Editorial Board and Contents
Publication date: February 2019Source: Trends in Genetics, Volume 35, Issue 2Author(s): (Source: Trends in Genetics)
Source: Trends in Genetics - January 15, 2019 Category: Genetics & Stem Cells Source Type: research

miRNA Targeting: Growing beyond the Seed
Publication date: Available online 9 January 2019Source: Trends in GeneticsAuthor(s): Laura B. Chipman, Amy E. PasquinellimiRNAs are small RNAs that guide Argonaute proteins to specific target mRNAs to repress their translation and stability. Canonically, miRNA targeting is reliant on base pairing of the seed region, nucleotides 2–7, of the miRNA to sites in mRNA 3′ untranslated regions. Recently, the 3′ half of the miRNA has gained attention for newly appreciated roles in regulating target specificity and regulation. In addition, the extent of pairing to the miRNA 3′ end can influence the stability...
Source: Trends in Genetics - January 10, 2019 Category: Genetics & Stem Cells Source Type: research

Translation of Small Open Reading Frames: Roles in Regulation and Evolutionary Innovation
Publication date: Available online 31 December 2018Source: Trends in GeneticsAuthor(s): Jorge Ruiz-Orera, M. Mar AlbàThe translatome can be defined as the sum of the RNA sequences that are translated into proteins in the cell by the ribosomal machinery. Until recently, it was generally assumed that the translatome was essentially restricted to evolutionary conserved proteins encoded by the set of annotated protein-coding genes. However, it has become increasingly clear that it also includes small regulatory open reading frames (ORFs), functional micropeptides, de novo proteins, and the pervasive translation of likel...
Source: Trends in Genetics - January 1, 2019 Category: Genetics & Stem Cells Source Type: research

Multiple Roles for Mono- and Poly(ADP-Ribose) in Regulating Stress Responses
Publication date: Available online 27 December 2018Source: Trends in GeneticsAuthor(s): Hongyun Qi, Brendan D. Price, Tovah A. DayAlthough stress-induced synthesis of mono(ADP-ribose) (mADPr) and poly(ADP-ribose) (pADPr) conjugates by pADPr polymerase (PARP) enzymes has been studied extensively, the removal and degradation of pADPr, as well as the fate of ADPr metabolites, have received less attention. The observations that stress-induced pADPr undergoes rapid turnover, and that deficiencies in ADPr degradation phenocopy loss of pADPr synthesis, suggest that ADPr degradation is fundamentally important to the cellular stres...
Source: Trends in Genetics - December 28, 2018 Category: Genetics & Stem Cells Source Type: research

Support for Living Stock Collections: A Mammalian Stock Center Perspective
Publication date: Available online 23 December 2018Source: Trends in GeneticsAuthor(s): Hippokratis KiarisThe living stock collections represent an indispensable resource for life scientists. Their uninterrupted operation should combine high quality standards, cost-effectiveness, wide accessibility, and sustainability. Mammalian stock collections, especially those involving diversified animals, face some unique challenges that may disrupt their smooth operation if not addressed. (Source: Trends in Genetics)
Source: Trends in Genetics - December 24, 2018 Category: Genetics & Stem Cells Source Type: research

Chromatin Interactions and Regulatory Elements in Cancer: From Bench to Bedside
Publication date: Available online 18 December 2018Source: Trends in GeneticsAuthor(s): Yi Xiang See, Benny Zhengjie Wang, Melissa J. FullwoodChromatin interactions regulate gene expression by bringing distal regulatory elements, such as super-enhancers, to promoters in close spatial proximity. It has been recognized that in cancer, chromatin interactions can be dysregulated, leading to aberrant oncogene expression. Chromatin interactions may potentially serve as biomarkers, or be modulated via CRISPR therapy and small molecule inhibitors against transcription. However, these methods face challenges that must be resolved a...
Source: Trends in Genetics - December 19, 2018 Category: Genetics & Stem Cells Source Type: research

