Expansion of LINEs and species-specific DNA repeats drives genome expansion in Asian Gypsy Moths

Abstract Two subspecies of Asian gypsy moth (AGM), Lymantria dispar asiatica and L. dispar japonica, pose a serious alien invasive threat to North American forests. Despite decades of research on the ecology and biology of this pest, limited AGM-specific genomic resources are currently available. Here, we report on the genome sequences and functional content of these AGM subspecies. The genomes of L.d. asiatica and L.d. japonica are the largest lepidopteran genomes sequenced to date, totaling 921 and 999 megabases, respectively. Large genome size in these subspecies is driven by the accumulation of specific classes of repeats. Genome-wide metabolic pathway reconstructions suggest strong genomic signatures of energy-related pathways in both subspecies, dominated by metabolic functions related to thermogenesis. The genome sequences reported here will provide tools for probing the molecular mechanisms underlying phenotypic traits that are thought to enhance AGM invasiveness.

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Alu-mediated weak CEBPA binding and slow B cell transdifferentiation in human

10.1101/2021.10.28.466072 ◽

2021 ◽

Author(s):

Ramil Nurtdinov ◽

Maria Sanz ◽

Amaya Abad ◽

Alexandre Esteban ◽

Sebastian Ullrich ◽

...

Keyword(s):

Molecular Mechanisms ◽

Biological Information ◽

Genome Sequences ◽

Binding Motifs ◽

Alu Repeats ◽

Natural Processes ◽

Cell Transdifferentiation ◽

Genome Wide ◽

Alu Repeat ◽

Species Specific

Many developmental and differentiation processes take substantially longer in human than in mouse. To investigate the molecular mechanisms underlying this phenomenon, here we have specifically focused on the transdifferentiation from B cells to macrophages. The process is triggered by exactly the same molecular mechanism -- the induction by the transcription factor (TF) CEBPA -- but takes three days in mouse and seven in human. In mouse, the speed of this process is known to be associated with Myc expression. We found that in this species, CEBPA binds strongly to the Myc promoter, efficiently down-regulating Myc. In human, in contrast, CEBPA does not bind this promoter, and MYC is indirectly and more slowly down-regulated. Attenuation of CEBPA binding is not specific to the MYC promoter, but a general trait of the human genome across multiple biological conditions. We traced back weak CEBPA binding to the primate-specific Alu repeat expansion. Many Alu repeats carry strong CEBPA binding motifs, which sequester CEBPA, and attenuate CEBPA binding genome-wide. We observed similar CEBPA and MYC dynamics in natural processes regulated by CEBPA, suggesting that CEBPA attenuation could underlie the longer duration in human processes controlled by this factor. Our work highlights the highly complex mode in which biological information is encoded in genome sequences, evolutionarily connecting, in an unexpected way, lineage-specific transposable element expansions to species-specific changes in developmental tempos.

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Genome-Wide Analysis of Protein Family Diversity Provides Insights into Species-Specific Protein Family Expansions in Insects

10.21203/rs.3.rs-864773/v1 ◽

2021 ◽

Author(s):

Mehmet DAYI

Keyword(s):

Copy Number ◽

Molecular Mechanisms ◽

Specific Protein ◽

Protein Family ◽

Insect Species ◽

Protein Families ◽

Family Diversity ◽

Genome Wide ◽

Wide Range ◽

Species Specific

Abstract Insects are one of the earliest land animals with more than 400 million years old history on Earth, and they compose more than 80% of species. Insects invade a wide range of ecosystems and are considered one of the most evolutionary successful organism groups. Today, many insect species’ genomes have been sequenced to encode molecular mechanisms behind this magnificent evolutionary plasticity. However, only limited genome-wide studies have been carried out to compare protein family diversity in insects. A total of 20 insect species belonging to seven insect orders and two morphogenesis groups were investigated for evolutionary relationships and to uncover protein family diversity in the present study. The phylogenetic analysis inferred from a total of 530 one-to-one single-copy ortholog genes were separated insects into two evolutionary clades based on morphogenesis. Protein family analyses showed that insects share core protein families that perform essential tasks in development and metabolic processes, such as Pkinase and Zinc Finger, cellular signaling and odorant perception (7tm), digestion of food molecules (Trypsin), and detoxification (p450) with copy number expansion compared to other protein families. Additionally, species-specific protein family expansion was observed in various protein families. This study provided insights into protein family diversity and variation among insects and highlights high copy number variation in protein families species-wide.

