A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues

Abstract Background Although considerable progress has been made towards annotating the noncoding portion of the human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized. This lack of functional annotation poses a substantial roadblock to agricultural research and diminishes the value of these species as model organisms. As active regulatory elements are typically characterized by chromatin accessibility, we implemented the Assay for Transposase Accessible Chromatin (ATAC-seq) to annotate and characterize regulatory elements in pigs and cattle, given a set of eight adult tissues. Results Overall, 306,304 and 273,594 active regulatory elements were identified in pig and cattle, respectively. 71,478 porcine and 47,454 bovine regulatory elements were highly tissue-specific and were correspondingly enriched for binding motifs of known tissue-specific transcription factors. However, in every tissue the most prevalent accessible motif corresponded to the insulator CTCF, suggesting pervasive involvement in 3-D chromatin organization. Taking advantage of a similar dataset in mouse, open chromatin in pig, cattle, and mice were compared, revealing that the conservation of regulatory elements, in terms of sequence identity and accessibility, was consistent with evolutionary distance; whereas pig and cattle shared about 20% of accessible sites, mice and ungulates only had about 10% of accessible sites in common. Furthermore, conservation of accessibility was more prevalent at promoters than at intergenic regions. Conclusions The lack of conserved accessibility at distal elements is consistent with rapid evolution of enhancers, and further emphasizes the need to annotate regulatory elements in individual species, rather than inferring elements based on homology. This atlas of chromatin accessibility in cattle and pig constitutes a substantial step towards annotating livestock genomes and dissecting the regulatory link between genome and phenome.

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A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues

10.1101/2020.08.13.249870 ◽

2020 ◽

Author(s):

Michelle M Halstead ◽

Colin Kern ◽

Perot Saelao ◽

Ying Wang ◽

Ganrea Chanthavixay ◽

...

Keyword(s):

Agricultural Research ◽

Rapid Evolution ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Model Organisms ◽

Individual Species ◽

Open Chromatin ◽

Tissue Specific ◽

Mouse Tissues ◽

Intergenic Regions

AbstractBackgroundAlthough considerable progress has been made towards annotating the noncoding portion of the human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized. This lack of functional annotation poses a substantial roadblock to agricultural research and diminishes the value of these species as model organisms. As active regulatory elements are typically characterized by chromatin accessibility, we implemented the Assay for Transposase Accessible Chromatin (ATAC-seq) to annotate and characterize regulatory elements in pigs and cattle, given a set of eight adult tissues.ResultsOverall, 306,304 and 273,594 active regulatory elements were identified in pig and cattle, respectively. 71,478 porcine and 47,454 bovine regulatory elements were highly tissue-specific and were correspondingly enriched for binding motifs of known tissue-specific transcription factors. However, in every tissue the most prevalent accessible motif corresponded to the insulator CTCF, suggesting pervasive involvement in 3-D chromatin organization. Taking advantage of a similar dataset in mouse, open chromatin in pig, cattle, and mice were compared, revealing that the conservation of regulatory elements, in terms of sequence identity and accessibility, was consistent with evolutionary distance; whereas pig and cattle shared about 20% of accessible sites, mice and ungulates only had about 10% of accessible sites in common. Furthermore, conservation of accessibility was more prevalent at promoters than at intergenic regions.ConclusionsThe lack of conserved accessibility at distal elements is consistent with rapid evolution of enhancers, and further emphasizes the need to annotate regulatory elements in individual species, rather than inferring elements based on homology. This atlas of chromatin accessibility in cattle and pig constitutes a substantial step towards annotating livestock genomes and dissecting the regulatory link between genome and phenome.

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Chromatin accessibility and regulatory vocabulary across indicine cattle tissues

Genome Biology ◽

10.1186/s13059-021-02489-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Pâmela A. Alexandre ◽

Marina Naval-Sánchez ◽

Moira Menzies ◽

Loan T. Nguyen ◽

Laercio R. Porto-Neto ◽

...