Editorial Board and Contents
Publication date: January 2019Source: Trends in Genetics, Volume 35, Issue 1Author(s): (Source: Trends in Genetics)
Source: Trends in Genetics - December 18, 2018 Category: Genetics & Stem Cells Source Type: research

Small Nucleolar RNAs Tell a Different Tale
Publication date: Available online 16 December 2018Source: Trends in GeneticsAuthor(s): Joanna Kufel, Pawel GrzechnikTranscribing RNA Polymerase II interacts with multiple factors that orchestrate maturation and stabilisation of messenger RNA. For the majority of noncoding RNAs, the polymerase complex employs entirely different strategies, which usually direct the nascent transcript to ribonucleolytic degradation. However, some noncoding RNA classes use endo- and exonucleases to achieve functionality. Here we review processing of small nucleolar RNAs that are transcribed by RNA Polymerase II as precursors, and whose 5&prim...
Source: Trends in Genetics - December 16, 2018 Category: Genetics & Stem Cells Source Type: research

Studying Transcriptional Enhancers: The Founder Fallacy, Validation Creep, and Other Biases
Publication date: Available online 13 December 2018Source: Trends in GeneticsAuthor(s): Marc S. HalfonTranscriptional enhancers play a major role in regulating metazoan gene expression. Recent developments in genomics and next-generation sequencing have accelerated and revitalized the study of this important class of sequence elements. Increased interest and attention, however, has also led to troubling trends in the enhancer literature. In this Opinion, I describe some of these issues and show how they arise from shifting and nonuniform enhancer definitions, and genome-era biases. I discuss how they can lead to interpreta...
Source: Trends in Genetics - December 13, 2018 Category: Genetics & Stem Cells Source Type: research

The Generic Facet of Hox Protein Function: (Trends in Genetics 34, 941–953, 2018)
Publication date: Available online 7 December 2018Source: Trends in GeneticsAuthor(s): Andrew J. Saurin, Marie Claire Delfini, Corinne Maurel-Zaffran, Yacine Graba (Source: Trends in Genetics)
Source: Trends in Genetics - December 8, 2018 Category: Genetics & Stem Cells Source Type: research

Non-duplex G-Quadruplex Structures Emerge as Mediators of Epigenetic Modifications
Publication date: Available online 4 December 2018Source: Trends in GeneticsAuthor(s): Ananda Kishore Mukherjee, Shalu Sharma, Shantanu ChowdhuryThe role of non-duplex DNA, the guanine-quadruplex structure in particular, is becoming widely appreciated. Increasing evidence in the last decade implicates quadruplexes in important processes such as transcription and replication. Interestingly, more recent work suggests roles for quadruplexes, in association with quadruplex-interacting proteins, in epigenetics through both DNA and histone modifications. Here, we review the effect of the quadruplex structure on post-replication ...
Source: Trends in Genetics - December 5, 2018 Category: Genetics & Stem Cells Source Type: research

Understanding Grass Domestication through Maize Mutants
Publication date: Available online 30 November 2018Source: Trends in GeneticsAuthor(s): Zhaobin Dong, Martin Alexander, George ChuckAs an economically important model crop plant, rich in genetic resources, maize has been useful for uncovering the genetic pathways responsible for domestication and plant improvement. However, several of the pathways that have been shown by recent studies to be important for domestication and/or yield in other grasses function differently in maize. In several cases, this unexpectedly wide functional divergence between genes from closely related grasses appears to be due to alternative modes o...
Source: Trends in Genetics - December 1, 2018 Category: Genetics & Stem Cells Source Type: research

Improving Estimates of Compensatory cis–trans Regulatory Divergence
Publication date: Available online 30 November 2018Source: Trends in GeneticsAuthor(s): Hunter B. Fraser (Source: Trends in Genetics)
Source: Trends in Genetics - December 1, 2018 Category: Genetics & Stem Cells Source Type: research

Inferring Compensatory Evolution of cis- and trans-Regulatory Variation
Publication date: Available online 29 November 2018Source: Trends in GeneticsAuthor(s): Xinwen Zhang, J.J. Emerson (Source: Trends in Genetics)
Source: Trends in Genetics - December 1, 2018 Category: Genetics & Stem Cells Source Type: research

