Refined genome-wide comparative map of the domestic horse, donkey and human based on cross-species chromosome painting: insight into the occasional fertility of mules

Pteropodidae and Hipposideridae are 2 of the 9 chiropteran families that occur on Madagascar. Despite major advancements in the systematic study of the island's bat fauna, few karyotypic data exist for endemic species. We utilized G- and C-banding in combination with chromosome painting with Myotismyotis probes to establish a genome-wide homology among Malagasy species belonging to the families Pteropodidae (Pteropus rufus 2n = 38; Rousettus madagascariensis, 2n = 36), Hipposideridae (Hipposideros commersoni s.s., 2n = 52), and a single South African representative of the Rhinolophidae (Rhinolophus clivosus, 2n = 58). Painting probes of M. myotis detected 26, 28, 28, and 29 regions of homology in R. madagascariensis, P. rufus, H. commersoni s.s, and R. clivosus, respectively. Translocations, pericentric inversions, and heterochromatin additions were responsible for karyotypic differences amongst the Malagasy pteropodids. Comparative chromosome painting revealed a novel pericentric inversion on P. rufus chromosome 4. Chromosomal characters suggest a close evolutionary relationship between Rousettus and Pteropus. H. commersoni s.s. shared several chromosomal characters with extralimital congeners but did not exhibit 2 chromosomal synapomorphies proposed for Hipposideridae. This study provides further insight into the ancestral karyotypes of pteropodid and hipposiderid bats and corroborates certain molecular phylogenetic hypotheses.

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Genome-wide correlation analysis to identify amplitude regulators of circadian transcriptome output

Scientific Reports ◽

10.1038/s41598-020-78851-9 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Evan S. Littleton ◽

Madison L. Childress ◽

Michaela L. Gosting ◽

Ayana N. Jackson ◽

Shihoko Kojima

Keyword(s):

Clock Genes ◽

Circadian System ◽

Average Level ◽

Relative Amplitude ◽

Critical Component ◽

Period 2 ◽

Genome Wide ◽

Mouse Tissues ◽

Rhythmic Gene ◽

Insight Into

AbstractCell-autonomous circadian system, consisting of core clock genes, generates near 24-h rhythms and regulates the downstream rhythmic gene expression. While it has become clear that the percentage of rhythmic genes varies among mouse tissues, it remains unclear how this variation can be generated, particularly when the clock machinery is nearly identical in all tissues. In this study, we sought to characterize circadian transcriptome datasets that are publicly available and identify the critical component(s) involved in creating this variation. We found that the relative amplitude of 13 genes and the average level of 197 genes correlated with the percentage of cycling genes. Of those, the correlation of Rorc in both relative amplitude and the average level was one of the strongest. In addition, the level of Per2AS, a novel non-coding transcript that is expressed at the Period 2 locus, was also linearly correlated, although with a much lesser degree compared to Rorc. Overall, our study provides insight into how the variation in the percentage of clock-controlled genes can be generated in mouse tissues and suggests that Rorc and potentially Per2AS are involved in regulating the amplitude of circadian transcriptome output.

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Phylogenomic study of the subfamily Caprinae by cross-species chromosome painting with Chinese muntjac paints

Chromosome Research ◽

10.1007/s10577-005-0977-6 ◽

2005 ◽

Vol 13 (4) ◽

pp. 389-399 ◽

Cited By ~ 18

Author(s):

Ling Huang ◽

Wenhui Nie ◽

Jinhuan Wang ◽

Weiting Su ◽

Fengtang Yang

Keyword(s):

Chromosome Painting ◽

Cross Species Chromosome Painting ◽

Phylogenomic Study

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Genome-wide identification of chitinase genes in Thalassiosira pseudonana and analysis of their expression under abiotic stresses

BMC Plant Biology ◽

10.1186/s12870-021-02849-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Haomiao Cheng ◽

Zhanru Shao ◽

Chang Lu ◽

Delin Duan

Keyword(s):

Abiotic Stresses ◽

Chitinase Activity ◽

Thalassiosira Pseudonana ◽

Centric Diatom ◽

Carbon And Nitrogen ◽

Genome Wide ◽

Duplication Events ◽

The Many ◽

Chitinase Genes ◽

Insight Into

Abstract Background The nitrogen-containing polysaccharide chitin is the second most abundant biopolymer on earth and is found in the cell walls of diatoms, where it serves as a scaffold for biosilica deposition. Diatom chitin is an important source of carbon and nitrogen in the marine environment, but surprisingly little is known about basic chitinase metabolism in diatoms. Results Here, we identify and fully characterize 24 chitinase genes from the model centric diatom Thalassiosira pseudonana. We demonstrate that their expression is broadly upregulated under abiotic stresses, despite the fact that chitinase activity itself remains unchanged, and we discuss several explanations for this result. We also examine the potential transcriptional complexity of the intron-rich T. pseudonana chitinase genes and provide evidence for two separate tandem duplication events during their evolution. Conclusions Given the many applications of chitin and chitin derivatives in suture production, wound healing, drug delivery, and other processes, new insight into diatom chitin metabolism has both theoretical and practical value.

