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Trends in Genetics: TIG

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https://www.readbyqxmd.com/read/28732599/evolutionary-dynamics-of-unreduced-gametes
#1
REVIEW
Julia M Kreiner, Paul Kron, Brian C Husband
Unreduced gametes, which have the somatic (2n) chromosome number, are an important precursor to polyploid formation and apomixis. The product of irregularities in meiosis, 2n gametes are expected to be rare and deleterious in most natural populations, contrary to their wide taxonomic distribution and the prevalence of polyploidy. To better understand this discrepancy, we review contemporary evidence related to four aspects of 2n gamete dynamics in natural populations: (i) estimates of their frequency; (ii) their environmental and genetic determinants; (iii) adaptive and nonadaptive processes regulating their evolution; and (iv) factors regulating their union and production of polyploids in diploid populations...
July 18, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28732598/high-throughput-imaging-for-the-discovery-of-cellular-mechanisms-of-disease
#2
REVIEW
Gianluca Pegoraro, Tom Misteli
High-throughput imaging (HTI) is a powerful tool in the discovery of cellular disease mechanisms. While traditional approaches to identify disease pathways often rely on knowledge of the causative genetic defect, HTI-based screens offer an unbiased discovery approach based on any morphological or functional defects of disease cells or tissues. In this review, we provide an overview of the use of HTI for the study of human disease mechanisms. We discuss key technical aspects of HTI and highlight representative examples of its practical applications for the discovery of molecular mechanisms of disease, focusing on infectious diseases and host-pathogen interactions, cancer, and rare genetic diseases...
July 18, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28720483/left-right-patterning-breaking-symmetry-to-asymmetric-morphogenesis
#3
REVIEW
Daniel T Grimes, Rebecca D Burdine
Vertebrates exhibit striking left-right (L-R) asymmetries in the structure and position of the internal organs. Symmetry is broken by motile cilia-generated asymmetric fluid flow, resulting in a signaling cascade - the Nodal-Pitx2 pathway - being robustly established within mesodermal tissue on the left side only. This pathway impinges upon various organ primordia to instruct their side-specific development. Recently, progress has been made in understanding both the breaking of embryonic L-R symmetry and how the Nodal-Pitx2 pathway controls lateralized cell differentiation, migration, and other aspects of cell behavior, as well as tissue-level mechanisms, that drive asymmetries in organ formation...
July 15, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28720482/time-to-go-bigger-emerging-patterns-in-macrogenetics
#4
Simon Blanchet, Jérôme G Prunier, Hanne De Kort
The increasing availability of large-scale and high-resolution data sets in population genetics is moving the field toward a novel research agenda. Here, we show how this shift toward macrogenetics should generate new perspectives and theories allowing the description, understanding, and prediction of patterns of genetic diversity at broad spatial, temporal, and taxonomic scales.
July 15, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28697848/roles-of-rnase-p-and-its-subunits
#5
REVIEW
Nayef Jarrous
Recent studies show that nuclear RNase P is linked to chromatin structure and function. Thus, variants of this ribonucleoprotein (RNP) complex bind to chromatin of small noncoding RNA genes; integrate into initiation complexes of RNA polymerase (Pol) III; repress histone H3.3 nucleosome deposition; control tRNA and PIWI-interacting RNA (piRNA) gene clusters for genome defense; and respond to Werner syndrome helicase (WRN)-related replication stress and DNA double-strand breaks (DSBs). Likewise, the related RNase MRP and RMRP-TERT (telomerase reverse transcriptase) are implicated in RNA-dependent RNA polymerization for chromatin silencing, whereas the telomerase carries out RNA-dependent DNA polymerization for telomere lengthening...
July 8, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28693826/genome-wide-mapping-of-the-nucleosome-landscape-by-micrococcal-nuclease-and-chemical-mapping
#6
REVIEW
Lilien N Voong, Liqun Xi, Ji-Ping Wang, Xiaozhong Wang
Nucleosomes regulate the transcription output of the genome by occluding the underlying DNA sequences from DNA-binding proteins that must act on it. Knowledge of the precise locations of nucleosomes in the genome is thus essential towards understanding how transcription is regulated. Current nucleosome-mapping strategies involve digesting chromatin with nucleases or chemical cleavage followed by high-throughput sequencing. In this review, we compare the traditional micrococcal nuclease (MNase)-based approach with a chemical cleavage strategy, with discussion on the important insights each has uncovered about the role of nucleosomes in shaping transcriptional processes...