Subcellular Heterogeneity of the microRNA Machinery
Publication date: Available online 30 November 2018Source: Trends in GeneticsAuthor(s): Michele TrabucchiDifferent methods have recently been developed to understand the subcellular localization and role of microRNAs (miRNAs) as well as small RNAs associated with Argonaute (AGO) proteins. The heterogeneity of the protein complexes associated with miRNAs, along with their subcellular localization, provides clues into their biochemical mechanism of function. Subcellular diversity indicates that miRNAs localized to different cellular regions could have different functions, including transcriptional regulation on chromatin or ...
Source: Trends in Genetics - December 1, 2018 Category: Genetics & Stem Cells Source Type: research

Post-Translational Modification, Phase Separation, and Robust Gene Transcription
Publication date: Available online 23 November 2018Source: Trends in GeneticsAuthor(s): Hari R. Singh, Yogesh B. OstwalA few recent reports reveal fundamental new insights into the intricate regulatory mechanisms that govern RNA polymerase II (Pol II)-mediated gene transcription. Whereas a histidine-rich domain (HRD) triggers phase separation, promoting transcription elongation, a phosphatase switch promotes transcription termination. A paradigm that might govern the underlying mechanisms leading to robust gene transcription is now starting to emerge. (Source: Trends in Genetics)
Source: Trends in Genetics - November 24, 2018 Category: Genetics & Stem Cells Source Type: research

Solving the Polyploid Mystery in Health and Disease
Publication date: Available online 21 November 2018Source: Trends in GeneticsAuthor(s): K.J. Gjelsvik, R. Besen-McNally, V.P. LosickPolyploidy (the more than doubling of a cell’s genome) frequently arises during organogenesis, tissue repair, and age-associated diseases. Despite its prevalence, major gaps exist in how polyploid cells emerge and affect tissue function. Studies have begun to elucidate the signals required for polyploid cell growth as well as the advantages and disadvantages of polyploidy in health and disease. This review highlights the recent advances on the role and regulation of polyploidy in Drosoph...
Source: Trends in Genetics - November 22, 2018 Category: Genetics & Stem Cells Source Type: research

RNA Splicing and Disease: Animal Models to Therapies
Publication date: Available online 19 November 2018Source: Trends in GeneticsAuthor(s): Matías Montes, Brianne L. Sanford, Daniel F. Comiskey, Dawn S. ChandlerAlternative splicing of pre-mRNA increases genetic diversity, and recent studies estimate that most human multiexon genes are alternatively spliced. If this process is not highly regulated and accurate, it leads to mis-splicing events, which may result in proteins with altered function. A growing body of work has implicated mis-splicing events in a range of diseases, including cancer, neurodegenerative diseases, and muscular dystrophies. Understanding the mech...
Source: Trends in Genetics - November 21, 2018 Category: Genetics & Stem Cells Source Type: research

Dissecting the Genetics of Osteoporosis using Systems Approaches
Publication date: Available online 20 November 2018Source: Trends in GeneticsAuthor(s): Basel M. Al-Barghouthi, Charles R. FarberOsteoporosis is a condition characterized by low bone mineral density (BMD) and an increased risk of fracture. Traits contributing to osteoporotic fracture are highly heritable, indicating that a comprehensive understanding of bone requires a thorough understanding of the genetic basis of bone traits. Towards this goal, genome-wide association studies (GWASs) have identified over 500 loci associated with bone traits. However, few of the responsible genes have been identified, and little is known ...
Source: Trends in Genetics - November 21, 2018 Category: Genetics & Stem Cells Source Type: research

Editorial Board and Contents
Publication date: December 2018Source: Trends in Genetics, Volume 34, Issue 12Author(s): (Source: Trends in Genetics)
Source: Trends in Genetics - November 21, 2018 Category: Genetics & Stem Cells Source Type: research

Knocking Out Enhancers to Enhance Epigenetic Research
Publication date: Available online 19 November 2018Source: Trends in GeneticsAuthor(s): Gregg Duester (Source: Trends in Genetics)
Source: Trends in Genetics - November 19, 2018 Category: Genetics & Stem Cells Source Type: research

