Week 1.1: Introduction, the landscape of the human genome Flashcards

Question

Where are ribosomal genes found?

Answer 1

``` Are found in clusters see diagram on page 5 which illustrates one such cluster; This 40 Kbp (Kilobase Pairs) long module is tandemly repeated 30-40 times on the short arms of human chromosomes 13, 14, 15, 21 and 22. They comprise about eight Mbp (mega base pairs) of the human genome. ``` Human 5S rDNA occur within 2.2 kb repeating elements organized in tandem of 35 to 175 copies per haploid genome on Chromosome 1. These ribosomal clusters under a microscope with suitable dye can be observed.

Answer 2

(FISH) Fluorescent in-situ hybridisation of human metaphase chromosomes. Green = rDNA, yellow = centromeres, red = telomeres. Recently as well as mRNA, within the DNA of a protein coding gene we find all sorts of other types of RNA some short, some long. ``` Short ncRNA’s (nc = non-coding) Long ncRNA’s (nc =non-coding) snoRNA miRNA (microRNAs) Some are 5’ to 3’ others are opposite direction ```

Answer 3

They bind to a protein called argonaute This is a clever way of controlling gene expression. The messenger RNA will be chopped up if too much small RNA is transcribed.

Answer 4

Argonaute proteins are the catalytic components of the RNA-induced silencing complex (RISC), the protein complex responsible for the gene silencing phenomenon known as RNA interference (RNAi).[1] Argonaute proteins bind different classes of small non-coding RNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs).[2] Small RNAs guide Argonaute proteins to their specific targets through sequence complementarity, which typically leads to silencing of the target. Some of the Argonaute proteins have endonuclease activity directed against messenger RNA (mRNA) strands that display extensive complementarity to their bound small RNA, and this is known as Slicer activity.

Answer 5

MicroRNA (miRNA) Small RNA, 22 nucleotides long, in the genome they form a hair-pin structure in RNA, that are cleaved out, exported from nucleus, and cut in two. > 1000 types. Often they are in introns or UTRs, and occur in arrays.

Answer 6

They often >1000bp, there is over 3000 types they are also involved in regulation of gene expression HOX cluster contains 39 protein-coding genes, was first discovered in drosophila, but produces 231 different long ncRNA’s. Some look like mRNA but act as anti-sense regulators, as they are transcribed in opposite direction. Function of vast majority unknown, usually present in genome as individual copies. Long dsRNA  cleaved by ‘dicer’  into siRNA (small-intron RNA)  these break up into single stranded RNA that then bind to reverse complement  they either guide argonaute complexes to cleave matching mRNA transcripts or guide argonaute complexes methylate DNA near newly synthesising mRNA

Answer 7

Piwi protein interacting RNA (piRNAs) 24-31 nucleotides long, over 15000 types, found in 89 clusters in genome, 10-75 Kb long Often the get processed from long RNA precursors, and processed to form piRNAs

Answer 8

Small nucleolar RNA (snoRNA) 60-300 nucleotides long, involved in maturation of ribosomal RNA, they carry out site-specific methylation, they change uridine into pseudouridine. Usually found in introns of protein coding genes, some found in clusters.

Answer 9

Pseudogenes and gene fragments Partial gene sequences that do not appear to code for viable proteins. Mutated copies of functional genes; “Processed” pseudogenes lack introns and promoters. Sometimes have a role in regulation of similar genes that code viable proteins. Especially when they produce an anti-sense RNA, or contain an inverted repeat.

Answer 10

LINEs, SINEs and LTRs Over 40% of the human genome, Retrotransposons can turn into RNA and then make to DNA : DNA  RNA  DNA Repeated elements, structured like RNA transcripts, not like protein-coding genes.

Answer 11

LINEs 20% Long interspersed elements We have about 0.5 million of them in genome. Only ~80-100 in most human genomes can still “jump” because they encode two proteins; • ORF1p: RNA-binding and acts as a nucleic acid chaperone • ORF2p: reverse transcriptase and endonuclease These allow the LINE element to be transcribed into RNA then this binds to ORF1p and then the ORF2p protein allow it to go back to DNA. These also promote the mobilisation of other parts of the genome, and can reshuffle parts of the genome. It also seems active in brain development Nature 479: 534–537 (2011) And implicated in disease Ann.Rev.Genom.Hum.Genet 12: 187-215 (2011)

Answer 12

SINE 13% Short interspersed elements, ~300 bp long Most common: Alu elements; 11% of genome Looks like7SL RNA gene (part of a RNP involved in protein trafficking) after deletion of a central sequence. It may be involved in regulation of gene expression; Nucleic Acids Research 34: 5491-5497 (2006)

Answer 13

LTRs – 8% Long terminal repeats are retro-virus like elements, named for their flanking “long terminal repeats”, human endogenous retroviral sequences (HERVs) Some are 6-11 Kbp long; Encode protease, reverse transcriptase, RNAse H and integrase genes Some are 1.5-3 Kbp long; Encode fewer or no genes ~240,000 copies in human genome

Answer 14

DNA transposons 3% Transpose via a DNA intermediate through a “cut-and-paste” mechanism not as common as retro-transposons that have a “copy-and-paste” mechanism. Large “autonomous” transposons encode transposase up to 40 Kbp. Small “non-autonomous” transposons; miniature inverted-repeat transposable elements, some encode miRNAs PLoS ONE 2(2): e203.

Answer 15

``` Microsatellites – 3% Simple Sequence Repeats (SSRs) ATATATATAT GCGCGCGC Length evolves rapidly due to slippage in replication – (often used in population genetics) ```

Answer 16

Other intergenetic 16% - we don’t really know…

Answer 17

``` Mitochondrial genome; • 16.6 Kb in length. Circular. • 66% protein coding genes • 32% RNA genes and regulatory sequences • 2% other sequences ```

Answer 18

Mitochondrial genome; It has 2 places where replication starts and because it has different codons it has to make its own tRNA. It has to make separate tRNA’s, it can be transcribed in both directions and is very information dense. Loads of RNA and proteins coded for. Some of its genes overlap, thus translated in more than one reading frame – this is clever as you can have two genes by two different proteins being coded for my same DNA in a single strand in the mitochondria. The MT-ATP6 and MT-ATP8 genes are transcribed in different reading frames from overlapping segments of the mitochondrial H strand.