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26-OR: Meta-analyses of Genome-Wide Association Studies for Proinsulin Provide Insight into Glycemic Trait Dysregulation

Diabetes ◽

10.2337/db21-26-or ◽

2021 ◽

Vol 70 (Supplement 1) ◽

pp. 26-OR

Author(s):

K. ALAINE BROADAWAY ◽

XIANYONOG YIN ◽

ALICE WILLIAMSON ◽

EMMA WILSON ◽

MAGIC INVESTIGATORS

Keyword(s):

Association Studies ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Meta Analyses ◽

Insight Into

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PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3

eLife ◽

10.7554/elife.10607 ◽

2016 ◽

Vol 5 ◽

Cited By ~ 14

Author(s):

Ho-Ryun Chung ◽

Chao Xu ◽

Alisa Fuchs ◽

Andreas Mund ◽

Martin Lange ◽

...

Keyword(s):

Dna Damage Response ◽

Size Exclusion ◽

X Ray ◽

Chip Sequencing ◽

X Ray Crystallography ◽

Genome Wide ◽

Damage Response ◽

Exclusion Chromatography ◽

Insight Into ◽

Binding Cell

PHF13 is a chromatin affiliated protein with a functional role in differentiation, cell division, DNA damage response and higher chromatin order. To gain insight into PHF13's ability to modulate these processes, we elucidate the mechanisms targeting PHF13 to chromatin, its genome wide localization and its molecular chromatin context. Size exclusion chromatography, mass spectrometry, X-ray crystallography and ChIP sequencing demonstrate that PHF13 binds chromatin in a multivalent fashion via direct interactions with H3K4me2/3 and DNA, and indirectly via interactions with PRC2 and RNA PolII. Furthermore, PHF13 depletion disrupted the interactions between PRC2, RNA PolII S5P, H3K4me3 and H3K27me3 and resulted in the up and down regulation of genes functionally enriched in transcriptional regulation, DNA binding, cell cycle, differentiation and chromatin organization. Together our findings argue that PHF13 is an H3K4me2/3 molecular reader and transcriptional co-regulator, affording it the ability to impact different chromatin processes.

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Hoxa1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on Hoxa1 targets

10.1101/092296 ◽

2016 ◽

Author(s):

Bony De Kumar ◽

Hugo J. Parker ◽

Ariel Paulson ◽

Mark E. Parrish ◽

Irina Pushel ◽

...

Keyword(s):

Es Cells ◽

Hox Proteins ◽

Binding Motifs ◽

Functional Roles ◽

Regulatory Interactions ◽

Mouse Es Cells ◽

Genome Wide ◽

A Genome ◽

Combinatorial Interactions ◽

Insight Into

AbstractHoxa1 has diverse functional roles in differentiation and development. We have identified and characterized properties of regions bound by Hoxa1 on a genome-wide basis in differentiating mouse ES cells. Hoxa1 bound regions are enriched for clusters of consensus binding motifs for Hox, Pbx and Meis and many display co-occupancy of Pbx and Meis. Pbx and Meis are members of the TALE family and genome-wide analysis of multiple TALE members (Pbx, Meis, TGIF, Prep1 and Prep2) show that nearly all Hoxa1 targets display occupancy of one or more TALE members. The combinatorial binding patterns of TALE proteins defines distinct classes of Hoxa1 targets and indicates a role as cofactors in modulating the specificity of Hox proteins. We also discovered extensive auto- and cross-regulatory interactions among the Hoxa1 and TALE genes. This study provides new insight into a regulatory network involving combinatorial interactions between Hoxa1 and TALE proteins.

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DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis

eLife ◽

10.7554/elife.00534 ◽

2013 ◽

Vol 2 ◽

Cited By ~ 221

Author(s):

Benjamin JM Taylor ◽

Serena Nik-Zainal ◽

Yee Ling Wu ◽

Lucy A Stebbings ◽

Keiran Raine ◽

...

Keyword(s):

Breast Cancer ◽

Abasic Site ◽

Dna Breaks ◽

Mutational Signatures ◽

Genome Wide ◽

Cancer Genomes ◽

Strand Breakage ◽

Cytidine Deamination ◽

Apobec Family ◽

Insight Into

Breast cancer genomes have revealed a novel form of mutation showers (kataegis) in which multiple same-strand substitutions at C:G pairs spaced one to several hundred nucleotides apart are clustered over kilobase-sized regions, often associated with sites of DNA rearrangement. We show kataegis can result from AID/APOBEC-catalysed cytidine deamination in the vicinity of DNA breaks, likely through action on single-stranded DNA exposed during resection. Cancer-like kataegis can be recapitulated by expression of AID/APOBEC family deaminases in yeast where it largely depends on uracil excision, which generates an abasic site for strand breakage. Localized kataegis can also be nucleated by an I-SceI-induced break. Genome-wide patterns of APOBEC3-catalyzed deamination in yeast reveal APOBEC3B and 3A as the deaminases whose mutational signatures are most similar to those of breast cancer kataegic mutations. Together with expression and functional assays, the results implicate APOBEC3B/A in breast cancer hypermutation and give insight into the mechanism of kataegis.

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