Keyword(s):

Motif Discovery ◽

Target Genes ◽

Developmental Stages ◽

Bos Taurus ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Model Organisms ◽

Open Chromatin ◽

Health And Disease ◽

Collaborative Efforts

Abstract Background Spatiotemporal changes in the chromatin accessibility landscape are essential to cell differentiation, development, health, and disease. The quest of identifying regulatory elements in open chromatin regions across different tissues and developmental stages is led by large international collaborative efforts mostly focusing on model organisms, such as ENCODE. Recently, the Functional Annotation of Animal Genomes (FAANG) has been established to unravel the regulatory elements in non-model organisms, including cattle. Now, we can transition from prediction to validation by experimentally identifying the regulatory elements in tropical indicine cattle. The identification of regulatory elements, their annotation and comparison with the taurine counterpart, holds high promise to link regulatory regions to adaptability traits and improve animal productivity and welfare. Results We generate open chromatin profiles for liver, muscle, and hypothalamus of indicine cattle through ATAC-seq. Using robust methods for motif discovery, motif enrichment and transcription factor binding sites, we identify potential master regulators of the epigenomic profile in these three tissues, namely HNF4, MEF2, and SOX factors, respectively. Integration with transcriptomic data allows us to confirm some of their target genes. Finally, by comparing our results with Bos taurus data we identify potential indicine-specific open chromatin regions and overlaps with indicine selective sweeps. Conclusions Our findings provide insights into the identification and analysis of regulatory elements in non-model organisms, the evolution of regulatory elements within two cattle subspecies as well as having an immediate impact on the animal genetics community in particular for a relevant productive species such as tropical cattle.

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Hepatic-Specific Accessibility of Igf1 Gene Enhancers Is Independent of Growth Hormone Signaling

Molecular Endocrinology ◽

10.1210/me.2013-1181 ◽

2013 ◽

Vol 27 (12) ◽

pp. 2080-2092 ◽

Cited By ~ 5

Author(s):

Mahalakshmi Santhanam ◽

Dennis J. Chia

Keyword(s):

Gene Regulation ◽

Gene Transcription ◽

Tissue Expression ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Open Chromatin ◽

Binding Motifs ◽

Tissue Specific ◽

Regulatory Domains ◽

Binding Domains

The diverse roles of IGF-1 in physiology include acting as the endocrine intermediate to elicit the anabolic actions of GH. The majority of serum IGF-1 is synthesized in liver, where GH stimulates Igf1 gene transcription via the transcription factor, signal transducer and activator of transcription (Stat)5b. We and others have identified multiple Stat5-binding domains at the Igf1 locus that function in gene regulation, but it remains unclear whether the roles of these domains are tissue specific. Survey of the chromatin landscape of regulatory domains can provide insight about mechanisms of gene regulation, with chromatin accessibility regarded as a hallmark feature of regulatory domains. We prepared chromatin from liver, kidney, and spleen of C57BL/6 mice, and used formaldehyde-associated isolation of regulatory elements to assess chromatin accessibility at the major Igf1 promoter and 7 -binding enhancers. Whereas the promoters of other prototypical tissue-specific genes are open in a tissue-specific way, the major Igf1 promoter is open in all 3 tissues, albeit moderately more so in liver. In contrast, chromatin accessibility at Igf1 Stat5-binding domains is essentially restricted to liver, indicating that the enhancers are driving extensive differences in tissue expression. Furthermore, studies with Ghrhrlit/lit mice reveal that prior GH exposure is not necessary to establish open chromatin at these domains. Lastly, formaldehyde-associated isolation of regulatory elements of human liver samples confirms open chromatin at IGF1 Promoter 1, but unexpectedly, homologous Stat5-binding motifs are not accessible. We conclude that robust GH-stimulated hepatic Igf1 gene transcription utilizes tissue-specific mechanisms of epigenetic regulation that are established independent of GH signaling.

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EPCO-31. EPIGENOMIC INTRATUMORAL HETEROGENEITY OF GLIOBLASTOMA IN THREE-DIMENSIONAL SPACE

Neuro-Oncology ◽

10.1093/neuonc/noaa215.310 ◽

2020 ◽

Vol 22 (Supplement_2) ◽

pp. ii76-ii76

Author(s):

Radhika Mathur ◽

Sriranga Iyyanki ◽

Stephanie Hilz ◽

Chibo Hong ◽

Joanna Phillips ◽

...

Keyword(s):

Spatial Organization ◽

Dimensional Space ◽

Three Dimensional ◽

Spatial Location ◽

Therapy Resistance ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Intratumoral Heterogeneity ◽

