scholarly journals Endogenous retroviruses drive species-specific germline transcriptomes in mammals

2020 ◽  
Author(s):  
Akihiko Sakashita ◽  
So Maezawa ◽  
Kris G. Alavattam ◽  
Masashi Yukawa ◽  
Artem Barski ◽  
...  
Keyword(s):  
Gene Activation ◽  
Endogenous Retroviruses ◽  
Evolutionary Divergence ◽  
Binding Motifs ◽  
Genome Wide ◽  
Germline Genes ◽  
Human Spermatogenesis ◽  
Species Specific ◽  
Accessible Chromatin

AbstractGene regulation in the germline ensures the production of high-quality gametes, long-term maintenance of the species, and speciation. Germline transcriptomes undergo dynamic changes after the mitosis-to-meiosis transition in males and have been subject to evolutionary divergence among mammals. However, the mechanism that underlies germline regulatory divergence remains undetermined. Here, we show that endogenous retroviruses influence species-specific germline transcriptomes in mammals. We show that the expression of endogenous retroviruses, particularly the evolutionarily young K family (ERVK), is associated with gene activation after the mitosis-to-meiosis transition in male mice. We demonstrate that accessible chromatin and H3K27ac, a marker of active enhancers, are tightly associated with ERVK loci as well as with the activation of neighboring evolutionarily young germline genes. Thus, ERVKs serve as evolutionarily novel enhancers in mouse spermatogenesis. These ERVK loci bear binding motifs for critical regulators of spermatogenesis such as A-MYB. The genome-wide transposition of ERVKs might have rewired germline gene expression in a species-specific manner. Notably, these features are present in human spermatogenesis, but independently evolved ERVs are associated with expression of germline genes, demonstrating the prevalence of ERV-driven mechanisms in mammals. Together, we propose a model whereby species-specific transcriptomes are fine-tuned by endogenous retroviruses in the mammalian germline.

scholarly journals Altered Transcription Factor Binding and Gene Bivalency in Islets of Intrauterine Growth Retarded Rats

Cells ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 1435
Author(s):  
Yu-Chin Lien ◽  
Paul Zhiping Wang ◽  
Xueqing Maggie Lu ◽  
Rebecca A. Simmons
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Transcription Factor Binding ◽  
Binding Motifs ◽  
Factor Binding ◽  
Intrauterine Growth ◽  
Gene Dysregulation ◽  
Genome Wide

Intrauterine growth retardation (IUGR), which induces epigenetic modifications and permanent changes in gene expression, has been associated with the development of type 2 diabetes. Using a rat model of IUGR, we performed ChIP-Seq to identify and map genome-wide histone modifications and gene dysregulation in islets from 2- and 10-week rats. IUGR induced significant changes in the enrichment of H3K4me3, H3K27me3, and H3K27Ac marks in both 2-wk and 10-wk islets, which were correlated with expression changes of multiple genes critical for islet function in IUGR islets. ChIP-Seq analysis showed that IUGR-induced histone mark changes were enriched at critical transcription factor binding motifs, such as C/EBPs, Ets1, Bcl6, Thrb, Ebf1, Sox9, and Mitf. These transcription factors were also identified as top upstream regulators in our previously published transcriptome study. In addition, our ChIP-seq data revealed more than 1000 potential bivalent genes as identified by enrichment of both H3K4me3 and H3K27me3. The poised state of many potential bivalent genes was altered by IUGR, particularly Acod1, Fgf21, Serpina11, Cdh16, Lrrc27, and Lrrc66, key islet genes. Collectively, our findings suggest alterations of histone modification in key transcription factors and genes that may contribute to long-term gene dysregulation and an abnormal islet phenotype in IUGR rats.

scholarly journals Species-specific differences in synaptic transmission and plasticity

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Prateep Beed ◽  
Saikat Ray ◽  
Laura Moreno Velasquez ◽  
Alexander Stumpf ◽  
Daniel Parthier ◽  
...  
Keyword(s):  
Synaptic Plasticity ◽  
Synaptic Transmission ◽  
Mossy Fiber ◽  
Mossy Fibers ◽  
Evolutionary Divergence ◽  
Short Term Plasticity ◽  
Species Specific ◽  
The Brain ◽  
Lower Expression

