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Transcription of genomic loci containing protein-coding genes often yields not only cognate mRNAs but also assorted noncoding RNAs (ncRNAs), which typically map in the vicinity of transcription start sites. A new study shows that far from being random byproducts of gene expression, many long ncRNAs (lncRNAs) are synthesized in a coordinate fashion and control important cellular processes, such as survival in the face of DNA damage.
Genetic and gene expression studies have suggested an important role for KLF14 in metabolic disease. A new study now identifies a network of genes whose expression is associated with KLF14 variation in trans, providing a framework for understanding how KLF14 influences disease risk.
A genome-wide association study has identified two new loci modifying pulmonary disease severity in cystic fibrosis. Although this data offers clues to pathways influencing pulmonary function, the underlying genes and mechanisms remain to be elucidated.
A new study reveals that the HMG-box transcription factor SOX2 coupled with the chromatin remodeling helicase CHD7 cooperatively regulate target genes that are essential during neural stem cell development. Notably, this complex controls the expression of several disease-associated genes, suggesting a possible mechanistic connection between five seemingly unrelated human genetic disorders.
A study characterizes the in vitro replicative capacity of over 70,000 clinical isolates of HIV-1 in the absence of drugs, or in the presence of one of 15 individual drugs. The largest survey of the effects of mutations on fitness undertaken in any organism, this study finds extensive pairwise interactions among over 1,800 variable sites identified through sequencing the protease and reverse transcriptase genes.
Current models of Mycobacterium tuberculosis latency presume very low mycobacterial replication and mutation rates. In contrast to these models, a study reporting whole-genome sequencing of mycobacteria isolated from infected macaques shows that the mutational capacity of M. tuberculosis during latency is not reduced, a finding with important implications for tuberculosis research and control.
Identifying causal variants for complex traits and understanding their function remain arduous tasks. A new study combines the advantages of gene mapping in livestock with elegant genetic and functional analyses to address these challenges and identifies candidate regulatory variants affecting stature in cattle.
MicroRNAs (miRNAs) regulate expression of more than one half of the genes in the human genome. A study now reports a new method for selectively silencing whole families of miRNAs, thus providing a new paradigm for disease therapy.
A new study successfully applies complementary whole-genome sequencing and imputation approaches to establish robust disease associations in an isolated population. This strategy is poised to help elucidate the role of variants at the low end of the allele frequency spectrum in the genetic architecture of complex traits.
New studies reveal that 20% of individuals with acute myeloid leukemia harbor somatic mutations in DNMT3A (encoding DNA methyltransferase 3A). Although these leukemias have some gene expression and DNA methylation changes, a direct link between mutant DNMT3A, epigenetic changes and pathogenesis remains to be established.
Expression of oncogenes in otherwise normal cells often leads to the activation of anti-oncogenic pathways through a poorly understood process described as 'oncogenic stress'. A new study implicates the Jnk pathway signaling in the activation of p53 in response to both K-Ras and Neu oncogene expression.
Follow-up studies of a Crohn's disease risk locus encompassing IRGM have revealed unexpected complexity. A new study shows that a synonymous variant in the IRGM coding region alters a binding site for miR-196 and modulates IRGM-dependent autophagy, adding to the list of possible mechanisms by which this locus influences disease risk.
A new study uses genome-wide SNP genotypes to identify a subset of children undergoing therapy for acute lymphoblastic leukemia that are at increased risk for relapse. Borrowing from the classical approach of admixture mapping, the work shows how genome-wide assessment of genetic ancestry can be used as a biomarker for disease outcome.
Two new studies show that mutations in tartrate-resistant acid phosphatase (TRAP) cause spondyloenchondrodysplasia, a rare recessive disease associated with short stature, brain calcifications and lupus-like autoimmunity. The complex clinical syndrome is probably mediated by impaired dephosphorylation of osteopontin.
A new study shows that the piRNA-binding protein Piwi interacts with Hsp90 and suppresses phenotypic variation in Drosophila melanogaster by preventing the expression of hidden epigenetic variation. This suggests that Hsp90 and Piwi function are dampened in times of stress to increase genetic and epigenetic variability, providing a last-ditch mechanism for a species to survive.
Two studies illustrate that with the appropriate resources and scale of study, most of the heritability of complex traits in maize is not missing, but can be located within the genome. Given that maize is one of the world's most important crop plants, this has implications for feeding a growing population with minimum carbon footprint as well as for understanding the genetics of complex traits in a range of species.
