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Trends in Genetics: TIG

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https://www.readbyqxmd.com/read/30366621/whole-genome-duplication-and-yeast-s-fruitful-way-of-life
#1
REVIEW
Ximena Escalera-Fanjul, Héctor Quezada, Lina Riego-Ruiz, Alicia González
Studies on the fate of Saccharomyces cerevisiae paralogous gene pairs that arose through a whole-genome duplication event have shown diversification of retained duplicated genes. Paralogous functional specialization often results in improved function and/or novel function that could contribute to the adaptation of the organism to a new lifestyle. Here, we analyze and discuss particular case studies of paralogous functional diversification that could have played a role in the acquisition of yeast fermentative metabolism...
October 23, 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30342790/genomic-and-phenomic-research-in-the-21st-century
#2
REVIEW
Scott Hebbring
The field of human genomics has changed dramatically over time. Initial genomic studies were predominantly restricted to rare disorders in small families. Over the past decade, researchers changed course from family-based studies and instead focused on common diseases and traits in populations of unrelated individuals. With further advancements in biobanking, computer science, electronic health record (EHR) data, and more affordable high-throughput genomics, we are experiencing a new paradigm in human genomic research...
October 17, 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30316580/post-transcriptional-regulatory-functions-of-mammalian-pumilio-proteins
#3
REVIEW
Aaron C Goldstrohm, Traci M Tanaka Hall, Katherine M McKenney
Mammalian Pumilio proteins, PUM1 and PUM2, are members of the PUF family of sequence-specific RNA-binding proteins. In this review, we explore their mechanisms, regulatory networks, biological functions, and relevance to diseases. Pumilio proteins bind an extensive network of mRNAs and repress protein expression by inhibiting translation and promoting mRNA decay. Opposingly, in certain contexts, they can activate protein expression. Pumilio proteins also regulate noncoding (nc)RNAs. The ncRNA, ncRNA activated by DNA damage (NORAD), can in turn modulate Pumilio activity...
October 10, 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30309754/rhythms-of-the-genome-circadian-dynamics-from-chromatin-topology-tissue-specific-gene-expression-to-behavior
#4
REVIEW
Jake Yeung, Felix Naef
Circadian rhythms in physiology and behavior evolved to resonate with daily cycles in the external environment. In mammals, organs orchestrate temporal physiology over the 24-h day, which requires extensive gene expression rhythms targeted to the right tissue. Although a core set of gene products oscillates across virtually all cell types, gene expression profiling across tissues over the 24-h day showed that rhythmic gene expression programs are tissue specific. We highlight recent progress in uncovering how the circadian clock interweaves with tissue-specific gene regulatory networks involving functions such as xenobiotic metabolism, glucose homeostasis, and sleep...
October 8, 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30292539/the-birth-of-the-3d-genome-during-early-embryonic-development
#5
REVIEW
Clemens B Hug, Juan M Vaquerizas
The 3D structure of chromatin in the nucleus is important for the regulation of gene expression and the correct deployment of developmental programs. The differentiation of germ cells and early embryonic development (when the zygotic genome is activated and transcription is taking place for the first time) are accompanied by dramatic changes in gene expression and the epigenetic landscape. Recent studies used Hi-C to investigate the 3D chromatin organization during these developmental transitions, uncovering remarkable remodeling of the 3D genome...
October 3, 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30287096/wake-up-sleepy-gene-reactivating-fetal-globin-for-%C3%AE-hemoglobinopathies
#6
REVIEW
Beeke Wienert, Gabriella E Martyn, Alister P W Funnell, Kate G R Quinlan, Merlin Crossley
Disorders in hemoglobin (hemoglobinopathies) were the first monogenic diseases to be characterized and remain among the most common and best understood genetic conditions. Moreover, the study of the β-globin locus provides a textbook example of developmental gene regulation. The fetal γ-globin genes (HBG1/HBG2) are ordinarily silenced around birth, whereupon their expression is replaced by the adult β-globin genes (HBB primarily and HBD). Over 50 years ago it was recognized that mutations that cause lifelong persistence of fetal γ-globin expression ameliorate the debilitating effects of mutations in β-globin...
