear Genome

Human idiogram

Mitochondrial Genome

Eukaryotic mitochondrial genomes
  • In humans this genome is maternally inherited.
  • Exists as multiple copies within the matrix of each mitochondrion within the cytoplasm of cells.
  • In 1981 the human mitochondrial genome was sequenced.
  • The genome is a small circular DNA molecule 16,568 bp in length containing 37 genes.
    • 24 genes specify RNA molecules involved in protein synthesis (22 transfer RNAs (tRNA) and 2 ribosomal RNAs (rRNA))
    • 13 genes encode proteins required for the biochemical reactions that make up respiration.

Swapping mitochondrial DNA mammalian oocytes.jpg

Swapping mitochondrial DNA mammalian oocytes[3] Assisted Reproductive Technology

Links: Mitochondria | 16569 bp Homo sapiens mitochondrion | Mitochondrial DNA Deletion Syndromes

Chromosome Regions

Chromosome Abnormalities

Ploidy refers to the chromosomal genetic content of cells. Euploidy (euploid) is the genetic term used to describe the normal cell genome chromosomal set (n, 2n, 3n) or complement for a species, in humans this is diploid (2n).

The terms used to describe the classes of numerical chromosomal abnormalities include:

  • Aneuploidy are chromosome mutations in which chromosome number is abnormal (increased or reduced), nondisjunction in meiosis or mitosis (anaphase of meiosis I, sister chromatids fail to disjoin at either meiosis II or at mitosis) is the cause of most aneuploids.
  • Polyploidy includes triploidy, usually due to two sperm fertilizing a single egg.
  • Mixoploidy includes mosaicism, where there are two or more genetically different cell lines in an individual.

Links: Abnormal Development - Genetic | Trisomy 21 | Trisomy 18 | Trisomy 13)

Some Human Disease Gene Locations

Human genetics chromosomes 1-4.jpg

Human genetics chromosomes 5-8.jpg

Human genetics chromosomes 9-12.jpg

Human genetics chromosomes 17-20.jpg

Human genetics chromosomes 21-XY.jpg

Inheritance Genetics

Pedigree chart

Inheritance Pattern images: Autosomal dominant inheritance | Autosomal recessive inheritance | X-Linked dominant (affected father) | X-Linked dominant (affected mother) | X-Linked recessive (affected father) | X-Linked recessive (carrier mother) | Mitochondrial genome inheritance | Codominant inheritance | Genogram symbols | Genetics


A clinical diagram constructed to show an individual's family relationships and medical history, more detailed than a pedigree chart including non-genetic factors such as family emotional and social relationships. Additional colour coded symbols and connectors are used to show these relationships and interactions.

Genogram symbols.jpg

DNA Sequencing

Changes in genes can occur by a number of different methods including mutations, deletions and epigenetic modifications. Specific changes in DNA sequences can also be detected by a range of techniques, including direct sequencing of the DNA.

Recent technological developments have improved how DNA sequencing occurs and we are said to now be up to the "third generation" of sequencing techniques.[4]

DNA sequencing methods.jpg DNA sequencing methods third-generation.jpg
First and second generation sequencing[4] Third generation sequencing[4]

Using Genetic Databases

This exercise is an exploration of the available WWW and other database resources that relate to Human genetic diseases. The exercise is to explore the Human genome and its relationship to examples of know human genetic diseases that affect development and impact on health.

To start with, think of a specific Human disease and see what you can find out about:

  • Known gene?
  • What are the major effects of the disorder?
  • Does it have an effect/role in development?
  • Known mutations?
  • Likely hood of mortality?
  • History of the disease?
  • Who discovered the cause of the disease?
  • Most recent published data relationg to the disease?
  • What therapies are being explored?
  • Where to next?

Genetic Editing

CRISPR/Cas9 interaction with target DNA
File:CRISPR/Cas9 interaction with target DNA

Originally a more general approach was used to study the fly model of development, where random genome mutation (random mutagenesis) was carried out to identify a specific fly phenotype and then researchers would go back and find the gene that had been altered.

More recently in vertebrate models of development, mainly in mice, genetic editing was carried to to "knock out" (KO mice) a specific gene and then to look for a specific phenotype. Generally targeting known genetic disorder genes, but later a range of genes involved in signalling, proliferation, migration, cell cytoskeleton. This technology has developed to the stage where we can now not only "knock out" but also "knock in" as well as "transiently knock out" (at a specific stage) a specific gene of interest. This KO technology was complex and required long term projects to generate these knock out animal models.


More recently a new technology called CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease 9) has allowed more accurate and faster genetic editing. There has been concern in the scientific community that this technique may be applied to the human genome, and lead to "germ line" changes in the human genome. See also review.[5]

CRISPR History  
Like any great discovery, some contention as to who writes the history...

