To understand how hematopoietic stem cells (HSC) regulate renewal and differentiation, researchers performed bisulfite sequencing with the HiSeq 2000 system to evaluate genome-wide methylation. Sequencing results and additional functional assays identified the transcription factor and chromatin remodeler Satb1 as a critical regulator of HSC fate, promoting quiescence and repressing differentiation.
Read more at PubMed »
Will B, Vogler TO, Bartholdy B, Garrett-Bakelman F, Mayer J, et al. Satb1 regulates the self-renewal of hematopoietic stem cells by promoting quiescence and repressing differentiation commitment Nature Immunology
To investigate the evolution of the turtle body plan, researchers assembled draft genomes of soft-shell and green sea turtles. RNA sequencing and comparative analysis identified changes in genes and gene regulation that occurred after divergence from the bird–crocodilian lineage. Results indicate that a highly conservative period in vertebrate evolution was followed by embryonic re-patterning in turtles to yield the shell structure.
Read more at PubMed »
Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, et al. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan Nature Genetics
To characterize the response of marine species to increasing ocean acidification, researchers measured genome-wide shifts in allele frequency in purple sea urchins. Though morphology showed little response to the acidic environment, widespread genetic changes demonstrated the capacity of sea urchins to rapidly adapt in response to environmental change.
Read more at PubMed »
Pespeni MH, Sanford E, Gaylord B, Hill TM, Hosfelt JD, et al. Evolutionary change during experimental ocean acidification PNAS
The coelacanth lineage of lobe-finned fish demonstrates potential evolutionary significance for understanding vertebrate adaptation to land. Researchers assembled and annotated the genome of the African coelacanth, revealing genetic changes involved in the tetrapod land transition. Comparative phylogenetic analysis indicated that the lungfish, not the coelacanth, is the closest living relative of the tetrapod ancestor.
Read more at PubMed »
Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, et al. The African coelacanth genome provides insights into tetrapod evolution Nature
To better understand metastatic prostate cancer, researchers used the MiSeq system to perform whole-genome sequencing of plasma DNA from cancer patients. Plasma DNA profiling revealed multiple copy number aberrations and novel chromosomal rearrangements. This approach provided genomic signatures within two days, representing a noninvasive method for investigating the genomic landscape of prostate cancer.
Read more at PubMed »
Heitzer E, Ulz P, Belic J, Gutschi S, Quehenberger F, et al. Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing Genome Medicine
To identify susceptibility loci specific to estrogen receptor (ER)-negative tumors, researchers used the iCOGS custom genotyping array to perform genome-wide association studies of breast cancer cases. They identified SNPs at four loci associated with ER-negative but not ER-positive breast cancer. These findings support hypotheses for distinct etiological pathways associated with invasive ER-negative and ER-positive breast cancers.
Read more at PubMed »
Garcia-Closas M, Couch FJ, Lindstrom S, Michailidou K, Schmidt MK, et al. Genome-wide association studies identify four ER negative-specific breast cancer risk loci Nature Genetics
Using the iCOGS custom genotyping array, researchers performed genome-wide analysis studies of DNA from prostate cancer samples. They evaluated the association between SNPs and prostate cancer, identifying 23 new prostate cancer susceptibility loci. Along with those previously known, these new loci explain approximately 30% of the familial risk of prostate cancer.
Read more at PubMed »
Eeles RA, Olama AA, Benlloch S, Saunders EJ, Leongamornlert DA, et al. Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array Nature Genetics
Guenons, one of the most diverse groups of primates, are endemic to sub-Saharan Africa. To investigate the mechanisms driving guenon diversity, researchers sequenced mitochondrial genomes from museum-preserved specimens. Sequences indicated evolutionary relationships between species and subspecies and suggested that fluctuations in forest cover drove guenon diversification.
Read more at PubMed »
Guschanski K, Krause J, Sawyer S, Valente LM, Bailey S, et al. Next-generation museomics disentangles one of the largest primate radiations Systematic Biology