Abstract Synaptic transmission and plasticity in the hippocampus are integral factors in learning and memory. While there has been intense investigation of these critical mechanisms in the brain of rodents, we lack a broader understanding of the generality of these processes across species. We investigated one of the smallest animals with conserved hippocampal macroanatomy—the Etruscan shrew, and found that while synaptic properties and plasticity in CA1 Schaffer collateral synapses were similar to mice, CA3 mossy fiber synapses showed striking differences in synaptic plasticity between shrews and mice. Shrew mossy fibers have lower long term plasticity compared to mice. Short term plasticity and the expression of a key protein involved in it, synaptotagmin 7 were also markedly lower at the mossy fibers in shrews than in mice. We also observed similar lower expression of synaptotagmin 7 in the mossy fibers of bats that are evolutionarily closer to shrews than mice. Species specific differences in synaptic plasticity and the key molecules regulating it, highlight the evolutionary divergence of neuronal circuit functions.

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

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.

scholarly journals Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Puneet Sharma ◽  
Jie Wu ◽  
Benedikt S. Nilges ◽  
Sebastian A. Leidel
Keyword(s):  
Human Cells ◽  
Ribosome Profiling ◽  
Model Organisms ◽  
Treatment Conditions ◽  
Genome Wide ◽  
Optimized Protocol ◽  
Gene Level ◽  
Translation Inhibitor ◽  
Species Specific ◽  
Conformational Restrictions

AbstractRibosome profiling measures genome-wide translation dynamics at sub-codon resolution. Cycloheximide (CHX), a widely used translation inhibitor to arrest ribosomes in these experiments, has been shown to induce biases in yeast, questioning its use. However, whether such biases are present in datasets of other organisms including humans is unknown. Here we compare different CHX-treatment conditions in human cells and yeast in parallel experiments using an optimized protocol. We find that human ribosomes are not susceptible to conformational restrictions by CHX, nor does it distort gene-level measurements of ribosome occupancy, measured decoding speed or the translational ramp. Furthermore, CHX-induced codon-specific biases on ribosome occupancy are not detectable in human cells or other model organisms. This shows that reported biases of CHX are species-specific and that CHX does not affect the outcome of ribosome profiling experiments in most settings. Our findings provide a solid framework to conduct and analyze ribosome profiling experiments.

scholarly journals A Genome-Wide Scan for Evidence of Selection in a Maize Population Under Long-Term Artificial Selection for Ear Number

Genetics ◽  
2013 ◽  
Vol 196 (3) ◽  
pp. 829-840 ◽  
Author(s):  
Timothy M. Beissinger ◽  
Candice N. Hirsch ◽  
Brieanne Vaillancourt ◽  
Shweta Deshpande ◽  
Kerrie Barry ◽  
...  
Keyword(s):  
Artificial Selection ◽  
Maize Population ◽  
Genome Wide ◽  
A Genome ◽  
Selection For ◽  
Ear Number ◽  
Genome Wide Scan

scholarly journals PGC7 suppresses TET3 for protecting DNA methylation

2013 ◽  
Vol 42 (5) ◽  
pp. 2893-2905 ◽  
Author(s):  
Chunjing Bian ◽  
Xiaochun Yu
Keyword(s):  
Dna Methylation ◽  
Molecular Mechanism ◽  
Biological Process ◽  
Cpg Islands ◽  
Binding Motifs ◽  
Genome Wide Analysis ◽  
Dna Motif ◽  
Genome Wide

Abstract Ten-eleven translocation (TET) family enzymes convert 5-methylcytosine to 5-hydroxylmethylcytosine. However, the molecular mechanism that regulates this biological process is not clear. Here, we show the evidence that PGC7 (also known as Dppa3 or Stella) interacts with TET2 and TET3 both in vitro and in vivo to suppress the enzymatic activity of TET2 and TET3. Moreover, lacking PGC7 induces the loss of DNA methylation at imprinting loci. Genome-wide analysis of PGC7 reveals a consensus DNA motif that is recognized by PGC7. The CpG islands surrounding the PGC7-binding motifs are hypermethylated. Taken together, our study demonstrates a molecular mechanism by which PGC7 protects DNA methylation from TET family enzyme-dependent oxidation.