Links: Nature News 12 March 2015


  1. Andreas Bolzer, Gregor Kreth, Irina Solovei, Daniela Koehler, Kaan Saracoglu, Christine Fauth, Stefan Müller, Roland Eils, Christoph Cremer, Michael R Speicher, Thomas Cremer Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol.: 2005, 3(5);e157 PubMed 15839726 | PLoS Biol.
  2. Eric A Shoubridge Developmental biology: Asexual healing. Nature: 2009, 461(7262);354-5 PubMed 19759608
  3. 4.0 4.1 4.2 Eric E Schadt, Steve Turner, Andrew Kasarskis A window into third-generation sequencing. Hum. Mol. Genet.: 2010, 19(R2);R227-40 PubMed 20858600 | Hum Mol Genet.
  4. Geir K Sandve, Sveinung Gundersen, Morten Johansen, Ingrid K Glad, Krishanthi Gunathasan, Lars Holden, Marit Holden, Knut Liestøl, Ståle Nygård, Vegard Nygaard, Jonas Paulsen, Halfdan Rydbeck, Kai Trengereid, Trevor Clancy, Finn Drabløs, Egil Ferkingstad, Matús Kalas, Tonje Lien, Morten B Rye, Arnoldo Frigessi, Eivind Hovig The Genomic HyperBrowser: an analysis web server for genome-scale data. Nucleic Acids Res.: 2013, 41(Web Server issue);W133-41 PubMed 23632163
  5. Martin Jinek, Krzysztof Chylinski, Ines Fonfara, Michael Hauer, Jennifer A Doudna, Emmanuelle Charpentier A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science: 2012, 337(6096);816-21 PubMed 22745249
  6. Eric S Lander The Heroes of CRISPR. Cell: 2016, 164(1-2);18-28 PubMed 26771483

Online Textbooks

  • Genomes (2nd edition) Brown, T.A. New York and London: Garland Science ; c2002 PMID20821850
  • Introduction to Genetic Analysis Griffiths, Anthony J.F.; Miller, Jeffrey H.; Suzuki, David T.; Lewontin, Richard C.; Gelbart, William M. New York: W. H. Freeman & Co.; c1999
  • Modern Genetic Analysis Griffiths, Anthony J.F.; Gelbart, William M.; Miller, Jeffrey H.; Lewontin, Richard C. New York: W. H. Freeman & Co.; c1999
  • Human Molecular Genetics 2 Strachan, Tom and Read, Andrew P. New York and London: Garland Science; c1999
  • Genetics for Surgeons Morrison, Patrick J.; Spence, Roy A.J., authors Hatchwell, Eli, series editor London: Remedica; c2000
  • Sequence - Evolution - Function: Computational Approaches in Comparative Genomics Koonin, Eugene V; Galperin, Michael Y. Norwell (MA): Kluwer Academic Publishers ; c2003
  • The Genetic Landscape of Diabetes [Internet] Dean, Laura; McEntyre, J.R. Bethesda (MD): National Library of Medicine (US), NCBI; 2004 Jun
  • Madame Curie Bioscience Database Chapters taken from the Madame Curie Bioscience Database (formerly, Eurekah Bioscience Database) and Landes Bioscience and Springer Science+Business Media; c2009


Magdalena Götz, Wieland B Huttner The cell biology of neurogenesis. Nat. Rev. Mol. Cell Biol.: 2005, 6(10);777-88 PubMed 16314867


Search PubMed

Not easy to generate a good search term for this topic.

Search "Genetic Development" All (151839) Review (31389) Free Full Text (54818)

