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Current Opinion in Genetics & Development

Joshua M Akey, Anna Di Rienzo
No abstract text is available yet for this article.
November 23, 2016: Current Opinion in Genetics & Development
Ignacio Maeso, Rafael D Acemel, José Luis Gómez-Skarmeta
The recent advances in our understanding of the 3D organization of the chromatin together with an almost unlimited ability to detect cis-regulatory elements genome-wide using different biochemical signatures has provided us with an unprecedented power to study gene regulation. It is now possible to profile the complete regulatory apparatus controlling the spatio-temporal expression of any given gene, the so-called gene Regulatory Landscapes (RLs). Here we review several studies over the last two years demonstrating the functional consequences of altering RL structure in development, disease and evolution...
November 11, 2016: Current Opinion in Genetics & Development
Marcia Holsbach Beltrame, Meagan A Rubel, Sarah A Tishkoff
Africa is the origin of anatomically modern humans and a continent of linguistic, cultural, environmental, phenotypic, and genetic diversity. However, African populations remain underrepresented in genetic studies, which have largely focused on individuals with European and Asian ancestry. The expansion of high-throughput 'omic' technologies to interrogate multiple tissue types across many biomolecules-DNA, proteins, epigenetic modifications, metabolites, and others-has heralded a new era of investigation into African history...
October 31, 2016: Current Opinion in Genetics & Development
Andrew Seeber, Susan M Gasser
Chromatin is organized and segmented into a landscape of domains that serve multiple purposes. In contrast to transcription, which is controlled by defined sequences at distinct sites, DNA damage can occur anywhere. Repair accordingly must occur everywhere, yet it is inevitably affected by its chromatin environment. In this review, we summarize recent work investigating how changes in chromatin organization facilitate and/or guide DNA double-strand break repair. In addition, we examine new live cell studies on the dynamics of chromatin and the mechanisms that regulate its movement...
October 31, 2016: Current Opinion in Genetics & Development
Nicoletta Bobola, Samir Merabet
Homeodomain proteins are evolutionary conserved proteins present in the entire eukaryote kingdom. They execute functions that are essential for life, both in developing and adult organisms. Most homeodomain proteins act as transcription factors and bind DNA to control the activity of other genes. In contrast to their similar DNA binding specificity, homeodomain proteins execute highly diverse and context-dependent functions. Several factors, including genome accessibility, DNA shape, combinatorial binding and the ability to interact with many transcriptional partners, diversify the activity of homeodomain proteins and culminate in the activation of highly dynamic, context-specific transcriptional programs...
October 18, 2016: Current Opinion in Genetics & Development
Yuval B Simons, Guy Sella
Over the past decade, there has been both great interest and confusion about whether recent demographic events-notably the Out-of-Africa-bottleneck and recent population growth-have led to differences in mutation load among human populations. The confusion can be traced to the use of different summary statistics to measure load, which lead to apparently conflicting results. We argue, however, that when statistics more directly related to load are used, the results of different studies and data sets consistently reveal little or no difference in the load of non-synonymous mutations among human populations...
October 13, 2016: Current Opinion in Genetics & Development
Lauren Alpert Sugden, Sohini Ramachandran
Human population genomic studies have repeatedly observed a decrease in heterozygosity and an increase in linkage disequilibrium with geographic distance from Africa. While multiple demographic models can generate these patterns, many studies invoke the serial founder effect model, in which populations expand from a single origin and each new population's founders represent a subset of genetic variation in the previous population. The model assumes no admixture with archaic hominins, however, recent studies have identified loci in Homo sapiens bearing signatures of archaic introgression...
October 13, 2016: Current Opinion in Genetics & Development
Martin Kuhlwilm, Marc de Manuel, Alexander Nater, Maja P Greminger, Michael Krützen, Tomas Marques-Bonet
The great apes are the closest living relatives of humans. Chimpanzees and bonobos group together with humans, while gorillas and orangutans are more divergent from humans. Here, we review insights into their evolution pertaining to the topology of species and subspecies and the reconstruction of their demography based on genome-wide variation. These advances have only become possible recently through next-generation sequencing technologies. Given the close relationship to humans, they provide an important evolutionary context for human genetics...
October 4, 2016: Current Opinion in Genetics & Development
Feng Gao, Alon Keinan
The advent of next-generation sequencing technology has allowed the collection of vast amounts of genetic variation data. A recurring discovery from studying larger and larger samples of individuals had been the extreme, previously unexpected, excess of very rare genetic variants, which has been shown to be mostly due to the recent explosive growth of human populations. Here, we review recent literature that inferred recent changes in population size in different human populations and with different methodologies, with many pointing to recent explosive growth, especially in European populations for which more data has been available...
October 3, 2016: Current Opinion in Genetics & Development
Kaustubh Adhikari, Javier Mendoza-Revilla, Juan Camilo Chacón-Duque, Macarena Fuentes-Guajardo, Andrés Ruiz-Linares
Latin Americans arguably represent the largest recently admixed populations in the world. This reflects a history of massive settlement by immigrants (mostly Europeans and Africans) and their variable admixture with Natives, starting in 1492. This process resulted in the population of Latin America showing an extensive genetic and phenotypic diversity. Here we review how genetic analyses are being applied to examine the demographic history of this population, including patterns of mating, population structure and ancestry...
September 27, 2016: Current Opinion in Genetics & Development
Torsten Günther, Mattias Jakobsson
Genomic information from ancient human remains is beginning to show its full potential for learning about human prehistory. We review the last few years' dramatic finds about European prehistory based on genomic data from humans that lived many millennia ago and relate it to modern-day patterns of genomic variation. The early times, the Upper Paleolithic, appears to contain several population turn-overs followed by more stable populations after the Last Glacial Maximum and during the Mesolithic. Some 11000 years ago the migrations driving the Neolithic transition start from around Anatolia and reach the north and the west of Europe millennia later followed by major migrations during the Bronze Age...
