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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 21, 2023 |
| Title |
Epigenomic analysis of regulatory evolution in mole rats |
| Organisms |
Mus musculus; Cavia porcellus; Heterocephalus glaber; Fukomys damarensis |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
Changes in gene regulation have long been though to underlie most phenotypic differences between species. Subterranean rodents, and in particular the naked mole-rat (NMR), have attracted substantial attention due to their proposed phenotypic adaptations, which include hypoxia tolerance, metabolic changes and cancer resistance. However, it is largely unknown what regulatory changes may associate with these phenotypic traits, and whether these are unique to the NMR, the mole-rat clade or also present in other mammals. Here, we undertook a comparative genomics approach to identify genome-wide promoter and enhancer regions harbouring epigenomic hallmarks of regulatory activity, in heart and liver from two mole-rat species (NMR and DMR) and two rodent outgroups. To identify promoters and enhancers displaying robust shifts in regulatory activity in the mole-rat clade, we adapted and applied a phylogenetic modeling approach to quantitatively compare epigenomic signals at orthologous locations, while accounting for phylogenetic distance and inter-species variation. This method identified thousands of orthologous promoter and enhancer regions with increased activity in ancestral or single-species mole-rat branches, as well as hundreds of promoters and enhancers with reduced activity in mole-rats versus other rodents. These elements underlie both shared tissue-specific changes in gene regulation associated with mole-rat evolution, which include metabolic and functional adaptations in heart and liver. Moreover, by comparing mole-rat specific changes in promoters and enhancers between ancestral and single-species branches, our data revealed a number of candidate pathways with stepwise regulatory changes during mole-rat evolution. Lastly, we analysed the genomic properties of non-alignable promoters and enhancers in mole-rats, and report (i) their overlap with specific repetitive elements and transcription factor binding sites; and (ii) their association with metabolic gene functions. On the whole, these comparative analyses reveal mole-rat specific epigenomic changes across orthologous and non-mappable promoters and enhancers - which inform previously reported mole-rat adaptations from a gene regulation perspective.
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| Overall design |
Chromatin immunoprecipitation sequencing (ChIP-seq) for histone postranslational modifications H3K27ac, H3K4me3 and H3K4me1 in liver and heart tissues from naked mole-rat, damaraland mole-rat, guinea pig and mouse (with three to six biological replicates)
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| Contributor(s) |
Parey E, Fernandez-Aroca D, Frost S, Berthelot C, Villar D |
| Citation(s) |
37625847 |
| |
| Submission date |
Jan 16, 2023 |
| Last update date |
Nov 16, 2023 |
| Contact name |
Diego Villar |
| E-mail(s) |
d.villarlozano@qmul.ac.uk
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| Phone |
+447775847664
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| Organization name |
