Jack Chen, Associate Professor

Department of Molecular Biology and Biochemistry
Simon Fraser University

Office: SSB8111
Phone: (778)782-4823
Email: chenn(at)sfu.ca

B.Sc., Fudan University, Shanghai
Ph.D., Chinese Academy of Sciences, Qingdao

Reconstructing and functional analysis of transcriptome

REVIEWS & BACKGROUND (of C. briggsae)

Exploring plant transcriptomes using ultra high-throughput sequencing (Wang et al., Briefings in Functional Genomics, 2010)
New Tools for Investigating the Comparative Biology of Caenorhabditis briggsae and C. elegans (Zhao et al., Genetics, 2010)
Bias and Evolution of the Mutationally Accessible Phenotypic Space in a Developmental System (Braendle et al., PLoS Genetics, 2010)
Molecular population genetics and phenotypic sensitivity to ethanol for a globally diverse sample of the nematode Caenorhabditis briggsae (Cutter et al., Molecular Ecology, 2010)
Comparing Mutational and Standing Genetic Variability for Fitness and Size in Caenorhabditis briggsae and C. elegans (Salomon et al., Genetics, 2009)
Spontaneous Mutational and Standing Genetic (Co)variation at Dinucleotide Microsatellites in Caenorhabditis briggsae and Caenorhabditis elegans (Phillips et al., Molecular Biology & Evolution, 2009)
Knockdown of SKN-1 and the Wnt effe ctor TCF/POP-1 reveals differences in endomesoderm specification in C. briggsae as c ompared with C. elegans (Lin et al., Developmental Biology, 2009)
Comparative peptidomics of Caenorhabditis elegans versus C. briggsae by LCMALDI-TOF MS (Husson et al., Petides, 2009)
Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution (Haerty et al., BMC Genomics, 2008)
Genome evolution in Caenorhabditis (Thomas, Briefings in Functional Genomics, 2008)
On the potential for extinction by Muller's Ratchet in Caenorhabditis elegans (Loewe et al., BMC Evolutionary Biology, 2008)
Evolutionary dynamics of nematode operons: Easy come, slow go (Qiang and Zhang, Genome Research, 2008)
Muller's Ratchet and compensatory mutation in Caenorhabditis briggsae mitochondrial genome evolution (Howe et al., BMC Evolutionary Biology, 2008)
Comparative analysis of embryonic cell lineage between Caenorhabditis briggsae and Caenorhabditis elegans (Zhao et al., Developmental Biology, 2008)
nGASP the nematode genome annotation assessment project (Coghlan et al., BMC Bioinformatics, 2008)
Identification of phylogenetically conserved sequence motifs in microRNA 5' flanking sites from C. elegans and C. briggsae (Heikkinen et al., BMC Molecular Biology, 2008)
Multigenome DNA sequence conservation identifies Hox cis-regulatory elements (Kuntz et al., Genome Research, 2008)
The Caenorhabditis globin gene family reveals extensive nematode-specific radiation and diversification (Hoogewijs et al., BMC Evolutionary Biology, 2008)
The Caenorhabditis chemoreceptor gene families (Thomas and Robertson, BMC Biology, 2008)
Hakuna Nematoda: genetic and phenotypic diversity in African isolates of Caenorhabditis elegans and C. briggsae (Dolgin et al., Heredity, 2007)
Widespread Evolutionary Conservation of Alternatively Spliced Exons in Caenorhabditis (Irimia et al., Molecular Biology and Evolution, 2007)
Note: This report shows that alternative splicing is evolutionaarily conserved in many Caenorhabditis species.
Terms: cassette exons -- as an internal exon that can be either included or completely spliced out from the mRNA transcripts (i.e., not considering cases that are due to use of AS boundaries).; constitutive exons -- those exons included in all transcripts. Exons can also be divided into major forms & minor forms.
Poly-G/poly-C tracts in the genomes of Caenorhabditis (Zhao et al., BMC Geneomics, 2007)
A comparative genomic analysis of the small heat shock proteins in Caenorhabditis elegans and briggsae (Aevermann and Waters, Genetica, 2007)
Comparison of C. elegans and C. briggsae Genome Sequences Reveals Extensive Conservation of Chromosome Organization and Synteny (Hillier et al., PLoS Biology, 2007)
High Qualitative and Quantitative Conservation of Alternative Splicing in Caenorhabditis elegans and Caenorhabditis briggsae (Rukov et al., Molecular Biology & Evolution, 2007)
Note: This project shows that most of these alternative splice events present in Caenorhabditis elegans are conserved in Caenorhabditis briggsae.
Cryptic Quantitative Evolution of the Vulva Intercellular Signaling Network in Caenorhabditis (Felix, Current Biology, 2007)
Comparative Genomics and Adaptive Selection of the ATP-Binding-Cassette Gene Family in Caenorhabditis Species (Zhao et al., Genetics, 2007)
Genetic Analysis of Dauer Formation in Caenorhabditis briggsae (Inoue et al., Genetics, 2007)
Genomics and biology of the nematode Caenorhabditis briggsae (Gupta et al., WormBook, 2007)
Identification of ciliary and ciliopathy genes in Caenorhabditis elegans throug h comparative genomics (Chen et al., Genome Biology, 2006)
Patterns of Nucleotide Polymorphism Distinguish Temperate and Tropical Wild Isolates of Caenorhabditis briggsae (Cutter et al., Genetics, 2006)
Overview of gene structure (Spieth and Lawson, WormBook, 2006)
AceView: a comprehensive cDNA-supported gene and transcripts annotation (Thierry-Mieg and Thierry-Mieg, Genome Biology, 2006)
C. elegans noncoding RNA genes (Stricklin et al., 2005)
Alternative splicing in C. elegans (Alan Zahler, WormBook, 2005)
Note: This reviews describes reviews that genes are alternatively spliced in tissue-specific, developmentally-regulated, and hormone-responsive manners, providing an additional mechanism for regulation of gene expression.
ORFeomics: correcting the wiggle in worm genes (Boone and Andrews, Nature Genetics, 2003)
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics (Stein et al., PLoS Biology, 2003)
What does a worm want with 20,000 genes? (Hodgkin, Genome Biology, 2001)

