A mouse tissue atlas of small noncoding RNA

Small noncoding RNAs (ncRNAs) play a vital role in a broad range of biological processes both in health and disease. A comprehensive quantitative reference of small ncRNA expression would significantly advance our understanding of ncRNA roles in shaping tissue functions. Here, we systematically profiled the levels of five ncRNA classes (microRNA [miRNA], small nucleolar RNA [snoRNA], small nuclear RNA [snRNA], small Cajal body-specific RNA [scaRNA], and transfer RNA [tRNA] fragments) across 11 mouse tissues by deep sequencing. Using 14 biological replicates spanning both sexes, we identified that ∼30% of small ncRNAs are distributed across the body in a tissue-specific manner with some also being sexually dimorphic. We found that some miRNAs are subject to “arm switching” between healthy tissues and that tRNA fragments are retained within tissues in both a gene- and a tissue-specific manner. Out of 11 profiled tissues, we confirmed that brain contains the largest number of unique small ncRNA transcripts, some of which were previously annotated while others are identified in this study. Furthermore, by combining these findings with single-cell chromatin accessibility (scATAC-seq) data, we were able to connect identified brain-specific ncRNAs with their cell types of origin. These results yield the most comprehensive characterization of specific and ubiquitous small RNAs in individual murine tissues to date, and we expect that these data will be a resource for the further identification of ncRNAs involved in tissue function in health and dysfunction in disease.

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A mouse tissue atlas of small non-coding RNA

10.1101/430561 ◽

2018 ◽

Cited By ~ 3

Author(s):

Alina Isakova ◽

Tobias Fehlmann ◽

Andreas Keller ◽

Stephen R. Quake

Keyword(s):

Distribution Patterns ◽

Cell Types ◽

Vital Role ◽

The Body ◽

Mouse Tissue ◽

List Type ◽

Tissue Specific ◽

Small Ncrnas ◽

Mouse Tissues ◽

Specific Manner

SUMMARYSmall non-coding RNAs (ncRNAs) play a vital role in a broad range of biological processes both in health and disease. A comprehensive quantitative reference of small ncRNA expression would significantly advance our understanding of ncRNA roles in shaping tissue functions. Here, we systematically profiled the levels of five ncRNA classes (miRNA, snoRNA, snRNA, scaRNA and tRNA fragments) across eleven mouse tissues by deep sequencing. Using fourteen biological replicates spanning both sexes, we identified that ~ 30% of small ncRNAs are distributed across the body in a tissue-specific manner with some are also being sexually dimorphic. We found that miRNAs are subject to “arm switching” between healthy tissues and that tRNA fragments are retained within tissues in both a gene- and a tissue-specific manner. Out of eleven profiled tissues we confirmed that brain contains the largest number of unique small ncRNA transcripts, some of which were previously annotated while others are identified for the first time in this study. Furthermore, by combining these findings with single-cell ATAC-seq data, we were able to connect identified brain-specific ncRNA with their cell types of origin. These results yield the most comprehensive characterization of specific and ubiquitous small RNAs in individual murine tissues to date, and we expect that this data will be a resource for the further identification of ncRNAs involved in tissue-function in health and dysfunction in disease.HIGHLIGHTS-An atlas of tissue levels of multiple small ncRNA classes generated from 14 biological replicates of both sexes across 11 tissues-Distinct distribution patterns of miRNA arms and tRNA fragments across tissues suggest the existence of tissue-specific mechanisms of ncRNA cleavage and retention-miRNA expression is sex specific in healthy tissues-Small RNA-seq and scATAC-seq data integration produce a detailed map of cell-type specific ncRNA profiles in the mouse brain

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Tentacle Morphological Variation Coincides with Differential Expression of Toxins in Sea Anemones

Toxins ◽

10.3390/toxins13070452 ◽

2021 ◽

Vol 13 (7) ◽

pp. 452

Author(s):

Lauren M. Ashwood ◽

Michela L. Mitchell ◽

Bruno Madio ◽

David A. Hurwood ◽

Glenn F. King ◽

...

Keyword(s):

Differential Expression ◽

Morphological Variation ◽

Expression Profiles ◽

The Body ◽

Sea Anemones ◽

Tissue Specific ◽

Venom Composition ◽

Specific Manner ◽

Branched Structures ◽

Morphological Variants

Phylum Cnidaria is an ancient venomous group defined by the presence of cnidae, specialised organelles that serve as venom delivery systems. The distribution of cnidae across the body plan is linked to regionalisation of venom production, with tissue-specific venom composition observed in multiple actiniarian species. In this study, we assess whether morphological variants of tentacles are associated with distinct toxin expression profiles and investigate the functional significance of specialised tentacular structures. Using five sea anemone species, we analysed differential expression of toxin-like transcripts and found that expression levels differ significantly across tentacular structures when substantial morphological variation is present. Therefore, the differential expression of toxin genes is associated with morphological variation of tentacular structures in a tissue-specific manner. Furthermore, the unique toxin profile of spherical tentacular structures in families Aliciidae and Thalassianthidae indicate that vesicles and nematospheres may function to protect branched structures that host a large number of photosynthetic symbionts. Thus, hosting zooxanthellae may account for the tentacle-specific toxin expression profiles observed in the current study. Overall, specialised tentacular structures serve unique ecological roles and, in order to fulfil their functions, they possess distinct venom cocktails.

