Developmental Genetics BIOL 5330 Final

genome

all the genetic information in an organism’s chromosomes

chromosome

linear arrangement of genes and other DNA

gene

fundamental unit of heredity that carries information from one generation to the next

central dogma

DNA → RNA → Protein

gene parts in order

5’ UTR, promoter, exon, intron, exon, 3’ UTR

protein structure basics

N terminal, binding domain, transmembrane domains, protein specific motif, modification site, protein-protein interaction domain, cellular targeting sequence, c-terminus

allele

one of a series of alternative forms of a given gene at a single locus that differ in DNA sequence and often result in altered protein expression

locus

a specific place on a chromosome

genotype

genetic make-up of the organism as distinguished from its physical appearance

phenotype

observable properties of an organism produced by its genotype

co-dominant/semi-dominant

blue + yellow = green; mixture of both

epigenetics

study of changes in organism caused by modifications of gene expression rather than alterations in genetic code, often heritable changes

common epigenetic mechanisms

DNA methylation, histone modification/histone variants, regulatory non-coding RNAs

mutation

change in genetic composition

physical mutation

direct change of the DNA sequence: deletions, substitutions, transpositions, insertions

substitutions

missense, nonsense, silent

silent mutations

change in DNA that does not affect the amino acid coded for

leaky mutation

only partial loss of function

conditional mutation

effect dependent on certain conditions

dominant negative mutation

mutant gene product, which adversely affects the wild-type gene product in the same cell. Usually works in an antagonistic manner often MORE DETRIMENTAL than a null allele

homeotic mutation

one developmental pattern replaced by another

transgenic organism

organism that has its genome altered by the addition of DNA

most popular transgenic mechanisms

marker/reporter, over expression, antisense and RNAi, specific promoter targeting, and tagging

model system

system, area, or organism that is simple and informative to work with that applies to other systems, areas, or organisms

genetic model organism

representative organism from a genetic perspective, such as a simple genome or well studied genetics

developmental model organism

representative organism from a developmental perspective with similar developmental processes that are well or easy to study

what makes a good genetic model organism

ease of use/study, ease of data generation, readily available, strong link of results applying to related systems, used by many researchers

specifically, short generation time, small size, large number of progeny, genetic manipulation, genome sequenced and annotated, link to relevant process and economic importance

what makes a good developmental model organism

specifically, short generation time, ability to have large numbers for examination, ease of ability to examine developmental process, ability to manipulate, genetic model commonalities

what makes a good developmental genetic model organism

specifically, must combine strong characteristics of both genetic and developmental systems

why is C. elegans a good developmental genetic model organism

short life cycle, small size, easy to care for, lots of progeny, great genetics and lots of mutants, small sequenced genome, complete lineage of all 959 adult cells known, clear body

why is drosophila melongaster a good developmental genetic model organism

short generation time, small, ease of care, 100 years of research, multiple developmental life stages, great genetics, sequenced genome, lots of molecular tools

why are zebrafish good developmental genetic model organisms

small, rapidly developing vertebrate, easy to maintain, lots of transparent embryos, mutants, RNAi, mutants, sequenced genome

why are mice good developmental genetic model organisms

small vertabrate, very similar to human development, sequenced genome, many molecular tools

mutagens

agents that cause genetic mutations, which can lead to changes in DNA sequence

forward mutant screen

screening mutant phenotypes to find the gene(s) responsible for altered phenotype effects

reverse mutant screens

mutating a specific gene to find what function it has

forward genetics

know the phenotype, want the gene

reverse genetics

know the gene, want the phenotype

Specific benefit of using CRISPR

site directed DNA editing

transposons

sections of DNA that can move, jump, or hop to other places in the same genome

transcript expression analyses basic methodolgies

northern blot, RT-PCR, realtime PCR, microarray, RNA-seq

transcription factor

protein that binds to DNA and affects the transcription of that gene

cis-regulatory element

5-25 base pair stretch of DNA that regulates expression of a gene on the same stretch of DNA via protein binding