Tumor Evolution ◽

Open Chromatin

Abstract Treatment failure in glioblastoma is often attributed to intratumoral heterogeneity (ITH), which fosters tumor evolution and generation of therapy-resistant clones. While ITH in glioblastoma has been well-characterized at the genomic and transcriptomic levels, the extent of ITH at the epigenomic level and its biological and clinical significance are not well understood. In collaboration with neurosurgeons, neuropathologists, and biomedical imaging experts, we have established a novel topographical approach towards characterizing epigenomic ITH in three-dimensional (3-D) space. We utilize pre-operative MRI scans to define tumor volume and then utilize 3-D surgical neuro-navigation to intra-operatively acquire 10+ samples representing maximal anatomical diversity. The precise spatial location of each sample is mapped by 3-D coordinates, enabling tumors to be visualized in 360-degrees and providing unprecedented insight into their spatial organization and patterning. For each sample, we conduct assay for transposase-accessible chromatin using sequencing (ATAC-Seq), which provides information on the genomic locations of open chromatin, DNA-binding proteins, and individual nucleosomes at nucleotide resolution. We additionally conduct whole-exome sequencing and RNA sequencing for each spatially mapped sample. Integrative analysis of these datasets reveals distinct patterns of chromatin accessibility within glioblastoma tumors, as well as their associations with genetically defined clonal expansions. Our analysis further reveals how differences in chromatin accessibility within tumors reflect underlying transcription factor activity at gene regulatory elements, including both promoters and enhancers, and drive expression of particular gene expression sets, including neuronal and immune programs. Collectively, this work provides the most comprehensive characterization of epigenomic ITH to date, establishing its importance for driving tumor evolution and therapy resistance in glioblastoma. As a resource for further investigation, we have provided our datasets on an interactive data sharing platform – The 3D Glioma Atlas – that enables 360-degree visualization of both genomic and epigenomic ITH.

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Dynamics of Cardiomyocyte Transcriptome and Chromatin Landscape Demarcates Key Events of Heart Development

10.1101/488593 ◽

2018 ◽

Author(s):

Michal Pawlak ◽

Katarzyna Z. Kedzierska ◽

Maciej Migdal ◽

Karim Abu Nahia ◽

Jordan A. Ramilowski ◽

...

Keyword(s):

Heart Development ◽

Regulatory Networks ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Proximal Promoter ◽

Global Changes ◽

Open Chromatin ◽

Sequence Motifs ◽

Loss Of Function ◽

Heart Looping

ABSTRACTThe development of an organ involves dynamic regulation of gene transcription and complex multipathway interactions. To better understand transcriptional regulatory mechanism driving heart development and the consequences of its disruption, we isolated cardiomyocytes (CMs) from wild-type zebrafish embryos at 24, 48 and 72 hours post fertilization corresponding to heart looping, chamber formation and heart maturation, and from mutant lines carrying loss-of-function mutations in gata5, tbx5a and hand2, transcription factors (TFs) required for proper heart development. The integration of CM transcriptomics (RNA-seq) and genome-wide chromatin accessibility maps (ATAC-seq) unravelled dynamic regulatory networks driving crucial events of heart development. These networks contained key cardiac TFs including Gata5/6, Nkx2.5, Tbx5/20, and Hand2, and are associated with open chromatin regions enriched for DNA sequence motifs belonging to the family of the corresponding TFs. These networks were disrupted in cardiac TF mutants, indicating their importance in proper heart development. The most prominent gene expression changes, which correlated with chromatin accessibility modifications within their proximal promoter regions, occurred between heart looping and chamber formation, and were associated with metabolic and hematopoietic/cardiac switch during CM maturation. Furthermore, loss of function of cardiac TFs Gata5, Tbx5a, and Hand2 affected the cardiac regulatory networks and caused global changes in chromatin accessibility profile. Among regions with differential chromatin accessibility in mutants were highly conserved non-coding elements which represent putative cis regulatory elements with potential role in heart development and disease. Altogether, our results revealed the dynamic regulatory landscape at key stages of heart development and identified molecular drivers of heart morphogenesis.

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Chromatin accessibility changes at intergenic regions associates with ovarian cancer drug resistance

10.1101/2021.02.24.432641 ◽

2021 ◽

Author(s):

John Gallon ◽

Erick Loomis ◽

Edward Curry ◽

Nicholas Martin ◽

Leigh Brody ◽

...

Keyword(s):

Ovarian Cancer ◽

Drug Resistance ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Cancer Drug ◽

Gene Promoters ◽

Altered Expression ◽

Platinum Based Chemotherapy ◽

Resistant Lines ◽

Intergenic Regions

AbstractWe have investigated how genomic distribution of chromatin accessibilities alter during acquisition of resistance to carboplatin-based chemotherapy using matched ovarian cell lines from high grade serous ovarian cancer (HGSOC) patients before and after becoming clinically resistant to platinum-based chemotherapy. Resistant lines show altered chromatin accessibility at intergenic regions, but less so at gene promoters. Super-enhancers, as defined by clusters of cis-regulatory elements, at these intergenic regions show chromatin changes that are associated with altered expression of linked genes, with enrichment for genes involved in the Fanconi anemia/BRCA DNA damage response pathway. Further, genome-wide distribution of platinum adducts associates with the chromatin changes observed and distinguish sensitive from resistant lines. In the resistant line, we observe fewer adducts around gene promoters and more adducts at intergenic regions. Thus, chromatin changes at intergenic regulators of gene expression are associated with in vivo derived drug resistance and Pt-adduct distribution in patient-derived HGSOC drug resistance models.