September 26, 2016: Current Opinion in Genetics & Development
John Novembre, Benjamin M Peter
Empowered by modern genotyping and large samples, population structure can be accurately described and quantified even when it only explains a fraction of a percent of total genetic variance. This is especially relevant and interesting for humans, where fine-scale population structure can both confound disease-mapping studies and reveal the history of migration and divergence that shaped our species' diversity. Here we review notable recent advances in the detection, use, and understanding of population structure...
September 20, 2016: Current Opinion in Genetics & Development
Jeffrey D Wall, Debora Yoshihara Caldeira Brandt
Modern humans evolved in Southern or Eastern Africa, and spread from there across the rest of the world. As they expanded across Africa and Eurasia, they encountered other hominin groups. The extent to which modern and 'archaic' human groups interbred is an area of active research, and while we know that modern humans interbred with Neanderthals and Denisovans, there is not yet agreement on how many admixture events there were or on how much Neanderthal or Denisovan DNA can be found in contemporary genomes...
September 20, 2016: Current Opinion in Genetics & Development
Nicole Creanza, Marcus W Feldman
Both genetic variation and certain culturally transmitted phenotypes show geographic signatures of human demographic history. As a result of the human cultural predisposition to migrate to new areas, humans have adapted to a large number of different environments. Migration to new environments alters genetic selection pressures, and comparative genetic studies have pinpointed numerous likely targets of this selection. However, humans also exhibit many cultural adaptations to new environments, such as practices related to clothing, shelter, and food...
September 16, 2016: Current Opinion in Genetics & Development
Charles N Rotimi, Fasil Tekola-Ayele, Jennifer L Baker, Daniel Shriner
The trans-Atlantic slave trade brought millions of Africans to the New World. Advances in genomics are providing novel insights into the history and health of Africans and the diasporan populations. Recent examples reviewed here include the unraveling of substantial hunter-gatherer and 'Eurasian' admixtures across sub-Saharan Africa, expanding our understanding of ancestral African genetics; the global ubiquity of mixed ancestry; the revealing of African ancestry in Latin Americans that likely derived from the slave trade; and understanding of the ancestral backgrounds of APOL1 and LPL found to influence kidney disease and lipid levels, respectively, providing specific insights into disease etiology and health disparities...
September 16, 2016: Current Opinion in Genetics & Development
Ricardo Mallarino, Hopi E Hoekstra, Marie Manceau
For decades, mammalian developmental genetic studies have focused almost entirely on two laboratory models: Mus and Rattus, species that breed readily in the laboratory and for which a wealth of molecular and genetic resources exist. These species alone, however, do not capture the remarkable diversity of morphological, behavioural and physiological traits seen across rodents, a group that represents >40% of all mammal species. Due to new advances in molecular tools and genomic technologies, studying the developmental events underlying natural variation in a wide range of species for a wide range of traits has become increasingly feasible...
September 14, 2016: Current Opinion in Genetics & Development
Sarah F Becker, Sophie Jarriault
Elucidating the mechanisms underlying cell fate determination, cell identity maintenance and cell reprogramming in vivo is one of the main challenges in today's science. Such knowledge of fundamental importance will further provide new leads for early diagnostics and targeted therapy approaches both in regenerative medicine and cancer research. This review focuses on recent mechanistic findings and factors that influence the differentiated state of cells in direct reprogramming events, aka transdifferentiation...
October 2016: Current Opinion in Genetics & Development
B Duygu Özpolat, Alexandra E Bely
Studies of annelid regeneration have greatly increased in frequency in recent years, providing new insights into the developmental basis and evolution of regeneration. In this review, we summarize recent findings related to regeneration in annelids, focusing on molecular and developmental studies of epimorphic (blastema-based) regeneration, morphallactic (tissue-remodeling based) regeneration, and development and regeneration of putative stem cells of the posterior growth zone and germline. Regeneration is being investigated in a broad range of annelids spanning the phylum, and comparing findings among species reveals both widely conserved features that may be ancestral for the phylum as well as features that are variable across the group...
October 2016: Current Opinion in Genetics & Development
Randall Widelitz, Cheng-Ming Chuong
Stem cell and microenvironment molecular interactions have been studied in detail but regenerative behavior at the organ population level has remained unexplored. Organ renewal can occur continuously or in cyclic episodes. Progenitors may be distributed as one entity or compartmentalized into multiple units. Multiple units offer advantages as each unit can be regulated differently in different body regions or physiological stages, adapting animals to their niche with flexible functional forms. Using the hair paradigm, we show how periodic patterning can convert one morphogenetic field into many hair germs, how follicles can be renewed with different cycle times and phenotypes in a region-specific manner, and how new properties, such as regenerative waves and quorum sensing, emerge to coordinate collective regenerative behavior...
October 2016: Current Opinion in Genetics & Development
Andrew R Gehrke, Mansi Srivastava
The molecular mechanisms underlying whole-body regeneration are best understood in the planarian flatworm Schmidtea mediterranea, where a heterogeneous population of somatic stem cells called neoblasts provides new tissue for regeneration of essentially any missing body part. Studies on Schmidtea have provided a detailed description of neoblasts and their role in regeneration, but comparatively little is known about the evolutionary history of these cells and their underlying developmental programs. Acoels, an understudied group of aquatic worms that are also capable of extensive whole-body regeneration, have arisen as an attractive group to study the evolution of regenerative processes due to their phylogenetically distant position relative to flatworms...
October 2016: Current Opinion in Genetics & Development
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