Transcriptomics - bioinformatics.uni-muenster.de

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Prof. Dr. Jürgen Gadau

Transcriptomics

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What is transcriptomics?

• The sum of all transcribed components (RNA) of a genome (DNA) is referred to as its transcriptom.

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What does my laboratory do?N. giraulti ♂

N. vitripennis ♂

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HDL

N. giraulti ♂

N. vitripennis ♂

Male Courtship behavior

Male sex pheromone evolution

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V… G… V… G…

F2 Hybrid breakdown

PrezygoticPostzygotic

Functional and Comparative Genomics of speciation and species differences

Cuticular hydrocarbon pattern –species and sex recognition

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Evolution of Gene Regulation –Phenotypic Plasticity

Reproductive division of labor

Worker Subcastes

non-reproductive division of labor

AggressionCOOPERATION AND CONFLICT

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What is Functional Genomics?

…and how does transcriptomicsfactor in?

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• Functional genomics is a field of molecular biology that attempts to make use of the vast wealth of data produced by genomic and transcriptomic projects (such as genome sequencing projects and RNA-seq) to describe gene (and protein) functions and interactions.

• Functional genomics uses genomic data to study gene and protein expression and function on a global scale (genome-wide or system-wide), focusing on gene transcription, translation and protein-protein interactions, and often involving high-throughput methods.

Some Definitions…

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Genotype to phenotype

• Classic Mendelian genetics and how we teach Genetics/Evolution is looking at a single locus that we can map.

• One gene (white) à 1 character

• Organisms or the genetic architecture of complex/simple traits are much more complex.

*In January 1910, more than a century ago, Thomas Hunt Morgan discovered his first Drosophila mutant, a white-eyed male (Morgan 1910).

White-eyed mutant*

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From Genotype to Phenotype…is a little bit more complex than we

usually think!

Envi

ronm

ent

Good flier

Bad flier

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Environment

Developm

entGenotype-Phenotype-Fitness-Map

Phenotype-SpaceGenotype-Space Aggressive -> Monogyny

Cooperative -> Polygyny

Fitness

…Or Behavior

GENE-EXPRESSION

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…one more complication

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Fixed Genetic Differences versus

Phenotypic Plasticity

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Any Questions?

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qPCR

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Methods to measure Generegulation

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RNA-SEQ/MICROARRAY INTRODUCTION

Microarray

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RNA-Seq

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What are the advantages of RNA-Seq vs Microarray?

• Prior sequence (genome or transcriptome) not required

• Microarrays are costly and time consuming to design and produce and are just for one species

• Greater dynamic range and sensitivity than microarrays

• Improved ability to discriminate regions of high sequence identity

• Greater multiplexing of samples

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Typical RNA-Seq Strategy

~300 bpinsert size

Library Construction

Illumina HiSeq 2000•104 bp paired end reads

Sequencing Assemblyor Alignment

Contigsnext-gen

104 bp reads

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https://galaxyproject.org/tutorials/rb_rnaseq/

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Transcriptome pipeline using UNIX-based tools

BowtieCreates reference genome index for alignment

(based on Broad Anocar2.0 assembly)

TophatAligns RNA-Seq reads to reference index

Cufflinks and CuffdiffTool for quantification and statistical analysis

of RNAseq reads , also can improve annotation

IGV/Tablet/ApolloViewers for output of RNA-Seq output from

Cufflinks

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Tools for RNA-Seq Analysis (mostly UNIX/Linux)

• Bowtie: http://bowtie-bio.sourceforge.net/index.shtml• Tophat: http://tophat.cbcb.umd.edu/• Samtools: http://samtools.sourceforge.net/• Picard tools: http://picard.sourceforge.net/• Cufflinks: http://cufflinks.cbcb.umd.edu/• Apollo: http://apollo.berkeleybop.org/current/index.html• IGV: http://www.broadinstitute.org/igv/• ABySS: http://www.bcgsc.ca/platform/bioinfo/software/abyss

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Resources Needed

• Genomic sequence in fasta format– For alignment of RNA sequence

• Annotations in GTF (General Feature Format) format– For binning RNAseq reads into transcripts for

quantitative analysis, as well as to help with annotation in Apollo

• RNAseq reads in FASTQ format (sequenced and quality score)

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Bowtie

Creates reference genome index for alignment• Commands needed:

– Bowtie-build –f (for fasta file) reference_in.faout_file_name

– Runtime: ~4 hrs for vertebrate genome• Output:

– 6 files that will be used by tophat

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Tophat

Aligns RNAseq reads to reference index• Commands needed

– tophat –r (average gap distance for paired reads) –o (output directory) reference_input (name you gave output in bowtie) RNAseq_reads_1.fastq RNAseq_reads_2.fastq

– Runtime: multiple days• Output

– Read allignments in .bam or .sam format– Junctions, insertion and deletion as .bed format

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Tophat aligns reads to reference genome

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CufflinksTool for quantification and statistical analysis of RNAseqreads• Commands used:

– Cufflinks –G (.GTF annotation file) input_file.sam• Basic command that gives FPKM values and errors for each

transcript in a tab delimited file• Runtime: several hours (goes for all cuff programs)

– Cuffcompare reference_annotation.gtf input_file_tissue1.gtf (from cufflinks) input_file_tissue2.gtf

• Secondary analysis using output from cufflinks. Gives data on pooled transcript levels, a .GTF file for annotation based on all tissues, major isoforms found (if annotated in reference .GTF file)

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Cufflinks quantifies expression level based on FPKM

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012345

Ttn

Acta1

Mef2a

Mstn

FPKM = Fragments per kilobase-pair per million sequenced reads

FPKM

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RPKM (FPKM avoids counting fragments twice in paired end

sequencing)• Count up the total reads in a sample and divide

that number by 1,000,000 – this is our “per million” scaling factor.

• Divide the read counts by the “per million” scaling factor. This normalizes for sequencing depth, giving you reads per million (RPM)

• Divide the RPM values by the length of the gene, in kilobases. This gives you RPKM.

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WHAT TO DO WITH TRANSCRIPTOMIC DATA?

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• Sequencing cDNA• mRNA vs unprocessed RNA (depends on

library prep but you want to get rid of the ribosomal RNAs)

• Annotate coding SNPS• Transcript isoforms • Splice junctions• Count abundance of transcripts

Transcripts found by RNA-Seq

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Review: Elements of protein coding genes

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Review: Processed transcript

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Review: Alternate splicing

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Gene Orthology vs. Paralogy

Ancestor Gene A

lizard Gene A1 Gene A2

mouse Gene A1 Gene A2

paralogs

orthologues

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• Not all genes in the genome encode proteins. • Human Chromosome 11, has 1,300 protein-coding genes

and 200 noncoding RNA genes, whose final product is an RNA, not a protein.

• Some are involved in the regulation of other genes, whereas others may play structural roles in various nuclear or cytoplasmic processes.

• MicroRNA (miRNA) genes, are noncoding RNA genes. There are at least 250 in the human genome

• miRNAs are short 22-nucleotide-long noncoding RNAs, at least some of which control the expression or repression of other genes during development.

From Thompson, Medical Genetics

Review: Non-protein coding genes

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Long non-coding RNAs where they come from

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Long non-coding RNAs have many functions in transcription

and translation

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Validation of your RNASeqresults: different methods

– Rerun the same sample on the same instrument – Use multiple sequencing methods for the same

sample.• Quantatative

– qPCR– RNA seq– Microarrays

• Qualitative– PCR– In situ

– Run multiple samples of same tissue type

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How does RT-qPCR work?

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How does RT-qPCR work?