Queen Mary University of London
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| Street address |
4 Newark Street, Blizard Institute
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| City |
London |
| ZIP/Postal code |
E1 2AT |
| Country |
United Kingdom |
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| Platforms (13)
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| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
| GPL24046 |
Illumina NextSeq 500 (Heterocephalus glaber) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL26775 |
Illumina HiSeq 4000 (Heterocephalus glaber) |
| GPL28700 |
Illumina HiSeq 4000 (Fukomys damarensis) |
| GPL29163 |
Illumina NextSeq 500 (Cavia porcellus) |
| GPL30172 |
NextSeq 2000 (Mus musculus) |
| GPL30845 |
Illumina NovaSeq 6000 (Heterocephalus glaber) |
| GPL32213 |
Illumina HiSeq 4000 (Cavia porcellus) |
| GPL33024 |
Illumina NextSeq 500 (Fukomys damarensis) |
| GPL33572 |
Illumina NovaSeq 6000 (Fukomys damarensis) |
| GPL33573 |
NextSeq 2000 (Heterocephalus glaber) |
| GPL33574 |
NextSeq 2000 (Fukomys damarensis) |
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| Samples (160)
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| GSM6935923 |
Mouse, Heart, H3K4me3, 33016, do14466 |
| GSM6935924 |
Mouse, Heart, H3K4me1, 33017, do14467 |
| GSM6935925 |
Mouse, Heart, H3K27ac, 33018, do14468 |
| GSM6935926 |
NMR, Liver, H3K4me3, NMR32, do16798 |
| GSM6935927 |
NMR, Liver, H3K27ac, NMR32, do16799 |
| GSM6935928 |
NMR, Liver, H3K4me1, NMR32, do16800 |
| GSM6935929 |
NMR, Liver, H3K4me3, NMR35, do16801 |
| GSM6935930 |
NMR, Liver, H3K27ac, NMR35, do16802 |
| GSM6935931 |
NMR, Liver, H3K4me1, NMR35, do16803 |
| GSM6935932 |
DMR, Heart, H3K4me3, DMR2, do16804 |
| GSM6935933 |
DMR, Heart, H3K27ac, DMR2, do16805 |
| GSM6935934 |
DMR, Heart, H3K4me1, DMR2, do16806 |
| GSM6935935 |
DMR, Heart, H3K4me3, DMR4, do16807 |
| GSM6935936 |
DMR, Heart, H3K27ac, DMR4, do16808 |
| GSM6935937 |
DMR, Heart, H3K4me1, DMR4, do16809 |
| GSM6935938 |
NMR, Liver, input, NMR32, do16810 |
| GSM6935939 |
NMR, Liver, input, NMR35, do16811 |
| GSM6935940 |
DMR, Heart, input, DMR2, do16812 |
| GSM6935941 |
DMR, Heart, input, DMR4, do16813 |
| GSM6935942 |
DMR, Liver, H3K27ac, DMR2, do17584 |
| GSM6935943 |
DMR, Liver, H3K4me1, DMR2, do17585 |
| GSM6935944 |
NMR, Liver, H3K4me3, NMR34, do17586 |
| GSM6935945 |
NMR, Liver, H3K27ac, NMR34, do17587 |
| GSM6935946 |
NMR, Liver, H3K4me1, NMR34, do17588 |
| GSM6935947 |
NMR, Heart, H3K4me3, NMR35, do17589 |
| GSM6935948 |
NMR, Heart, H3K27ac, NMR35, do17590 |
| GSM6935949 |
GuineaPig, Heart, H3K4me3, GuineaPig7, do17592 |
| GSM6935950 |
GuineaPig, Heart, H3K27ac, GuineaPig7, do17593 |
| GSM6935951 |
GuineaPig, Heart, H3K4me1, GuineaPig7, do17594 |
| GSM6935952 |
DMR, Liver, input, DMR2, do17595 |
| GSM6935953 |
NMR, Liver, input, NMR34, do17596 |
| GSM6935954 |
NMR, Heart, input, NMR35, do17597 |
| GSM6935955 |
GuineaPig, Heart, input, GuineaPig7, do17598 |
| GSM6935956 |
DMR, Liver, H3K4me3, DMR1, do17599 |
| GSM6935957 |
DMR, Liver, H3K27ac, DMR1, do17600 |
| GSM6935958 |
DMR, Liver, H3K4me1, DMR1, do17601 |
| GSM6935959 |
DMR, Liver, H3K4me3, DMR4, do17602 |
| GSM6935960 |
DMR, Liver, H3K27ac, DMR4, do17603 |
| GSM6935961 |
DMR, Liver, H3K4me1, DMR4, do17604 |
| GSM6935962 |
NMR, Heart, H3K4me1, NMR30, do17606 |
| GSM6935963 |
