Gene Structure and Organization

General Gene Organization

(1) Possible regulation of transcription – specific trans-acting proteins (transcription factors)

(2) Possible regulation of RNA processing – splicing/ alternative splicing; polyadenylation / alternative polyadenylation; mRNA stability (short vs long lived mRNA)

(3) Possible regulation of mRNA transport – cREV (ie HIV REV Þ binds and leads to rapid export)

(4) Regulation of translation – feedback regulation – protein product itself inhibits translation of mRNA

(5) Possible regulation of protein transport – if a memb protein must get to the surface of a cell

Coordination of multiple regulated steps is what determine the final level of protein product

Genomic constituents:

1- 2% protein coding genes
98 – 99%: RNA coding genes (ie rRNA genes); pseudogenes (looks like genes but do not produce functional protein products); repetitive DNA (ie dispersed repitition or satellite DNA); spacer DNA of unknown function

Repetitive Sequences

Interspersed repetitive sequences

~30% of DNA
short interspersed repeats (SINES) (100 – 500 bp)

ex: Alu sequence (Fig 2)
10⁶ copies in genome; Alu sequence is similar to ~300 nt 75L RNA which is part of the signal recognition particle; Alu sequence arose thru reverse transcriptase of 75L RNA

long interspersed repeats (LINES) (>500 bp)

Clustered repetitive sequences

satellite sequence
localized in centromeres

Tandemly Repeated Genes

Multiple copies of the same set of sequence lying in a series

Ex: rRNA genes for 18s / 5.8s / 28s Þ 13 kb repeating units » 100 copies

Ex: contain histone genes in tandem repeats

Single gene copies can produce large amounts of product thus tandem repeats aren’t here to yield more product

ex: silkworm – silk fibrin protein

1 gene Þ 10⁴ mRNA Þ 10⁹ silk fibrin proteins (huge)

due to optimizing each regulatory step and adds up to Ý level of final protein

Gene Families

Members of a gene family = homologous DNA sequence within a chromosome – location means nothing

Probably arised due to gene duplication

Totipotency and Chromatin

All cells have same DNA – specific regulated expression through chromatin

not a fixed state – changes with different transcription patterns
heterochromatin is dense, transcriptionally inactive
euchromatin is less dense (as in "puffs"), transcriptionally active