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Genome evolution in trypanosomatid parasites

Parasitology ◽

10.1017/s0031182014000894 ◽

2014 ◽

Vol 142 (S1) ◽

pp. S40-S56 ◽

Cited By ~ 39

Author(s):

ANDREW P. JACKSON

Keyword(s):

Comparative Genomics ◽

Genome Evolution ◽

Genome Sequencing ◽

Molecular Mechanisms ◽

Genome Sequences ◽

Parasitic Lifestyle ◽

Trypanosomatid Parasites ◽

The Many ◽

Species Specific ◽

Fresh Impetus

SUMMARYA decade of genome sequencing has transformed our understanding of how trypanosomatid parasites have evolved and provided fresh impetus to explaining the origins of parasitism in the Kinetoplastida. In this review, I will consider the many ways in which genome sequences have influenced our view of genomic reduction in trypanosomatids; how species-specific genes, and the genomic domains they occupy, have illuminated the innovations in trypanosomatid genomes; and how comparative genomics has exposed the molecular mechanisms responsible for innovation and adaptation to a parasitic lifestyle.

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Faculty Opinions recommendation of Genome-wide detection of tandem DNA repeats that are expanded in autism.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.738385928.793577268 ◽

2020 ◽

Author(s):

Branko Aleksic

Keyword(s):

Dna Repeats ◽

Genome Wide

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Artificial Intelligence for epigenetics: towards personalized medicine

Current Medicinal Chemistry ◽

10.2174/0929867327666201117142006 ◽

2020 ◽

Vol 27 ◽

Author(s):

Giulia De Riso ◽

Sergio Cocozza

Keyword(s):

Biological Sciences ◽

Artificial Intelligence ◽

Personalized Medicine ◽

Molecular Mechanisms ◽

Genomic Sequence ◽

Health Care Interventions ◽

Genome Wide ◽

Genetic And Environmental Factors ◽

Opening Up ◽

Omic Data

: Epigenetics is a field of biological sciences focused on the study of reversible, heritable changes in gene function not due to modifications of the genomic sequence. These changes are the result of a complex cross-talk between several molecular mechanisms, that is in turn orchestrated by genetic and environmental factors. The epigenetic profile captures the unique regulatory landscape and the exposure to environmental stimuli of an individual. It thus constitutes a valuable reservoir of information for personalized medicine, which is aimed at customizing health-care interventions based on the unique characteristics of each individual. Nowadays, the complex milieu of epigenomic marks can be studied at the genome-wide level thanks to massive, highthroughput technologies. This new experimental approach is opening up new and interesting knowledge perspectives. However, the analysis of these complex omic data requires to face important analytic issues. Artificial Intelligence, and in particular Machine Learning, are emerging as powerful resources to decipher epigenomic data. In this review, we will first describe the most used ML approaches in epigenomics. We then will recapitulate some of the recent applications of ML to epigenomic analysis. Finally, we will provide some examples of how the ML approach to epigenetic data can be useful for personalized medicine.

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Genetic analysis of amyotrophic lateral sclerosis identifies contributing pathways and cell types

Science Advances ◽

10.1126/sciadv.abd9036 ◽

2021 ◽

Vol 7 (3) ◽

pp. eabd9036

Author(s):

Sara Saez-Atienzar ◽

Sara Bandres-Ciga ◽

Rebekah G. Langston ◽

Jonggeol J. Kim ◽

Shing Wan Choi ◽

...

Keyword(s):

Amyotrophic Lateral Sclerosis ◽

Membrane Trafficking ◽

Molecular Mechanisms ◽

Cell Types ◽

Polygenic Risk Score ◽

Genome Wide ◽

Genome Wide Data ◽

Data Driven Approach ◽

Single Nucleus ◽

Lateral Sclerosis

Despite the considerable progress in unraveling the genetic causes of amyotrophic lateral sclerosis (ALS), we do not fully understand the molecular mechanisms underlying the disease. We analyzed genome-wide data involving 78,500 individuals using a polygenic risk score approach to identify the biological pathways and cell types involved in ALS. This data-driven approach identified multiple aspects of the biology underlying the disease that resolved into broader themes, namely, neuron projection morphogenesis, membrane trafficking, and signal transduction mediated by ribonucleotides. We also found that genomic risk in ALS maps consistently to GABAergic interneurons and oligodendrocytes, as confirmed in human single-nucleus RNA-seq data. Using two-sample Mendelian randomization, we nominated six differentially expressed genes (ATG16L2, ACSL5, MAP1LC3A, MAPKAPK3, PLXNB2, and SCFD1) within the significant pathways as relevant to ALS. We conclude that the disparate genetic etiologies of this fatal neurological disease converge on a smaller number of final common pathways and cell types.