Whole-Genome Duplication and Yeast’s Fruitful Way of Life
Publication date: Available online 23 October 2018Source: Trends in GeneticsAuthor(s): Ximena Escalera-Fanjul, Héctor Quezada, Lina Riego-Ruiz, Alicia GonzálezStudies 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 hav...
Source: Trends in Genetics - October 25, 2018 Category: Genetics & Stem Cells Source Type: research

Genomic and Phenomic Research in the 21st Century
Publication date: Available online 17 October 2018Source: Trends in GeneticsAuthor(s): Scott HebbringThe 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. Rapi...
Source: Trends in Genetics - October 18, 2018 Category: Genetics & Stem Cells Source Type: research

Editorial Board and Contents
Publication date: November 2018Source: Trends in Genetics, Volume 34, Issue 11Author(s): (Source: Trends in Genetics)
Source: Trends in Genetics - October 16, 2018 Category: Genetics & Stem Cells Source Type: research

Post-transcriptional Regulatory Functions of Mammalian Pumilio Proteins
Publication date: Available online 10 October 2018Source: Trends in GeneticsAuthor(s): Aaron C. Goldstrohm, Traci M. Tanaka Hall, Katherine M. McKenneyMammalian 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 (...
Source: Trends in Genetics - October 11, 2018 Category: Genetics & Stem Cells Source Type: research

Rhythms of the Genome: Circadian Dynamics from Chromatin Topology, Tissue-Specific Gene Expression, to Behavior
Publication date: Available online 8 October 2018Source: Trends in GeneticsAuthor(s): Jake Yeung, Felix NaefCircadian 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 cir...
Source: Trends in Genetics - October 9, 2018 Category: Genetics & Stem Cells Source Type: research

Improving Estimates of Compensatory cis–trans Regulatory Divergence
Publication date: Available online 27 September 2018Source: Trends in GeneticsAuthor(s): Hunter B. FraserInterspecific 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 biolo...
Source: Trends in Genetics - October 5, 2018 Category: Genetics & Stem Cells Source Type: research

Wake-up Sleepy Gene: Reactivating Fetal Globin for β-Hemoglobinopathies
Publication date: Available online 1 October 2018Source: Trends in GeneticsAuthor(s): Beeke Wienert, Gabriella E. Martyn, Alister P.W. Funnell, Kate G.R. Quinlan, Merlin CrossleyDisorders 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...
Source: Trends in Genetics - October 5, 2018 Category: Genetics & Stem Cells Source Type: research

The Birth of the 3D Genome during Early Embryonic Development
Publication date: Available online 3 October 2018Source: Trends in GeneticsAuthor(s): Clemens B. Hug, Juan M. VaquerizasThe 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, uncover...
Source: Trends in Genetics - October 5, 2018 Category: Genetics & Stem Cells Source Type: research

The Generic Facet of Hox Protein Function
Publication date: Available online 18 September 2018Source: Trends in GeneticsAuthor(s): Andrew J. Saurin, Marie Claire Delfini, Corinne Maurel-Zaffran, Yacine GrabaHox 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,...
Source: Trends in Genetics - September 20, 2018 Category: Genetics & Stem Cells Source Type: research

Easy Access to and Applications of the Sequences of All Protein-Coding Genes of All Sequenced Mouse Strains
Publication date: Available online 19 September 2018Source: Trends in GeneticsAuthor(s): Steven Timmermans, Claude LibertAn 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. (Source: Trends in Genetics)
Source: Trends in Genetics - September 20, 2018 Category: Genetics & Stem Cells Source Type: research

Editorial Board and Contents
Publication date: October 2018Source: Trends in Genetics, Volume 34, Issue 10Author(s): (Source: Trends in Genetics)
Source: Trends in Genetics - September 20, 2018 Category: Genetics & Stem Cells Source Type: research