GuineaPig, Heart, H3K4me3, GuineaPig8, do17607 |
| GSM6935964 |
GuineaPig, Heart, H3K27ac, GuineaPig8, do17608 |
| GSM6935965 |
GuineaPig, Heart, H3K4me1, GuineaPig8, do17609 |
| GSM6935966 |
DMR, Liver, input, DMR1, do17610 |
| GSM6935967 |
DMR, Liver, input, DMR4, do17611 |
| GSM6935968 |
NMR, Heart, input, NMR30, do17612 |
| GSM6935969 |
GuineaPig, Heart, input, GuineaPig8, do17613 |
| GSM6935970 |
Mouse, Heart, H3K4me3, 17_36584, do17627 |
| GSM6935971 |
Mouse, Heart, H3K27ac, 17_36584, do17628 |
| GSM6935972 |
Mouse, Heart, H3K4me3, 45884_45885_45886, do17726 |
| GSM6935973 |
Mouse, Heart, H3K27ac, 45884_45885_45886, do17727 |
| GSM6935974 |
Mouse, Heart, H3K4me1, 45884_45885_45886, do17728 |
| GSM6935975 |
Mouse, Heart, input, 45884_45885_45886, do17732 |
| GSM6935976 |
GuineaPig, Liver, H3K4me3, GuineaPig7, do2342 |
| GSM6935977 |
GuineaPig, Liver, H3K4me3, GuineaPig8, do2346 |
| GSM6935978 |
GuineaPig, Liver, H3K4me3, GuineaPig9, do2350 |
| GSM6935979 |
GuineaPig, Liver, input, GuineaPig7, do2422 |
| GSM6935980 |
GuineaPig, Liver, input, GuineaPig9, do2424 |
| GSM6935981 |
GuineaPig, Liver, input, GuineaPig8, do2432 |
| GSM6935982 |
GuineaPig, Liver, H3K4me1, GuineaPig7, do3023 |
| GSM6935983 |
GuineaPig, Liver, H3K4me1, GuineaPig8, do3024 |
| GSM6935984 |
GuineaPig, Liver, H3K4me1, GuineaPig9, do3025 |
| GSM6935985 |
GuineaPig, Liver, H3K27ac, GuineaPig7, do3044 |
| GSM6935986 |
GuineaPig, Liver, H3K27ac, GuineaPig8, do3045 |
| GSM6935987 |
GuineaPig, Liver, H3K27ac, GuineaPig9, do3046 |
| GSM6935988 |
Mouse, Liver, H3K27ac, 85920, do3128 |
| GSM6935989 |
Mouse, Liver, H3K27ac, 85921, do3129 |
| GSM6935990 |
Mouse, Liver, H3K27ac, 85923, do3130 |
| GSM6935991 |
Mouse, Liver, H3K27ac, 85924, do3131 |
| GSM6935992 |
Mouse, Liver, H3K4me3, 85920, do3134 |
| GSM6935993 |
Mouse, Liver, H3K4me3, 85921, do3135 |
| GSM6935994 |
Mouse, Liver, H3K4me3, 85923, do3136 |
| GSM6935995 |
Mouse, Liver, H3K4me3, 85924, do3137 |
| GSM6935996 |
Mouse, Liver, input, 85920, do3148 |
| GSM6935997 |
Mouse, Liver, input, 85921, do3149 |
| GSM6935998 |
Mouse, Liver, input, 85923, do3150 |
| GSM6935999 |
Mouse, Liver, input, 85924, do3151 |
| GSM6936000 |
Mouse, Liver, H3K4me1, 85920, do3166 |
| GSM6936001 |
Mouse, Liver, H3K4me1, 85921, do3167 |
| GSM6936002 |
Mouse, Liver, H3K4me1, 85923, do3168 |
| GSM6936003 |
Mouse, Liver, H3K4me1, 85924, do3169 |
| GSM6936004 |
Mouse, Heart, input, 75191, do4092 |
| GSM6936005 |
Mouse, Heart, H3K27ac, 73317, do4245 |
| GSM6936006 |
Mouse, Heart, H3K4me3, 6839, do4436 |
| GSM6936007 |
Mouse, Heart, H3K27ac, 6839, do4441 |
| GSM6936008 |
Mouse, Heart, H3K4me3, 6837, do8329 |
| GSM6936009 |
Mouse, Heart, H3K4me3, 6842, do8334 |
| GSM6936010 |
Mouse, Heart, H3K27ac, 6837, do8339 |
| GSM6936011 |
DMR, Heart, H3K4me3, DMR1, vl0001 |
| GSM6936012 |
DMR, Heart, H3K27ac, DMR1, vl0002 |
| GSM6936013 |
DMR, Heart, H3K4me1, DMR1, vl0003 |
| GSM6936014 |
NMR, Heart, H3K4me3, NMR31, vl0004 |
| GSM6936015 |
NMR, Heart, H3K27ac, NMR31, vl0005 |
| GSM6936016 |
NMR, Heart, H3K4me1, NMR31, vl0006 |
| GSM6936017 |
GuineaPig, Heart, H3K27ac, GuineaPig9, vl0007 |
| GSM6936018 |
GuineaPig, Heart, H3K4me1, GuineaPig9, vl0008 |
| GSM6936019 |
GuineaPig, Heart, input, GuineaPig9, vl0009 |
| GSM6936020 |
NMR, Liver, H3K4me3, NMR31, vl0042 |
| GSM6936021 |
NMR, Liver, H3K27ac, NMR31, vl0043 |
| GSM6936022 |
NMR, Liver, H3K4me1, NMR31, vl0044 |