October 1, 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30270122/improving-estimates-of-compensatory-cis-trans-regulatory-divergence
#7
Hunter B Fraser
Interspecific hybrids have played a key role in research on gene expression regulation. A growing number of studies have measured genome-wide allele-specific expression in hybrids and observed that cis-regulatory changes often oppose trans-acting changes affecting the same genes, suggesting stabilizing selection for compensatory changes. However, the most common method for estimating these effects is biased, producing artifactual patterns of compensatory evolution. Here I introduce a simple modification leveraging biological replicates that ameliorates the bias...
September 27, 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30243593/easy-access-to-and-applications-of-the-sequences-of-all-protein-coding-genes-of-all-sequenced-mouse-strains
#8
Steven Timmermans, Claude Libert
An easily accessible and searchable overview of all protein sequences in the 36 genome-sequenced mouse strains, compared to those in the reference strain C57BL/6J, is now available, as well as an overview of the aberrant proteins in this reference strain. We provide an insight into the advantages of using these databases.
September 19, 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30241969/the-generic-facet-of-hox-protein-function
#9
REVIEW
Andrew J Saurin, Marie Claire Delfini, Corinne Maurel-Zaffran, Yacine Graba
Hox transcription factors are essential to promote morphological diversification of the animal body. A substantial number of studies have focused on how Hox proteins reach functional specificity, an issue that arises from the fact that these transcription factors control distinct developmental functions despite sharing similar molecular properties. In this review, we highlight that, besides specific functions, for which these transcription factors are renowned, Hox proteins also often have nonspecific functions...
September 18, 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30220472/drilling-for-insight-forecasting-phenotype-from-genotype
#10
Ali Torkamani
The manifestation of disease can vary substantially from person to person. Yet, much of the emphasis of genomics in individualized medicine has been on linking genetic variants to broad disease categories. A new approach takes a first step towards predicting detailed phenotypic information from disease-causative variants.
September 13, 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30217559/parallels-between-mammalian-mechanisms-of-monoallelic-gene-expression
#11
REVIEW
Ahmed Amine Khamlichi, Robert Feil
Different types of monoallelic gene expression are present in mammals, some of which are highly flexible, whereas others are more rigid. These include allelic exclusion at antigen receptor loci, the expression of olfactory receptor genes, genomic imprinting, X-chromosome inactivation, and random monoallelic expression (MAE). Although these processes play diverse biological roles, and arose through different selective pressures, the underlying epigenetic mechanisms show striking resemblances. Regulatory transcriptional events are important in all systems, particularly in the specification of MAE...
September 11, 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30195580/pimp-my-ribosome-ribosomal-protein-paralogs-specify-translational-control
#12
REVIEW
Jeffrey E Gerst
The ability of cells to grow and divide, differentiate and function, and even senesce is dependent on the fine-tuning of both gene and protein expression. Protein concentration in the cell is regulated not only at the transcriptional and post-translational levels, but also at the level of translation. Ribosomes, the molecular machines behind translation, were once considered to be an invariant driving force behind protein expression. However, studies over the past decade paint a rather different picture; namely, that ribosomes constitute an additional layer of regulatory control that might define which subsets of mRNAs are translated, to what extent, and to what purpose...
September 5, 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30166071/analysis-of-epistasis-in-natural-traits-using-model-organisms
#13
REVIEW
Richard F Campbell, Patrick T McGrath, Annalise B Paaby
The ability to detect and understand epistasis in natural populations is important for understanding how biological traits are influenced by genetic variation. However, identification and characterization of epistasis in natural populations remains difficult due to statistical issues that arise as a result of multiple comparisons, and the fact that most genetic variants segregate at low allele frequencies. In this review, we discuss how model organisms may be used to manipulate genotypic combinations to power the detection of epistasis as well as test interactions between specific genes...
August 27, 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30144941/epigenetic-environmental-memories-in-plants-establishment-maintenance-and-reprogramming
#14
REVIEW
Yuehui He, Zicong Li
Plants are immobile and must respond to or endure fluctuating surroundings and diverse environmental challenges. Environmental inputs often induce chromatin modifications at various responsive genes and consequent changes in their expression. Environment-induced chromatin marks at certain loci are transmittable through cell divisions after relief from the original external signals, leading to acquired 'memorization' of environmental experiences in plants, namely epigenetic environmental memories, which enable plants to adapt to environmental changes or to perform better when events recur...