Abstract 62: Molecular Basis of Regulatory Variation at Coronary Heart Disease-Associated Loci

2015 ◽  
Vol 35 (suppl_1) ◽  
Author(s):  
Clint L Miller ◽  
Milos Pjanic ◽  
Jonathan D Lee ◽  
Boxiang Liu ◽  
William J Greenleaf ◽  
...  
Keyword(s):  
Coronary Heart Disease ◽  
Heart Disease ◽  
Chromatin Immunoprecipitation ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Regulatory Mechanisms ◽  
Tgf Beta ◽  
Genome Wide ◽  
Context Specific ◽  
Accessible Chromatin

Genome-wide association studies have identified 46 replicated genetic loci for coronary heart disease (CHD), and 104 loci associated at a 5% false discovery rate. However, the regulatory mechanisms of these associations largely remain elusive. Given that the majority of these CHD-associated loci reside in non-coding regions, they are predicted to function via context-specific gene regulation. Recent high-throughput assays of regulatory function include the assay for transposase-accessible chromatin using sequencing (ATAC-seq) and chromatin immunoprecipitation-sequencing (ChIP-seq). ATAC-seq utilizes a Tn5 transposase to fragment and tag accessible DNA sequences, which are often coupled to transcription factor occupancy identified by ChIP-seq. Importantly, this assay may reveal the spatio-temporal regulatory profiles in limited numbers of primary cells. Using ATAC-seq in human coronary artery smooth muscle cells (HCASMC) we identified 147,173 accessible chromatin peaks in control versus 198,976 peaks in TGF-beta-stimulated cells (136,446 shared peaks). Using de novo motif enrichment analysis we identified significant enrichment of specific AP-1 family members (29.2% vs. 5.1% background), chromatin remodeling, and SMC differentiation transcription factors. Using functional enrichment analysis of ChIP-seq and CHD-overlapping regions we observed enrichment of the hypoxia inducible factor 1 (HIF-1) and TGF-beta signaling pathways (1.5x10 -22 and 5.6x10 -18 , respectively) and relevant phenotypes, including cell migration and blood vessel morphology. Finally, we utilized these regulatory maps to explore the causal mechanisms underlying CHD-associated variants at four loci using haplotype-specific chromatin immunoprecipitation (haploChIP) and luciferase reporter assays. Taken together, these results suggest that genome-wide approaches such as ATAC-seq can be leveraged to map context-specific regulatory mechanisms of non-coding variants associated with complex diseases such as CHD, and reveal new biological and molecular insights into targeting heritable disease risk.

scholarly journals Loss of Heterozygosity and Base Mutation Rates Vary Among Saccharomyces cerevisiae Hybrid Strains

2020 ◽  
Vol 10 (9) ◽  
pp. 3309-3319 ◽  
Author(s):  
Ajith V Pankajam ◽  
Suman Dash ◽  
Asma Saifudeen ◽  
Abhishek Dutta ◽  
Koodali T Nishant
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Loss Of Heterozygosity ◽  
Mutation Rates ◽  
Single Nucleotide ◽  
Single Nucleotide Mutation ◽  
Genome Wide ◽  
Nucleotide Mutation ◽  
Specific Variation ◽  
Chromosomal Changes ◽  
Species Specific

Abstract A growing body of evidence suggests that mutation rates exhibit intra-species specific variation. We estimated genome-wide loss of heterozygosity (LOH), gross chromosomal changes, and single nucleotide mutation rates to determine intra-species specific differences in hybrid and homozygous strains of Saccharomyces cerevisiae. The mutation accumulation lines of the S. cerevisiae hybrid backgrounds - S288c/YJM789 (S/Y) and S288c/RM11-1a (S/R) were analyzed along with the homozygous diploids RM11, S288c, and YJM145. LOH was extensive in both S/Y and S/R hybrid backgrounds. The S/Y background also showed longer LOH tracts, gross chromosomal changes, and aneuploidy. Short copy number aberrations were observed in the S/R background. LOH data from the S/Y and S/R hybrids were used to construct a LOH map for S288c to identify hotspots. Further, we observe up to a sixfold difference in single nucleotide mutation rates among the S. cerevisiae S/Y and S/R genetic backgrounds. Our results demonstrate LOH is common during mitotic divisions in S. cerevisiae hybrids and also highlight genome-wide differences in LOH patterns and rates of single nucleotide mutations between commonly used S. cerevisiae hybrid genetic backgrounds.

Sign in / Sign up

Export Citation Format

Share Document