Drilling for Insight: Forecasting Phenotype from Genotype
Publication date: Available online 13 September 2018Source: Trends in GeneticsAuthor(s): Ali TorkamaniThe 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. (Source: Trends in Genetics)
Source: Trends in Genetics - September 14, 2018 Category: Genetics & Stem Cells Source Type: research

Parallels between Mammalian Mechanisms of Monoallelic Gene Expression
Publication date: Available online 11 September 2018Source: Trends in GeneticsAuthor(s): Ahmed Amine Khamlichi, Robert FeilDifferent 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...
Source: Trends in Genetics - September 12, 2018 Category: Genetics & Stem Cells Source Type: research

Pimp My Ribosome: Ribosomal Protein Paralogs Specify Translational Control
Publication date: Available online 5 September 2018Source: Trends in GeneticsAuthor(s): Jeffrey E. GerstThe 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 rib...
Source: Trends in Genetics - September 6, 2018 Category: Genetics & Stem Cells Source Type: research

Transposons, p53 and Genome Security
Publication date: Available online 5 September 2018Source: Trends in GeneticsAuthor(s): Bhavana Tiwari, Amanda E. Jones, John M. Abramsp53, 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 ex...
Source: Trends in Genetics - September 6, 2018 Category: Genetics & Stem Cells Source Type: research

RNA, Action through Interactions
Publication date: Available online 31 August 2018Source: Trends in GeneticsAuthor(s): Tri C. Nguyen, Kathia Zaleta-Rivera, Xuerui Huang, Xiaofeng Dai, Sheng ZhongAs 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 struct...
Source: Trends in Genetics - September 1, 2018 Category: Genetics & Stem Cells Source Type: research

The Neural Mechanisms of Sexually Dimorphic Aggressive Behaviors
Publication date: Available online 30 August 2018Source: Trends in GeneticsAuthor(s): Koichi Hashikawa, Yoshiko Hashikawa, Julieta Lischinsky, Dayu LinAggression 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 d...
Source: Trends in Genetics - August 31, 2018 Category: Genetics & Stem Cells Source Type: research

Analysis of Epistasis in Natural Traits Using Model Organisms
Publication date: Available online 27 August 2018Source: Trends in GeneticsAuthor(s): Richard F. Campbell, Patrick T. McGrath, Annalise B. PaabyThe 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 gen...
Source: Trends in Genetics - August 28, 2018 Category: Genetics & Stem Cells Source Type: research

Co-expression in Single-Cell Analysis: Saving Grace or Original Sin?
Publication date: Available online 23 August 2018Source: Trends in GeneticsAuthor(s): Megan Crow, Jesse GillisAs 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 fro...
Source: Trends in Genetics - August 24, 2018 Category: Genetics & Stem Cells Source Type: research

Epigenetic Environmental Memories in Plants: Establishment, Maintenance, and Reprogramming
Publication date: Available online 22 August 2018Source: Trends in GeneticsAuthor(s): Yuehui He, Zicong LiPlants 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 enab...
Source: Trends in Genetics - August 23, 2018 Category: Genetics & Stem Cells Source Type: research

Enter the Matrix: Factorization Uncovers Knowledge from Omics
Publication date: Available online 22 August 2018Source: Trends in GeneticsAuthor(s): 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. FertigOmics 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 ...
Source: Trends in Genetics - August 22, 2018 Category: Genetics & Stem Cells Source Type: research

Complex-Trait Prediction in the Era of Big Data
Publication date: Available online 20 August 2018Source: Trends in GeneticsAuthor(s): Gustavo de los Campos, Ana Ines Vazquez, Stephen Hsu, Louis LelloAccurate 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 hun...
Source: Trends in Genetics - August 21, 2018 Category: Genetics & Stem Cells Source Type: research

Giving the Genes a Shuffle: Using Natural Variation to Understand Host Genetic Contributions to Viral Infections
Publication date: Available online 18 August 2018Source: Trends in GeneticsAuthor(s): Sarah R. Leist, Ralph S. BaricThe laboratory mouse has proved an invaluable model to identify host factors that regulate the progression and outcome of virus-induced disease. The paradigm is to use single-gene knockouts in inbred mouse strains or genetic mapping studies using biparental mouse populations. However, genetic variation among these mouse strains is limited compared with the diversity seen in human populations. To address this disconnect, a multiparental mouse population has been developed to specifically dissect the multigenet...
Source: Trends in Genetics - August 18, 2018 Category: Genetics & Stem Cells Source Type: research