TATA box

cis-element, 5’-TATAA-3’ at -25b of which the TBP (TATA box binding protein binds and allows RNA polymerase II to bind and transcription to start

enhancer

cis-regulatory element that can increase transcription levels over large distances and can be 5’ or 3’ to the promoter they are involved in regulating

repressor

protein that can bind to specific sites on DNA to prevent transcription with RNA polymerase binding

major classes of transcription factors

basic domain, zinc related, helix turn helix, beta scaffold factors

steps of signaling pathways

ligand → receptor → signaling cascade → transcription factor

major signaling pathways in development

receptor tyrosine kinase (RTK), jak/stat, hedgehog, TFGbeta/BMP, Wnt/Wingless - beta-catenin, notch

notch signal transduction pathway

the receptor is called notch and is bound by a ligand from another signaling cell, it does have transcription factors

self-reinforcing signal

that maintains or enhances its own signaling process within a cellular context, often through positive feedback mechanisms

autocrine loop

activation of genes to synthesize and bind an activation signal within the cell

paracrine loop

activation of a signal in once cell that activates its neighbor, that in turn activates the original cell

mechanisms for eliminating a signal once it has been initiated at the receptor

sequestration (receptor removal), down regulation (receptor destruction), inactivation (blocking signaling from receptor)

mechanisms for eliminating a signal once it has been initiated during signaling

inactivation (blocking cascade), feedback (negative signal loop)

g-protein receptors

largest family of cell-surface receptors in yeast to humans, contains alpha, beta and gamma subunits, alpha subunits binds GDP/GTP

fertilization

union of parental gametes form a zygote

cleavage

zygote divides by mitosis to forma multicellular structure called a blastocyst

gastrulation

blastocyst cells form three primary germ layers, which are the basic cellular structures from which all body tissues develop

organogenesis

three primary germ layers arrange themselves in ways that give rise to all organs in the body

steps of fertlization

1. sperm contacts egg

2. sperm or its nucleus enters its egg

3. egg becomes activated and developmental changes begin

4. sperm and egg nuclei fuse

after fertilization, what happens

aerobic respiration increases, enzyme systems become activated, a burst of protein synthesis begins

cleavage gives rise to what

rapid increase in cell number NOT accompanied by significant cell growth

karyokinesis

mitotic division of the cell nucleus

holoblastic cleavage

egg contains little or no yolk, and cleavage occurs evenly throughout

meroblastic cleavage

egg composed almost entirely of yolk, cleavage is incomplete or occurring only in part of the embryo

three major body axes

dorsal-ventral, anterior-posterior, lateral/left-right

why would it be important to override site of sperm entry in establishing axis polarity

to properly develop in response to an important environmental cue

ectoderm

innermost layer, will form gut

mesoderm

middle layer, will form muscles, circulatory system, blood and many different organs

ectoderm

outermost layer, forms skin and nervous system

three events of gastrulation

1. three primary germ layers are established

2. basic body plan is established, including the primary body axes

3. cell movement occurs allowing new interactions with neighboring cells that were not initially nearby. Paves the way for inductive interactions and the beginning of organogenesis

invagination

in-folding of a cell sheet into the embryo

involution

in-turning of a cell sheet over the basal surface of an outer layer

ingression

migration of individual cells into the embryo

delamination

splitting or migration of one cell sheet into two sheets

epiboly

expansion of one cell sheet over other cells

fate maps

diagrams that show the developmental fate of different cell regions in an embryo

beta-catenin is a transcription factor activated by the

Wnt pathway

the first rudimentary organs are

neural tube and neural crest

neural tube and neural crest are formed from

ectoderm

neural tube

developing central nervous system

neurulation

is the process by which the neural tube is formed during development

first organ system to develop

nervous system

TGF-betas and SHH (sonic hedgehog) expression and interaction with their proteins and pathways control what

dorsal-ventral axis specification

stages of sporophyte development

1. embryogenesis

2. vegetative development

3. reproductive development

establishment of root-shoot axis

1. apical cell: becomes all shoot tissue (SAM)

2. basal cell: becomes all root tissue (RAM) and forms the suspensor (linking embryo to parent

three basic tissue systems in plants

dermal, ground and vascular