Search Pubmed: Genetic Development | Genome

Genetic Terms

Molecular Development

  • antisense - a sequence of DNA that is complementary usually to coding sequence of DNA or mRNA. Has been used experimentally to perturb or block gene expression. Also a mechanism that has been found to occur naturally as a regulatory mechanism.
  • autosomal inheritance - some hereditary diseases are described as autosomal which means that the disease is due to a DNA error in one of the 22 pairs that are not sex chromosomes. Both boys and girls can then inherit this error. If the error is in a sex chromosome, the inheritance is said to be sex-linked.
  • base - another term for nucleotide (usually a t c g).
  • base pair - Double stranded DNA has nucleotides A-T, C-G, paired by hydrogen bonds (2 for AT, 3 for GC). Note this means that GC is harder to separate that AT.
  • cis-acting elements - DNA sequences that through transcription factors or other trans-acting elements or factors, regulate the expression of genes on the same chromosome.
  • DNMT - DNA methyltransferase.
  • DNA - DeoxyriboNucleic Acid. The genetic material found in mammalian chromosomes and mitochondria. Consisting of 4 nucleic acids (ATCG) that combine in a triptych (3 nucleotide codon) code for protein amino acids (3nt=1aa).
  • DNA duplex - double stranded base-paired DNA forming a helix.
  • dominant inheritance - With autosomal dominant inheritance, there is an error in one of the 22 chromosome pairs. But the damaged gene dominates over the normal gene received from the other parent. If one of the parents has a disease caused by an autosomal dominant gene, all the children will have a 50 per cent risk of inheriting the dominant gene and a 50 per cent chance of not inheriting it. The children who do not inherit the damaged dominant gene will not themselves suffer from the disease, nor will they be able to pass the gene on to future children. This type of inheritance is present for example in Huntington's disease.
  • enhancer - A cis-regulatory sequence that can regulate levels of transcription from an adjacent promoter. Many tissue-specific enhancers can determine spatial patterns of gene expression in higher eukaryotes. Enhancers can act on promoters over many tens of kilobases of DNA and can be 5' or 3' to the promoter they regulate.
  • exon - a block of protein encoding sequence of DNA in a gene. Many proteins are made of several exons "stitched" or spliced together by editing out non-coding (intron) sequences.
  • fasta - a format for listing DNA sequence, where the first line has descritive information followed on the next line by the sequence without numbering.
  • GC repeat - a string of GC sequence repeated several times. Also associated with GC expansion, a mutational process that may lead eventually to serious gene expression effects.
  • gene - a sequence of DNA that encodes an individual protein.
  • genetic code - the 3 nucleotide sequence that forms a codon for a single amino acid or stop. See the gene code.
  • genome - the complete genetic information in the form of DNA available to a specific species.
  • hairpin loop - a folding of RNA generated by base pairing making a "===()" structure, the end loop and or stem of this structure can then interact with proteins or other RNA.
  • HyperD - hypermethylated domain
  • HypoD - hypomethylated domain
  • igDMR - imprinted germline differentially methylated regions
  • intron - a block of DNA within a gene not encoding a protein. Edited, spliced, out during transcription into mRNA. Originally thought not to contain any information, but more and more this appears not to be the case. Some intron sequences have been shown to regulate gene expression during development (eg c elegans, Lin 14)
  • karyotype - [Greek, karyon = kernel or nucleus + typos= stamp] The chromosomal makeup of a cell.
  • mRNA - messenger, transcribed from DNA in the nucleus and in mitochondria. Is translated by the ribosome in the cytoplasm (or mitochondrial matrix). Intermediate step in gene expression. (DNA-> mRNA-> protein).
  • mutation - any process which results in the alteration of the DNA sequence. Some conservative mutations may have no effect on the final amino acid encoded.
  • ncRNA - non-coding RNA.
  • ploidy - refers to the chromosomal genetic content of cells.
  • promoter - A regulatory region a short distance upstream from the 5' end of a transcription start site that acts as the binding site for RNA polymerase II. A region of DNA to which RNA polymerase IIbinds in order to initiate transcription.
  • point mutation - a change in a single nucleotide.
  • recessive inheritance - With autosomal recessive inheritance, the diseased individual has inherited the same gene damage from both father and mother. The damage is found on both chromosomes in the pair. But as this is not ´dominant gene damageª, neither father nor mother show any sign of disease, they are healthy carriers of the gene. We are all carriers of about five recessive genes of this type, but as spouses are seldom carriers of exactly the same damaged gene(s), all will probably go well in the next generation.
  • regulatory sequence - (regulatory region, regulatory area) is a segment of DNA where regulatory proteins such as transcription factors bind preferentially.
  • ribosome - complex of rRNA and ribosomal proteins, bind mRNA and translate it into protein.
  • RNA - RiboNucleic Acid. The intermediate nucleic acid involved in gene expression. It comes in 3 forms: tRNA, mRNA, rRNA.
  • rRNA - ribosomal, translates mRNA into protein. rRNA provides the "scaffolding" on which many ribosomal proteins are assembled as 2 subunits that themselves assemble to form a ribosome. rRNA genes are localized to the nucleolus in the nucleus, a sometimes visible region of DNA usually constantly being transcribed.
  • telomere - regions at the end of chromosomes. Shortening of the telomeres is thought to be associated with cellular aging. The enzyme that maintains the telomere is called telomerase. Introducing this gene into a cell can extend the cells lifespan.
  • transcription factor - a protein which binds to DNA activating (usually) gene expression. There are many different ways and forms that this activation can take place, but most transcription factors fall into specific classes (eg zinc fingers, helix loop helix).
  • tRNA - transfer, binds single amino acids acts as a "donor' for protein synthesis.
Other Terms Lists  
Terms Lists: ART | Birth | Bone | Cardiovascular | Gastrointestinal | Genetic | Hearing | Heart | Immune | Integumentary | Neural | Oocyte | Palate | Placenta | Renal | Spermatozoa | Ultrasound | Vision | Historic | Glossary

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Cite this page: Hill, M.A. (2016) Embryology Molecular Development - Genetics. Retrieved December 8, 2016, from

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© Dr Mark Hill 2016, UNSW Embryology ISBN: 978 0 7334 2609 4 - UNSW CRICOS Provider Code No. 00098G