JOURNAL CLUB

Chenghang Zong, Sijia Lu, Alec R. Chapman and X. Sunney Xie

Science, 338:1622-6 (2012)

SynopsisOne of my group's research activities is the study of variations in the genomes of single cells.  Single cell genomics is a difficult avenue of study because the methods used may themselves introduce errors and variations in datasets.  One of main approaches used in single cell genomics is whole genome amplification (WGS).  WGS often introduces biases during the amplification processes.  For example, genomic regions containing a large proportion of repeated sequences or high copy number genes may be over-represented in amplified genomic DNAs. In this manuscript, Zong et al describe a new method which minimises amplification bias during the amplification of DNA from single cells.  This allows for a better assessment of natural variations in the genomic DNAs.  Using this approach, the researchers evaluated changes in the genomes of individual cancer cells.  They discovered that cancer cells had a high rate of genome-level changes.  These changes included point mutations (Single Nucleotide Variations) and changes to the number of copies of genes (Copy Number Variations).  Indeed, the researchers estimated that the cancers calls had 10 times the mutation rates of non-cancerous cells.


Abstract: Kindred cells can have different genomes because of dynamic changes in DNA. Single-cell sequencing is needed to characterize these genomic differences but has been hindered by whole-genome amplification bias, resulting in low genome coverage. Here, we report on a new amplification method—multiple annealing and looping-based amplification cycles (MALBAC)—that offers high uniformity across the genome. Sequencing MALBAC-amplified DNA achieves 93% genome coverage ≥1x for a single human cell at 25x mean sequencing depth. We detected digitized copy-number variations (CNVs) of a single cancer cell. By sequencing three kindred cells, we were able to identify individual single-nucleotide variations (SNVs), with no false positives detected. We directly measured the genome-wide mutation rate of a cancer cell line and found that purine-pyrimidine exchanges occurred unusually frequently among the newly acquired SNVs. 


Characterization of a scavenger receptor cysteine-rich-domain-containing protein of the starfish, Asterina pectinifera: ApSRCR1 acts as an opsonin in the larval and adult innate immune systems

Ryohei Furukawa, Midori Matsumoto and Hiroyuki Kaneko

Developmental and Comparative Immunology 36:51–61 (2012)

AbstractProteins containing a scavenger receptor cysteine-rich (SRCR) domain (SRCR proteins) play an important role in the innate immune system of various metazoan animals. In the starfish Asterina pectinifera, mesenchyme cells and coelomocytes govern the two distinct innate immune systems of the larvae and adults, respectively. Here we identify a cDNA encoding a protein containing nine SRCR domains termed ApSRCR1, and present characterization of the molecular structure, expression, subcellular localization and function of ApSRCR1 protein during ontogenesis of this animal. ApSRCR1 protein is a membrane-type protein with a predicted molecular mass of approximately 120 kDa. During ontogenesis, ApSRCR1 protein is de novo synthesized and localizes to cytoplasmic vesicles in both mesenchyme cells and coelomocytes without translation of maternal mRNA; however, the net production and modification by N-glycosylation of ApSRCR1 protein differs in each cell type. In both types of cell, functional inhibition of ApSRCR1 protein leads to incompetent bacterial clearance and failure of aggregate formation. However, this inhibitory effect is weaker in the mesenchyme cells than in the coelomocytes. In the bacteria-sensitized adult, ApSRCR1 protein is up-regulated and digested to enable its secretion into the coelomic fluid. This secreted form of ApSRCR1 protein can apparently bind to bacteria. Overall, we show that ApSRCR1 protein is finely regulated for expression not only during development but also in a sensitive innate immunological situation, and thereupon acts as an opsonin for bacteria to different extents in the larvae and adults of A. pectinifera.


Unique system of photoreceptors in sea urchin tube feet

Esther M Ullrich-Lütera, Sam Dupont, Enrique Arboledac, Harald Hausend and Maria Ina Arnonec

Proceedings of the National Academy of Sciences USA, 108:208367-8372 (2011)

AbstractDifferent sea urchin species show a vast variety of responses to variations in light intensity; however, despite this behavioral evidence for photosensitivity, light sensing in these animals has remained an enigma. Genome information of the recently sequenced purple sea urchin (Strongylocentrotus purpuratus) allowed us to address this question from a previously unexplored molecular perspective by localizing expression of the rhabdomeric opsin Sp-opsin4 and Sp-pax6, two genes essential for photoreceptor function and development, respectively. Using a specifically designed antibody against Sp-Opsin4 and in situ hybridization for both genes, we detected expression in two distinct groups of photoreceptor cells (PRCs) located in the animal's numerous tube feet. Specific reactivity of the Sp-Opsin4 antibody with sea star optic cushions, which regulate phototaxis, suggests a similar visual function in sea urchins. Ultrastructural characterization of the sea urchin PRCs revealed them to be of a microvillar receptor type. Our data suggest that echinoderms, in contrast to chordates, deploy a microvillar, r-opsin–expressing PRC type for vision, a feature that has been so far documented only in protostome animals. Surprisingly, sea urchin PRCs lack any associated screening pigment. Indeed, one of the tube foot PRC clusters may account for directional vision by being shaded through the opaque calcite skeleton. The PRC axons connect to the animal internal nervous system, suggesting an integrative function beyond local short circuits. Because juveniles display no phototaxis until skeleton completion, we suggest a model in which the entire sea urchin, deploying its skeleton as PRC screening device, functions as a huge compound eye.


What is a gene, post-ENCODE? History and updated definition

Mark B. Gerstein,Can Bruce, Joel S. Rozowsky, Deyou Zheng, Jiang Du, Jan O. Korbel, Olof Emanuelsson, Zhengdong D. Zhang, Sherman Weissman and Michael Snyder.  

Genome Research. 17:669-681 (2007).

Synopsis:

This is an excellent review of the vagaries of gene finding in the age of genomics.  The author begins the narrative with an overview of the historical definitions of genes and then proceeds to the current ideas of genes and their structures.  The need for new, functional definitions of genes that explain established principles of genetics, together with the newer findings of genomics, is highlighted by the ENCODE project.

Abstract: While sequencing of the human genome surprised us with how many protein-coding genes there are, it did not fundamentally change our perspective on what a gene is. In contrast, the complex patterns of dispersed regulation and pervasive transcription uncovered by the ENCODE project, together with non-genic conservation and the abundance of noncoding RNA genes, have challenged the notion of the gene. To illustrate this, we review the evolution of operational definitions of a gene over the past century—from the abstract elements of heredity of Mendel and Morgan to the present-day ORFs enumerated in the sequence databanks. We then summarize the current ENCODE findings and provide a computational metaphor for the complexity. Finally, we propose a tentative update to the definition of a gene: A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products. Our definition sidesteps the complexities of regulation and transcription by removing the former altogether from the definition and arguing that final, functional gene products (rather than intermediate transcripts) should be used to group together entities associated with a single gene. It also manifests how integral the concept of biological function is in defining genes.

sham.nair@mq.edu.au
shamnair@gmail.com

© Sham Nair 2014