July 7, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28688671/mining-metagenomic-data-sets-for-ancient-dna-recommended-protocols-for-authentication
#7
REVIEW
Felix M Key, Cosimo Posth, Johannes Krause, Alexander Herbig, Kirsten I Bos
While a comparatively young area of research, investigations relying on ancient DNA data have been highly valuable in revealing snapshots of genetic variation in both the recent and the not-so-recent past. Born out of a tradition of single-locus PCR-based approaches that often target individual species, stringent criteria for both data acquisition and analysis were introduced early to establish high standards of data quality. Today, the immense volume of data made available through next-generation sequencing has significantly increased the analytical resolution offered by processing ancient tissues and permits parallel analyses of host and microbial communities...
July 5, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28669576/histone-h2a-monoubiquitination-in-neurodevelopmental-disorders
#8
REVIEW
Anshika Srivastava, Brian McGrath, Stephanie L Bielas
Covalent histone modifications play an essential role in gene regulation and cellular specification required for multicellular organism development. Monoubiquitination of histone H2A (H2AUb1) is a reversible transcriptionally repressive mark. Exchange of histone H2A monoubiquitination and deubiquitination reflects the succession of transcriptional profiles during development required to produce cellular diversity from pluripotent cells. Germ-line pathogenic variants in components of the H2AUb1 regulatory axis are being identified as the genetic basis of congenital neurodevelopmental disorders...
June 29, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28668385/driving-to-cancer-on-a-four-lane-expressway
#9
Lorenzo Galluzzi, Ilio Vitale
Recent findings from a prospective clinical study involving multiregion whole-exome sequencing suggest that driver mutations in cancer-relevant genes including EGFR and TP53 are often clonal and precede whole-genome duplication events in early lung carcinogenesis. This paves an expressway to extensive subclonal diversification, elevated intratumoral heterogeneity, and dismal disease outcome.
June 28, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28648452/advances-in-decoding-axolotl-limb-regeneration
#10
REVIEW
Brian J Haas, Jessica L Whited
Humans and other mammals are limited in their natural abilities to regenerate lost body parts. By contrast, many salamanders are highly regenerative and can spontaneously replace lost limbs even as adults. Because salamander limbs are anatomically similar to human limbs, knowing how they regenerate should provide important clues for regenerative medicine. Although interest in understanding the mechanics of this process has never wavered, until recently researchers have been vexed by seemingly impenetrable logistics of working with these creatures at a molecular level...
June 22, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28633980/the-genes-that-make-a-good-parent
#11
Reinmar Hager
What is the genetic basis of differences in parental care between promiscuous and monogamous mammal species? A team led by Hopi Hoekstra studied an intercross between deer mice and old-field mice that differ in their mating systems and parental behaviours. The authors discovered 12 genomic regions contributing to those differences and identified vasopressin as a regulator of nestbuilding behaviour.
June 17, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28629950/antibiotic-independent-adaptive-effects-of-antibiotic-resistance-mutations
#12
REVIEW
Ruth Hershberg
Antibiotic usage selects for the accumulation and spread of antibiotic-resistant bacteria. However, resistance can also accumulate in the absence of antibiotic exposure. Antibiotics are often designed to target widely distributed regulatory housekeeping genes. The targeting of such genes enables these antibiotics to be useful against a wider variety of pathogens. This review highlights work suggesting that regulatory housekeeping genes of the type targeted by many antibiotics function as hubs of adaptation to conditions unrelated to antibiotic exposure...
June 16, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28629949/the-diversity-of-long-noncoding-rnas-and-their-generation
#13
REVIEW
Huang Wu, Li Yang, Ling-Ling Chen
Long noncoding RNAs (lncRNAs) are emerging as potential key regulators in gene expression networks and exhibit a surprising range of shapes and sizes. Several distinct classes of lncRNAs are transcribed from different DNA elements, including promoters, enhancers, and intergenic regions in eukaryotic genomes. Additionally, others are derived from long primary transcripts with noncanonical RNA processing pathways, generating new RNA species with unexpected formats. These lncRNAs can be processed by several mechanisms, including ribonuclease P (RNase P) cleavage to generate mature 3' ends, capping by small nucleolar RNA (snoRNA)-protein (snoRNP) complexes at their ends, or the formation of circular structures...