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ATF3 drives senescence by reconstructing accessible chromatin profiles

10.1101/2020.08.13.249458 ◽

2020 ◽

Author(s):

Chao Zhang ◽

Xuebin Zhang ◽

Yiting Guan ◽

Xiaoke Huang ◽

Lijun Zhang ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Transcription Factors ◽

Regulatory Mechanism ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Dynamic Landscape ◽

Intergenic Regions ◽

Senescence Program ◽

Accessible Chromatin

AbstractChromatin architecture and gene expression profile undergo tremendous reestablishment during senescence. However, the regulatory mechanism between chromatin reconstruction and gene expression in senescence remain elusive. The chromatin accessibility is an excellent perspective to reveal the latent regulatory elements. Thus, we depicted the landscapes of chromatin accessibility and gene expression during HUVECs senescence. We found that chromatin accessibilities are re-distributed during senescence. The senescence related increased accessible regions (IARs) and the decreased accessible regions (DARs) are mainly distributed in distal intergenic regions. The DARs are correlated with the function declines caused by senescence, whereas the IARs are involved in the regulation for senescence program. Moreover, the heterochromatin contributes most of IARs in senescent cells. We identified that the AP-1 transcription factors, especially ATF3 is responsible for driving chromatin accessibility reconstruction in IARs. In particular, DNA methylation is negatively correlated with chromatin accessibility during senescence. AP-1 motifs with low DNA methylation may improve their binding affinity in IARs and further opens the chromatin nearby. Our results described a dynamic landscape of chromatin accessibility whose remodeling contributes to the senescence program. And we identified a cellular senescence regulator, AP-1, which promotes senescence through organizing the accessibility profile in IARs.

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Identification of distal regulatory regions in the human αIIb gene locus necessary for consistent, high-level megakaryocyte expression

Blood ◽

10.1182/blood-2002-05-1307 ◽

2002 ◽

Vol 100 (10) ◽

pp. 3588-3596 ◽

Cited By ~ 16

Author(s):

Michael A. Thornton ◽

Chunyan Zhang ◽

Maria A. Kowalska ◽

Mortimer Poncz

Keyword(s):

Gene Locus ◽

Tissue Specificity ◽

Mrna Level ◽

Regulatory Elements ◽

Proximal Promoter ◽

Regulatory Regions ◽

Platelet Surface ◽

Tissue Specific ◽

Intergenic Regions ◽

High Level

The αIIb/β3-integrin receptor is present at high levels only in megakaryocytes and platelets. Its presence on platelets is critical for hemostasis. The tissue-specific nature of this receptor's expression is secondary to the restricted expression of αIIb, and studies of the αIIb proximal promoter have served as a model of a megakaryocyte-specific promoter. We have examined the αIIb gene locus for distal regulatory elements. Sequence comparison between the human (h) and murine (m) αIIb loci revealed high levels of conservation at intergenic regions both 5′ and 3′ to the αIIb gene. Additionally, deoxyribonuclease (DNase) I sensitivity mapping defined tissue-specific hypersensitive (HS) sites that coincide, in part, with these conserved regions. Transgenic mice containing various lengths of the hαIIb gene locus, which included or excluded the various conserved/HS regions, demonstrated that the proximal promoter was sufficient for tissue specificity, but that a region 2.5 to 7.1 kb upstream of the hαIIb gene was necessary for consistent expression. Another region 2.2 to 7.4 kb downstream of the gene enhanced expression 1000-fold and led to levels of hαIIb mRNA that were about 30% of the native mαIIb mRNA level. These constructs also resulted in detectable hαIIb/mβ3 on the platelet surface. This work not only confirms the importance of the proximal promoter of the αIIb gene for tissue specificity, but also characterizes the distal organization of the αIIb gene locus and provides an initial localization of 2 important regulatory regions needed for the expression of the αIIb gene at high levels during megakaryopoiesis.

