scholarly journals An ancestral genomic sequence that serves as a nucleation site for de novo gene birth

2022 ◽  
Author(s):  
Nicholas Delihas
Keyword(s):  
De Novo ◽  
Developmental Process ◽  
Genomic Sequence ◽  
Primate Evolution ◽  
Nucleation Site ◽  
Intergenic Sequence ◽  
Trial And Error ◽  
Papio Anubis ◽  
Gamma Glutamyltransferase ◽  
De Novo Gene

A short non-coding sequence present between the gamma-glutamyltransferase 1 (GGT1) and gamma-glutamyltransferase 5 (GGT5) genes, termed a spacer sequence has been detected in the genomes of Mus musculus, the house mouse and in Philippine tarsier, a primitive ancestral primate. It is highly conserved during primate evolution with certain sequences being totally invariant from mouse to humans. Evidence is presented to show this intergenic sequence serves as a nucleation site for the initiation of diverse genes. We also outline the birth of the human lincRNA gene BCRP3 (BCR activator of RhoGEF and GTPase 3 pseudogene) during primate evolution. The gene developmental process involves sequence initiation, addition of a complex of tandem transposable elements and addition of a segment of another gene. The sequence, initially formed in the Old World Monkeys such as the Rhesus monkey (Macaca mulatta) and the baboon (Papio anubis), develops into different primate genes before evolving into the human BCRP3 gene; it appears to also include trial and error during sequence/gene formation. The protein gene, GGT5 may have also formed by spacer sequence initiation in an ancient ancestor such as zebrafish, but spacer and GGT5 gene sequence drift during evolution produced a divergence that precludes further assessment.

scholarly journals Functional cysteine-less subunits of the transporter associated with antigen processing (TAP1 and TAP2) by de novo gene assembly

FEBS Letters ◽  
2002 ◽  
Vol 533 (1) ◽  
pp. 42-46 ◽  
Author(s):  
Susanne Heintke ◽  
Min Chen ◽  
Ulrike Ritz ◽  
Brigitte Lankat-Buttgereit ◽  
Joachim Koch ◽  
...  
Keyword(s):  
Antigen Processing ◽  
De Novo ◽  
Gene Assembly ◽  
De Novo Gene

scholarly journals De Novo Sequencing, Assembly, and Annotation of Four Threespine Stickleback Genomes Based on Microfluidic Partitioned DNA Libraries

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 426 ◽  
Author(s):  
Daniel Berner ◽  
Marius Roesti ◽  
Steven Bilobram ◽  
Simon K. Chan ◽  
Heather Kirk ◽  
...  
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Gene Annotation ◽  
Model System ◽  
Threespine Stickleback ◽  
Evolutionary Genomics ◽  
Digital Repository ◽  
High Quality ◽  
De Novo Gene ◽  
Dna Libraries

The threespine stickleback is a geographically widespread and ecologically highly diverse fish that has emerged as a powerful model system for evolutionary genomics and developmental biology. Investigations in this species currently rely on a single high-quality reference genome, but would benefit from the availability of additional, independently sequenced and assembled genomes. We present here the assembly of four new stickleback genomes, based on the sequencing of microfluidic partitioned DNA libraries. The base pair lengths of the four genomes reach 92–101% of the standard reference genome length. Together with their de novo gene annotation, these assemblies offer a resource enhancing genomic investigations in stickleback. The genomes and their annotations are available from the Dryad Digital Repository (https://doi.org/10.5061/dryad.113j3h7).

scholarly journals De novo gene conversion in the RCA gene cluster (1q32) causes mutations in complement factor H associated with atypical hemolytic uremic syndrome

2006 ◽  
Vol 27 (3) ◽  
pp. 292-293 ◽  
Author(s):  
Stefan Heinen ◽  
Pilar Sanchez-Corral ◽  
Michael S Jackson ◽  
Lisa Strain ◽  
Judith A. Goodship ◽  
...  
Keyword(s):  
Hemolytic Uremic Syndrome ◽  
Gene Conversion ◽  
Gene Cluster ◽  
De Novo ◽  
Atypical Hemolytic Uremic Syndrome ◽  
Factor H ◽  
Complement Factor H ◽  
Complement Factor ◽  
De Novo Gene ◽  
Uremic Syndrome

scholarly journals Contribution of retrotransposition to developmental disorders

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Eugene J. Gardner ◽  
Elena Prigmore ◽  
Giuseppe Gallone ◽  
Petr Danecek ◽  
Kaitlin E. Samocha ◽  
...  
Keyword(s):  
Developmental Disorders ◽  
De Novo ◽  
Purifying Selection ◽  
Selective Constraint ◽  
Protein Coding ◽  
Genome Wide ◽  
De Novo Gene ◽  
The Impact ◽  
Transcribed Sequences