Methods

Supersplat--spliced RNAseq alignment (Bryant et al., Bioinformatics, 2010)
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments (Richard et al., NAR, 2010)
Staging worms for next-generation analysis (Baugh, Nature Method, 2009)
A simple method for directional transcriptome sequencing using Illumina technology (Croucher et al., NAR, 2009)
Transcriptome analysis by strand-specific sequencing of complementary DNA (Parkhomchuk et al., NAR, 2009)
Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq (Chepelev et al., NAR, 2009)
RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data (Cloonan et al., Bioinformatics, 2009)
Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing (Han et al., PNAS, 2009)
Statistical inferences for isoform expression in RNA-Seq (Jiang and Wong, Bioinformatics, 2009)
[BWA]Fast and accurate short read alignment with BurrowsWheeler transform (Li and Durbin, Bioinformatics, 2009)

C. elegans: ORFeome & RACE

Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome (Salehi-Ashtiani et al., Genome Research, 2009)
Note: This project was initiated based on the argument that "a full third of the ORFeome remains experimentally unverified".It expermentally examined ~2,000 unverified protein-coding genes using RACE and reconstructed ORF for close to 1,000. The method RACE was chosen since "RACE (rapid amplification of cDNA ends) (Bao and Hull 1993) can proactively explore protein-coding transcript models. Large-scale RACE has been hampered by low throughput, low specificity and sensitivity, and occasionally false capture of transcript ends." This project also reported the identificaiton of SL1, SL2, & alternative trans-splicing.
Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions (Wei et al., Genome Research, 2005)
C. elegans ORFeome Version 3.1: Increasing the Coverage of ORFeome Resources With Improved Gene Predictions (Lamesch et al., Genome Research, 2004)
Note: This ORFeome project was based on WS100, attempting to PCR amplify ~4200 ORFs missed in earlier attempts and for which new predictions were availabe in WS100. This effort helped to increase the ORFeome size to ~12,500 ORFs (Version 3.1). The paper argues that the application of comparative genomics analysis between C. elegans & C. briggsae will help improve C. elegans gene annotation.
C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression (Reboul et al., Nature Genetics, 2003)
Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans (Reboul et al., Nature Genetics, 2001)

C. elegans & worm SAGE, TEC-RED, RNAseq, TSS: protein-coding genes

RNA Pol II Accumulates at Promoters of Growth Genes During Developmental Arrest( Baugh et al., Science, 2009)
Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved (Yanai and Hunter, Genome Research, 2009)
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans (Hillier et al., Genome Research, 2009)
Note: Applying Solexa sequencing method (Illumina 1G, 36-base reads), this project provided support to many splice junctions, raising the confirmed splice junctions from 70,911 to 98,000 in C. elegans. Additional, the reads suggest at least 80 putative genes not found in any predicted gene sets. Furthermore, it identifies 10,778 SL1 & 2515 SL2 signals.
Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags (Shin et al., Genome Biology,2008)
Note: This study mapped 0.3 million 454 reads (each ~100 bp) to the C. elegans transcriptome & genome. The analysis confirmed many predicted gene, suggested the existence of novel genes and extension to existing genes, and identived L1-enriched genes. Since the library is 3'-transcript biased, there was not analysis of trans-splice sites. Before this project, WormBase contained 0.34 million ESTs obtained using the Sanger sequencing method.
Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations (Merrihew et al., Genome Research, 2008)
Genome annotation by high-throughput 5' RNA end determination (Hwang et al., PNAS, 2004)
Composition and dynamics of the Caenorhabditis elegans early embryonic transcriptome (Baugh et al., Development, 2003)

C. elegans & worm RNAseq: non-coding genes

Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae (Missal et al., J. Exp. Zoology, 2006)

Other systems

Integrative analysis of the melanoma transcriptome (Berger et al., Genome Research, 2010)
Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing (Wu et al., PNAS, 2010)
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing (Yassour et al., PNAS, 2009)
Benchmarking Next-Generation Transcriptome Sequencing for Functional and Evolutionary Genomics (Gibbons et al., Molecular Biology & Evolution, 2009)
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution (Wilhelm et al., Nature, 2008)
Stem cell transcriptome profiling via massive-scale mRNA sequencing (Cloonan et al., Nature Methods, 2008)
Mapping and quantifying mammalian transcriptomes by RNA-Seq (Mortazavi et al., Nature Methods, 2008)
A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome (Sultan et al., Science, 2008)
Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing (Morin et al., Biotechniques, 2008)
The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing (Nagalakshmi et al., Science, 2008)
Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology (Cheung et al., BMC Genomics, 2006)
Number and distribution of polyadenylated RNA sequences in yeast (Hereford and Rosbash, Cell, 1977)

Jack Chen, Associate Professor

Department of Molecular Biology and Biochemistry Simon Fraser University

Reconstructing and functional analysis of transcriptome

REVIEWS & BACKGROUND (of C. briggsae)

Methods

C. elegans: ORFeome & RACE

C. elegans & worm SAGE, TEC-RED, RNAseq, TSS: protein-coding genes

C. elegans & worm RNAseq: non-coding genes

Other systems

Department of Molecular Biology and Biochemistry
Simon Fraser University