June 16, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28545962/a-fundamental-unit-of-cell-size-in-bacteria
#14
Suckjoon Jun, Michael J Rust
A new study clarifies a relationship between growth, gene expression, and cell size in cyanobacteria. Quite unexpectedly, cyanobacteria and Escherichia coli appear to share an invariance principle to coordinate growth and chromosome replication. This principle allows quantitative predictions of cell size across a range of growth conditions in both organisms.
May 22, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28535931/the-dimensions-dynamics-and-relevance-of-the-mammalian-noncoding-transcriptome
#15
REVIEW
Ira W Deveson, Simon A Hardwick, Tim R Mercer, John S Mattick
The combination of pervasive transcription and prolific alternative splicing produces a mammalian transcriptome of great breadth and diversity. The majority of transcribed genomic bases are intronic, antisense, or intergenic to protein-coding genes, yielding a plethora of short and long non-protein-coding regulatory RNAs. Long noncoding RNAs (lncRNAs) share most aspects of their biogenesis, processing, and regulation with mRNAs. However, lncRNAs are typically expressed in more restricted patterns, frequently from enhancers, and exhibit almost universal alternative splicing...
May 20, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28528721/perspectives-on-gene-regulatory-network-evolution
#16
REVIEW
Marc S Halfon
Animal development proceeds through the activity of genes and their cis-regulatory modules (CRMs) working together in sets of gene regulatory networks (GRNs). The emergence of species-specific traits and novel structures results from evolutionary changes in GRNs. Recent work in a wide variety of animal models, and particularly in insects, has started to reveal the modes and mechanisms of GRN evolution. I discuss here various aspects of GRN evolution and argue that developmental system drift (DSD), in which conserved phenotype is nevertheless a result of changed genetic interactions, should regularly be viewed from the perspective of GRN evolution...
May 18, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28506494/sociomics-using-omic-approaches-to-understand-social-evolution
#17
REVIEW
Melanie Ghoul, Sandra B Andersen, Stuart A West
All of life is social, from genes cooperating to form organisms, to animals cooperating to form societies. Omic approaches offer exceptional opportunities to solve major outstanding problems in the study of how sociality evolves. First, omics can be used to clarify the extent and form of sociality in natural populations. This is especially useful in species where it is difficult to study social traits in natural populations, such as bacteria and other microbes. Second, omics can be used to examine the consequences of sociality for genome evolution and gene expression...
May 12, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28647055/uncovering-gene-regulatory-networks-controlling-plant-cell-differentiation
#18
REVIEW
Colleen Drapek, Erin E Sparks, Philip N Benfey
The development of multicellular organisms relies on the precise regulation of cellular differentiation. As such, there has been significant effort invested to understand the process through which an immature cell undergoes differentiation. In this review, we highlight key discoveries and advances that have contributed to our understanding of the transcriptional networks underlying Arabidopsis root endodermal differentiation. To conclude, we propose perspectives on how advances in molecular biology, microscopy, and nucleotide sequencing will provide the tools to test the biological significance of these gene regulatory networks (GRN)...
August 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28532625/v-d-j-recombination-exploits-dna-damage-responses-to-promote-immunity
#19
REVIEW
Rahul Arya, Craig H Bassing
It has been recognized for 40 years that the variable (diversity) joining [V(D)J] recombination-mediated assembly of diverse B and T lymphocyte antigen receptor (AgR) genes is not only essential for adaptive immunity, but also a risk for autoimmunity and lymphoid malignancies. Over the past few years, several studies have revealed that recombination-activating gene (RAG) endonuclease-induced DNA double-strand breaks (DSBs) transcend hazardous intermediates during antigen receptor gene assembly. RAG cleavage within the genomes of lymphocyte progenitors and immature lymphocytes regulates the expression of ubiquitous and lymphocyte-specific gene transcripts to control the differentiation and function of both adaptive and innate immune cell lineages...
July 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28457629/mosaicism-in-preimplantation-human-embryos-when-chromosomal-abnormalities-are-the-norm
#20
REVIEW
Rajiv C McCoy
Along with errors in meiosis, mitotic errors during post-zygotic cell division contribute to pervasive aneuploidy in human embryos. Relatively little is known, however, about the genesis of these errors or their fitness consequences. Rapid technological advances are helping to close this gap, revealing diverse molecular mechanisms contributing to mitotic error. These include altered cell cycle checkpoints, aberrations of the centrosome, and failed chromatid cohesion, mirroring findings from cancer biology. Recent studies are challenging the idea that mitotic error is abnormal, emphasizing that the fitness impacts of mosaicism depend on its scope and severity...
July 2017: Trends in Genetics: TIG
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