Beyond Promoters: How Genes Tweak Their Own Expression
Publication date: Available online 14 August 2018Source: Trends in GeneticsAuthor(s): Tamás Székely, Gábor BalázsiThe correct expression of genes is vital for cells to function. Schikora-Tamarit et al. show that, in addition to obeying their promoters, most genes can modulate their own expression by either buffering or amplification. This could help to avoid costly overexpression of proteins. (Source: Trends in Genetics)
Source: Trends in Genetics - August 15, 2018 Category: Genetics & Stem Cells Source Type: research

Editorial Board and Contents
Publication date: September 2018Source: Trends in Genetics, Volume 34, Issue 9Author(s): (Source: Trends in Genetics)
Source: Trends in Genetics - August 14, 2018 Category: Genetics & Stem Cells Source Type: research

Spermatogenesis and the Evolution of Mammalian Sex Chromosomes
Publication date: Available online 1 August 2018Source: Trends in GeneticsAuthor(s): Erica L. Larson, Emily E.K. Kopania, Jeffrey M. GoodDevelopmental constraint and sexual conflict shape the evolution of heteromorphic sex chromosomes. These contrasting forces are perhaps strongest during spermatogenesis in species with XY males. In this review, we consider how the unique regulatory environment and selective pressures of spermatogenesis interact to impact sex chromosome evolution in mammals. We explore how each developmental phase of spermatogenesis influences sex chromosome gene content, structure, and rate of molecular e...
Source: Trends in Genetics - August 2, 2018 Category: Genetics & Stem Cells Source Type: research

Nimble and Ready to Mingle: Transposon Outbursts of Early Development
Publication date: Available online 26 July 2018Source: Trends in GeneticsAuthor(s): Diego Rodriguez-Terrones, Maria-Elena Torres-PadillaTransposable elements are the largest individual constituent of mammalian genomes. These elements are highly diverse, a consequence of the multiplicity of genomic habitats that they inhabit and of the complex evolutionary histories that they have developed therein. Intriguingly, a surge of transposable element transcription occurs during mammalian preimplantation development, contributing to the establishment of totipotency and pluripotency and to the activation of the embryonic genome. Ho...
Source: Trends in Genetics - July 27, 2018 Category: Genetics & Stem Cells Source Type: research

New and Prospective Roles for lncRNAs in Organelle Formation and Function
Publication date: Available online 17 July 2018Source: Trends in GeneticsAuthor(s): Henry M. KrauseThe observation that long noncoding RNAs (lncRNAs) represent the majority of transcripts in humans has led to a rapid increase in interest and study. Most of this interest has focused on their roles in the nucleus. However, increasing evidence is beginning to reveal even more functions outside the nucleus, and even outside cells. Many of these roles are mediated by newly discovered properties, including the ability of lncRNAs to interact with lipids, membranes, and disordered protein domains, and to form differentially solubl...
Source: Trends in Genetics - July 18, 2018 Category: Genetics & Stem Cells Source Type: research

Strategies to Annotate and Characterize Long Noncoding RNAs: Advantages and Pitfalls
Publication date: Available online 17 July 2018Source: Trends in GeneticsAuthor(s): Huifen Cao, Claes Wahlestedt, Philipp KapranovThe past decade has seen an explosion of interest in long noncoding RNAs (lncRNAs). However, despite the massive volume of scientific data implicating these transcripts in a plethora of molecular and cellular processes, a great deal of controversy surrounds these RNAs. One of the main reasons for this lies in the multiple unique features of lncRNAs which limit the available methods used to characterize them. Combined with their vast numbers and inadequate classification, comprehensive annotation...
Source: Trends in Genetics - July 18, 2018 Category: Genetics & Stem Cells Source Type: research