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Epigenetics of Cellular Memory: Insights from the Chromatin Accessibility Landscape of the Mitotic Genome

Blood ◽

10.1182/blood.v124.21.4342.4342 ◽

2014 ◽

Vol 124 (21) ◽

pp. 4342-4342

Author(s):

Chris C.S. Hsiung ◽

Christapher Morrissey ◽

Maheshi Udugama ◽

Christopher Frank ◽

Cheryl A. Keller ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Transcription Factors ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Dnase I ◽

Specific Gene ◽

Tissue Specific ◽

Dnase I Sensitivity ◽

Mitotic Chromatin

Abstract Normal development requires the coordination of cell cycle progression and gene expression to produce physiologically appropriate cell numbers of various lineages. The concomitant dysregulation of these two cellular programs is central to many malignant and non-malignant hematologic diseases, yet researchers still lack clear, general principles of how intrinsic properties of cell division could influence transcriptional regulation. Mitosis is a unique phase of the cell cycle that dramatically disrupts transcription: chromosomes condense to form microscopically recognizable structures, the nucleus is disassembled, RNA synthesis ceases, and the transcription machinery and many transcription factors are evicted from mitotic chromatin. How cells “remember” tissue-specific transcriptional programs through mitotic divisions remains largely unknown. Some transcription factors, including the erythroid master regulator, GATA1, and certain chromatin features are known to remain associated with DNA during mitosis. These molecular entities have been proposed to serve as mitotic “bookmarks” -- molecules that store gene regulatory information at individual loci through mitosis. However, we have limited knowledge of the composition, mechanism and function of mitotic bookmarks. In this context, chromatin structure deserves special consideration, as chromosome condensation during mitosis could potentially hinder transcription factor binding. To obtain the first genome-wide view of chromatin accessibility during mitosis, we mapped the DNase I sensitivity of the interphase versus mitotic genome in two maturation stages in a murine erythroblast cell line, G1E. Despite microscopic condensation of chromosomes during mitosis, we found that DNase I sensitivity is extensively preserved throughout the mappable genome, indicating that mitotic chromatin is not as condensed as commonly presumed. Individual genes and cis-regulatory elements can maintain all, part of, or none of its interphase accessibility during mitosis, demonstrating that accessibility of mitotic chromatin is locally specified. Promoters generally maintain accessibility during mitosis; moreover, promoters with the highest degree of accessibility preservation in mitosis in G1E cells tend to also be accessible across many murine tissues in interphase. In contrast to promoters, we found that enhancer accessibility is preferentially lost during mitosis, raising the possibility that memory of enhancer regulation may be altered during mitosis. Since enhancers play crucial roles in specifying tissue-specific gene expression patterns, we propose that this phase of the cell cycle may be especially susceptible to resetting of transcriptional programs. This hypothesis is supported by our preliminary results that revealed aberrant RNA polymerase II re-engagement with the genome and transcript production in early G1. Thus, mitosis could be a source of gene expression heterogeneity, with potential implications for cell fate transitions in proliferative cells, such as during stem cell lineage commitment, experimental reprogramming, and tumorigenesis. Disclosures No relevant conflicts of interest to declare.

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A CTCF-Dependent Silencer Located in the Differentially Methylated Area May Regulate Expression of a Housekeeping Gene Overlapping a Tissue-Specific Gene Domain

Molecular and Cellular Biology ◽

10.1128/mcb.26.5.1589-1597.2006 ◽

2006 ◽

Vol 26 (5) ◽

pp. 1589-1597 ◽

Cited By ~ 28

Author(s):

Denis Klochkov ◽

Héctor Rincón-Arano ◽

Elena S. Ioudinkova ◽

Viviana Valadez-Graham ◽

Alexey Gavrilov ◽

...

Keyword(s):

Gene Transcription ◽

Globin Gene ◽

Housekeeping Gene ◽

Regulatory Elements ◽

Ctcf Binding ◽

Specific Gene ◽

Open Chromatin ◽

Erythroid Cells ◽

Tissue Specific ◽

In Erythroid Cells

ABSTRACT The tissue-specific chicken α-globin gene domain represents one of the paradigms, in terms of its constitutively open chromatin conformation and the location of several regulatory elements within the neighboring housekeeping gene. Here, we show that an 0.2-kb DNA fragment located ∼4 kb upstream to the chicken α-globin gene cluster contains a binding site for the multifunctional protein factor CTCF and possesses silencer activity which depends on CTCF binding, as demonstrated by site-directed mutagenesis of the CTCF recognition sequence. CTCF was found to be associated with this recognition site in erythroid cells but not in lymphoid cells where the site is methylated. A functional promoter directing the transcription of the apparently housekeeping ggPRX gene was found 120 bp from the CTCF-dependent silencer. The data are discussed in terms of the hypothesis that the CTCF-dependent silencer stabilizes the level of ggPRX gene transcription in erythroid cells where the promoter of this gene may be influenced by positive cis-regulatory signals activating α-globin gene transcription.

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