| GSM6936023 |
NMR, Heart, H3K4me3, NMR32, vl0045 |
| GSM6936024 |
NMR, Heart, H3K27ac, NMR32, vl0046 |
| GSM6936025 |
DMR, Heart, H3K4me3, DMR3, vl0047 |
| GSM6936026 |
DMR, Heart, H3K4me1, DMR3, vl0048 |
| GSM6936027 |
DMR, Heart, H3K4me3, DMR11, vl0049 |
| GSM6936028 |
DMR, Heart, H3K4me1, DMR11, vl0050 |
| GSM6936029 |
NMR, Heart, input, NMR32, vl0051 |
| GSM6936030 |
DMR, Heart, input, DMR3, vl0052 |
| GSM6936031 |
DMR, Heart, input, DMR11, vl0053 |
| GSM6936032 |
NMR, Heart, H3K4me1, NMR32, vl0054 |
| GSM6936033 |
DMR, Heart, H3K27ac, DMR3, vl0055 |
| GSM6936034 |
DMR, Heart, H3K27ac, DMR11, vl0056 |
| GSM6936035 |
NMR, Liver, input, NMR31, vl0057 |
| GSM6936036 |
DMR, Liver, H3K27ac, DMR3, vl0058 |
| GSM6936037 |
DMR, Liver, H3K4me1, DMR3, vl0059 |
| GSM6936038 |
DMR, Liver, H3K27ac, DMR6, vl0060 |
| GSM6936039 |
DMR, Liver, H3K4me1, DMR6, vl0061 |
| GSM6936040 |
NMR, Liver, H3K4me3, NMR30, vl0062 |
| GSM6936041 |
NMR, Liver, H3K27ac, NMR30, vl0063 |
| GSM6936042 |
NMR, Liver, H3K4me1, NMR30, vl0064 |
| GSM6936043 |
NMR, Heart, H3K4me3, NMR34, vl0065 |
| GSM6936044 |
GuineaPig, Heart, H3K4me3, GuineaPig9, vl0066 |
| GSM6936045 |
DMR, Heart, input, DMR1, vl0067 |
| GSM6936046 |
NMR, Heart, input, NMR31, vl0068 |
| GSM6936047 |
DMR, Liver, input, DMR6, vl0069 |
| GSM6936048 |
NMR, Liver, input, NMR30, vl0070 |
| GSM6936049 |
DMR, Liver, input, DMR3, vl0071 |
| GSM6936050 |
Mouse, Heart, H3K4me1, 17_3498, vl0081 |
| GSM6936051 |
Mouse, Heart, input, 17_3498, vl0141 |
| GSM6936052 |
Mouse, Heart, input, 17_3500, vl0142 |
| GSM6936053 |
Mouse, Heart, input, 17_3499, vl0159 |
| GSM6936054 |
Mouse, Heart, H3K4me1, 17_3501, vl0162 |
| GSM6936055 |
Mouse, Heart, H3K4me1, 17_3500, vl0203 |
| GSM7596681 |
DMR, Heart, TBX5, DMR6, vl0411 |
| GSM7596682 |
DMR, Liver, RXRA, DMR1, vl0412 |
| GSM7596683 |
DMR, Liver, FOXA1, DMR1, vl0413 |
| GSM7596684 |
DMR, Liver, HNF6, DMR1, vl0414 |
| GSM7596685 |
DMR, Liver, CEBPA, DMR1, vl0415 |
| GSM7596686 |
DMR, Heart, input, DMR6, vl0416 |
| GSM7596687 |
NMR, Liver, RXRA, NMR30, vl0417 |
| GSM7596688 |
NMR, Liver, RXRA, NMR35, vl0418 |
| GSM7596689 |
DMR, Liver, RXRA, DMR4, vl0419 |
| GSM7596690 |
NMR, Liver, FOXA1, NMR30, vl0420 |
| GSM7596691 |
NMR, Liver, FOXA1, NMR35, vl0421 |
| GSM7596692 |
DMR, Liver, FOXA1, DMR4, vl0422 |
| GSM7596693 |
NMR, Liver, HNF4A, NMR30, vl0423 |
| GSM7596694 |
NMR, Liver, HNF4A, NMR35, vl0424 |
| GSM7596695 |
DMR, Liver, HNF4A, DMR4, vl0425 |
| GSM7596696 |
NMR, Liver, CEBPA, NMR30, vl0426 |
| GSM7596697 |
NMR, Liver, CEBPA, NMR35, vl0427 |
| GSM7596698 |
DMR, Liver, CEBPA, DMR4, vl0428 |
| GSM7596699 |
NMR, Heart, Igf1r, 13562, vl0438 |
| GSM7596700 |
NMR, Heart, Igf1r, NMR35, vl0451 |
| GSM7596701 |
NMR, Liver, Ppargc1a, NMR34, vl0454 |
| GSM7596702 |
NMR, Heart, Ppargc1a, NMR35, vl0455 |
| GSM7596703 |
NMR, Heart, Nebl, NMR35, vl0459 |
| GSM7596704 |
NMR, Liver, Uox, NMR34, vl0460 |
| GSM7596705 |
NMR, Heart, Uox, NMR35, vl0461 |
| GSM7596706 |
DMR, Heart, Ppargc1a, DMR2, vl0465 |
| GSM7596707 |
DMR, Heart, Nebl, DMR2, vl0467 |
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| Relations |
| BioProject |
PRJNA924315 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE222972_RAW.tar |
202.1 Mb |
(http)(custom) |
TAR (of NARROWPEAK, WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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