Abstract Mobile genetic Elements (MEs) are segments of DNA which can copy themselves and other transcribed sequences through the process of retrotransposition (RT). In humans several disorders have been attributed to RT, but the role of RT in severe developmental disorders (DD) has not yet been explored. Here we identify RT-derived events in 9738 exome sequenced trios with DD-affected probands. We ascertain 9 de novo MEs, 4 of which are likely causative of the patient’s symptoms (0.04%), as well as 2 de novo gene retroduplications. Beyond identifying likely diagnostic RT events, we estimate genome-wide germline ME mutation rate and selective constraint and demonstrate that coding RT events have signatures of purifying selection equivalent to those of truncating mutations. Overall, our analysis represents a comprehensive interrogation of the impact of retrotransposition on protein coding genes and a framework for future evolutionary and disease studies.

Platelet microparticles reprogram macrophage gene expression and function

2016 ◽  
Vol 115 (02) ◽  
pp. 311-323 ◽  
Author(s):  
Matthieu Rousseau ◽  
Anne-Claire Duchez ◽  
Chan Ho C. Lee ◽  
Eric Boilard ◽  
Benoit Laffont ◽  
...  
Keyword(s):  
Actinomycin D ◽  
De Novo ◽  
Phagocytic Capacity ◽  
Human Macrophages ◽  
Mrna Targets ◽  
De Novo Gene ◽  
Supplementary Material ◽  
And Function ◽  
Microarray Analyses ◽  
Platelet Microparticles

SummaryPlatelet microparticles (MPs) represent the most abundant MPs subtype in the circulation, and can mediate intercellular communication through delivery of bioactives molecules, such as cytokines, proteins, lipids and RNAs. Here, we show that platelet MPs can be internalised by primary human macrophages and deliver functional miR-126–3p. The increase in macrophage miR-126–3p levels was not prevented by actinomycin D, suggesting that it was not due to de novo gene transcription. Platelet MPs dose-dependently downregulated expression of four predicted mRNA targets of miR-126–3p, two of which were confirmed also at the protein level. The mRNA downregulatory effects of platelet MPs were abrogated by expression of a neutralising miR-126–3p sponge, implying the involvement of miR-126–3p. Transcriptome-wide, microarray analyses revealed that as many as 66 microRNAs and 653 additional RNAs were significantly and differentially expressed in macrophages upon exposure to platelet MPs. More specifically, platelet MPs induced an upregulation of 34 microRNAs and a concomitant downregulation of 367 RNAs, including mRNAs encoding for cytokines/chemokines CCL4, CSF1 and TNF. These changes were associated with reduced CCL4, CSF1 and TNF cytokine/chemokine release by macrophages, and accompanied by a marked increase in their phagocytic capacity. These findings demonstrate that platelet MPs can modify the transcriptome of macrophages, and reprogram their function towards a phagocytic phenotype.Supplementary Material to this article is available online at www.thrombosis-online.com.

scholarly journals Accurate assembly of the olive baboon (Papio anubis) genome using long-read and Hi-C data

GigaScience ◽  
2020 ◽  
Vol 9 (12) ◽  
Author(s):  
Sanjit Singh Batra ◽  
Michal Levy-Sakin ◽  
Jacqueline Robinson ◽  
Joseph Guillory ◽  
Steffen Durinck ◽  
...  
Keyword(s):  
Single Molecule ◽  
De Novo ◽  
Poor Quality ◽  
Papio Anubis ◽  
Primate Model ◽  
De Novo Genome Assembly ◽  
Olive Baboon ◽  
Genetics Research ◽  
Long Read ◽  
Linkage Information

Abstract Background Baboons are a widely used nonhuman primate model for biomedical, evolutionary, and basic genetics research. Despite this importance, the genomic resources for baboons are limited. In particular, the current baboon reference genome Panu_3.0 is a highly fragmented, reference-guided (i.e., not fully de novo) assembly, and its poor quality inhibits our ability to conduct downstream genomic analyses. Findings Here we present a de novo genome assembly of the olive baboon (Papio anubis) that uses data from several recently developed single-molecule technologies. Our assembly, Panubis1.0, has an N50 contig size of ∼1.46 Mb (as opposed to 139 kb for Panu_3.0) and has single scaffolds that span each of the 20 autosomes and the X chromosome. Conclusions We highlight multiple lines of evidence (including Bionano Genomics data, pedigree linkage information, and linkage disequilibrium data) suggesting that there are several large assembly errors in Panu_3.0, which have been corrected in Panubis1.0.

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