August 22, 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30195581/transposons-p53-and-genome-security
#15
REVIEW
Bhavana Tiwari, Amanda E Jones, John M Abrams
p53, the most commonly mutated tumor suppressor, is a transcription factor known to regulate proliferation, senescence, and apoptosis. Compelling studies have found that p53 may prevent oncogenesis through effectors that are unrelated to these canonical processes and recent findings have uncovered ancient roles for p53 in the containment of mobile elements. Together, these developments raise the possibility that some p53-driven cancers could result from unrestrained transposons. Here, we explore evidence linking conserved features of p53 biology to the control of transposons...
November 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30177410/rna-action-through-interactions
#16
REVIEW
Tri C Nguyen, Kathia Zaleta-Rivera, Xuerui Huang, Xiaofeng Dai, Sheng Zhong
As transcription of the human genome is quite pervasive, it is possible that many novel functions of the noncoding genome have yet to be identified. Often the noncoding genome's functions are carried out by their RNA transcripts, which may rely on their structures and/or extensive interactions with other molecules. Recent technology developments are transforming the fields of RNA biology from studying one RNA at a time to transcriptome-wide mapping of structures and interactions. Here, we highlight the recent advances in transcriptome-wide RNA interaction analysis...
November 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30146183/co-expression-in-single-cell-analysis-saving-grace-or-original-sin
#17
REVIEW
Megan Crow, Jesse Gillis
As a fundamental unit of life, the cell has rightfully been the subject of intense investigation throughout the history of biology. Technical innovations now make it possible to assay cellular features at genomic scale, yielding breakthroughs in our understanding of the molecular organization of tissues, and even whole organisms. As these data accumulate we will soon be faced with a new challenge: making sense of the plethora of results. Early investigations into the replicability of cell type profiles inferred from single-cell RNA sequencing data have indicated that this is likely to be surprisingly straightforward due to consistent gene co-expression...
November 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30173869/the-neural-mechanisms-of-sexually-dimorphic-aggressive-behaviors
#18
REVIEW
Koichi Hashikawa, Yoshiko Hashikawa, Julieta Lischinsky, Dayu Lin
Aggression is a fundamental social behavior that is essential for competing for resources and protecting oneself and families in both males and females. As a result of natural selection, aggression is often displayed differentially between the sexes, typically at a higher level in males than females. Here, we highlight the behavioral differences between male and female aggression in rodents. We further outline the aggression circuits in males and females, and compare their differences at each circuit node. Lastly, we summarize our current understanding regarding the generation of sexually dimorphic aggression circuits during development and their maintenance during adulthood...
October 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30143323/enter-the-matrix-factorization-uncovers-knowledge-from-omics
#19
REVIEW
Genevieve L Stein-O'Brien, Raman Arora, Aedin C Culhane, Alexander V Favorov, Lana X Garmire, Casey S Greene, Loyal A Goff, Yifeng Li, Aloune Ngom, Michael F Ochs, Yanxun Xu, Elana J Fertig
Omics data contain signals from the molecular, physical, and kinetic inter- and intracellular interactions that control biological systems. Matrix factorization (MF) techniques can reveal low-dimensional structure from high-dimensional data that reflect these interactions. These techniques can uncover new biological knowledge from diverse high-throughput omics data in applications ranging from pathway discovery to timecourse analysis. We review exemplary applications of MF for systems-level analyses. We discuss appropriate applications of these methods, their limitations, and focus on the analysis of results to facilitate optimal biological interpretation...
October 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/30139641/complex-trait-prediction-in-the-era-of-big-data
#20
REVIEW
Gustavo de Los Campos, Ana Ines Vazquez, Stephen Hsu, Louis Lello
Accurate prediction of complex traits requires using a large number of DNA variants. Advances in statistical and machine learning methodology enable the identification of complex patterns in high-dimensional settings. However, training these highly parameterized methods requires very large data sets. Until recently, such data sets were not available. But the situation is changing rapidly as very large biomedical data sets comprising individual genotype-phenotype data for hundreds of thousands of individuals become available in public and private domains...
October 2018: Trends in Genetics: TIG
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