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Genome-Wide Mapping of Histone H3 Lysine 4 Trimethylation (H3K4me3) and Its Involvement in Fatty Acid Biosynthesis in Sunflower Developing Seeds

Plants ◽

10.3390/plants10040706 ◽

2021 ◽

Vol 10 (4) ◽

pp. 706

Author(s):

Antonio J. Moreno-Pérez ◽

Raquel Martins-Noguerol ◽

Cristina DeAndrés-Gil ◽

Mónica Venegas-Calerón ◽

Rosario Sánchez ◽

...

Keyword(s):

Fatty Acid ◽

Chromatin Remodeling ◽

Molecular Mechanisms ◽

Acid Metabolism ◽

Fatty Acid Biosynthesis ◽

Acid Synthesis ◽

Sunflower Seeds ◽

Acid Biosynthesis ◽

Functional Regions ◽

Genome Wide

Histone modifications are of paramount importance during plant development. Investigating chromatin remodeling in developing oilseeds sheds light on the molecular mechanisms controlling fatty acid metabolism and facilitates the identification of new functional regions in oil crop genomes. The present study characterizes the epigenetic modifications H3K4me3 in relationship with the expression of fatty acid-related genes and transcription factors in developing sunflower seeds. Two master transcriptional regulators identified in this analysis, VIV1 (homologous to Arabidopsis ABI3) and FUS3, cooperate in the regulation of WRINKLED 1, a transcriptional factor regulating glycolysis, and fatty acid synthesis in developing oilseeds.

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Genome-wide association study suggests that variation at the RCOR1 locus is associated with tinnitus in UK Biobank

Scientific Reports ◽

10.1038/s41598-021-85871-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Helena R. R. Wells ◽

Fatin N. Zainul Abidin ◽

Maxim B. Freidin ◽

Frances M. K. Williams ◽

Sally J. Dawson

Keyword(s):

Association Study ◽

Molecular Mechanisms ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Uk Biobank ◽

Significance Threshold ◽

Genome Wide ◽

Final Sample ◽

Close Proximity ◽

Repressor Complex

AbstractTinnitus is a prevalent condition in which perception of sound occurs without an external stimulus. It is often associated with pre-existing hearing loss or noise-induced damage to the auditory system. In some individuals it occurs frequently or even continuously and leads to considerable distress and difficulty sleeping. There is little knowledge of the molecular mechanisms involved in tinnitus which has hindered the development of treatments. Evidence suggests that tinnitus has a heritable component although previous genetic studies have not established specific risk factors. From a total of 172,608 UK Biobank participants who answered questions on tinnitus we performed a case–control genome-wide association study for self-reported tinnitus. Final sample size used in association analysis was N = 91,424. Three variants in close proximity to the RCOR1 gene reached genome wide significance: rs4906228 (p = 1.7E−08), rs4900545 (p = 1.8E−08) and 14:103042287_CT_C (p = 3.50E−08). RCOR1 encodes REST Corepressor 1, a component of a co-repressor complex involved in repressing neuronal gene expression in non-neuronal cells. Eleven other independent genetic loci reached a suggestive significance threshold of p < 1E−06.

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Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities

FEMS Microbiology Ecology ◽

10.1093/femsec/fiab017 ◽

2021 ◽

Vol 97 (3) ◽

Author(s):

Constantinos Xenophontos ◽

Martin Taubert ◽

W Stanley Harpole ◽

Kirsten Küsel

Keyword(s):

Bacterial Communities ◽

Species Interactions ◽

Phylogenetic Diversity ◽

Molecular Mechanisms ◽

Linear Models ◽

Theory Development ◽

Metabolic Diversity ◽

Community Functioning ◽

Metabolic Functions ◽

Independent Effects

ABSTRACT Quantifying the relative contributions of microbial species to ecosystem functioning is challenging, because of the distinct mechanisms associated with microbial phylogenetic and metabolic diversity. We constructed bacterial communities with different diversity traits and employed exoenzyme activities (EEAs) and carbon acquisition potential (CAP) from substrates as proxies of bacterial functioning to test the independent effects of these two aspects of biodiversity. We expected that metabolic diversity, but not phylogenetic diversity would be associated with greater ecological function. Phylogenetically relatedness should intensify species interactions and coexistence, therefore amplifying the influence of metabolic diversity. We examined the effects of each diversity treatment using linear models, while controlling for the other, and found that phylogenetic diversity strongly influenced community functioning, positively and negatively. Metabolic diversity, however, exhibited negative or non-significant relationships with community functioning. When controlling for different substrates, EEAs increased along with phylogenetic diversity but decreased with metabolic diversity. The strength of diversity effects was related to substrate chemistry and the molecular mechanisms associated with each substrate's degradation. EEAs of phylogenetically similar groups were strongly affected by within-genus interactions. These results highlight the unique flexibility of microbial metabolic functions that must be considered in further ecological theory development.

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