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Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

10.1101/2020.09.15.299123 ◽

2020 ◽

Author(s):

Timothy J. Durham ◽

Riza M. Daza ◽

Louis Gevirtzman ◽

Darren A. Cusanovich ◽

William Stafford Noble ◽

...

Keyword(s):

Gene Expression ◽

Single Cell ◽

Expression Patterns ◽

Cell Types ◽

Chromatin Accessibility ◽

Gene Expression Patterns ◽

Rna Seq ◽

Cell Type ◽

Tissue Specific ◽

C Elegans

AbstractRecently developed single cell technologies allow researchers to characterize cell states at ever greater resolution and scale. C. elegans is a particularly tractable system for studying development, and recent single cell RNA-seq studies characterized the gene expression patterns for nearly every cell type in the embryo and at the second larval stage (L2). Gene expression patterns are useful for learning about gene function and give insight into the biochemical state of different cell types; however, in order to understand these cell types, we must also determine how these gene expression levels are regulated. We present the first single cell ATAC-seq study in C. elegans. We collected data in L2 larvae to match the available single cell RNA-seq data set, and we identify tissue-specific chromatin accessibility patterns that align well with existing data, including the L2 single cell RNA-seq results. Using a novel implementation of the latent Dirichlet allocation algorithm, we leverage the single-cell resolution of the sci-ATAC-seq data to identify accessible loci at the level of individual cell types, providing new maps of putative cell type-specific gene regulatory sites, with promise for better understanding of cellular differentiation and gene regulation in the worm.

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In vivo tissue-specific chromatin profiling in Drosophila melanogaster using GFP-tagged nuclei

Genetics ◽

10.1093/genetics/iyab079 ◽

2021 ◽

Author(s):

Juan Jauregui-Lozano ◽

Kimaya Bakhle ◽

Vikki M Weake

Keyword(s):

Drosophila Melanogaster ◽

Cell Types ◽

Chromatin Accessibility ◽

Chromatin State ◽

Specific Cell ◽

Tissue Specific ◽

Histone Marks ◽

Chromatin Profiling ◽

Photoreceptor Neurons

Abstract The chromatin landscape defines cellular identity in multicellular organisms with unique patterns of DNA accessibility and histone marks decorating the genome of each cell type. Thus, profiling the chromatin state of different cell types in an intact organism under disease or physiological conditions can provide insight into how chromatin regulates cell homeostasis in vivo. To overcome the many challenges associated with characterizing chromatin state in specific cell types, we developed an improved approach to isolate Drosophila melanogaster nuclei tagged with a GFPKASH protein. The perinuclear space-localized KASH domain anchors GFP to the outer nuclear membrane, and expression of UAS-GFPKASH can be controlled by tissue-specific Gal4 drivers. Using this protocol, we profiled chromatin accessibility using an improved version of Assay for Transposable Accessible Chromatin followed by sequencing (ATAC-seq), called Omni-ATAC. In addition, we examined the distribution of histone marks using Chromatin immunoprecipitation followed by sequencing (ChIP-seq) and Cleavage Under Targets and Tagmentation (CUT&Tag) in adult photoreceptor neurons. We show that the chromatin landscape of photoreceptors reflects the transcriptional state of these cells, demonstrating the quality and reproducibility of our approach for profiling the transcriptome and epigenome of specific cell types in Drosophila.

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Rif1 functions in a tissue-specific manner to control replication timing through its PP1-binding motif

10.1101/870451 ◽

2019 ◽

Author(s):

Robin L. Armstrong ◽

Souradip Das ◽

Christina A. Hill ◽

Robert J. Duronio ◽

Jared T. Nordman

Keyword(s):

Cell Cycle ◽

Genome Stability ◽

Cell Lineage ◽

Replication Timing ◽

Cell Types ◽

Replication Initiation ◽

Control Factor ◽

Binding Motif ◽

Tissue Specific ◽

Specific Manner

AbstractReplication initiation in eukaryotic cells occurs asynchronously throughout S phase, yielding early and late replicating regions of the genome, a process known as replication timing (RT). RT changes during development to ensure accurate genome duplication and maintain genome stability. To understand the relative contributions that cell lineage, cell cycle, and replication initiation regulators have on RT, we utilized the powerful developmental systems available in Drosophila melanogaster. We generated and compared RT profiles from mitotic cells of different tissues and from mitotic and endocycling cells of the same tissue. Our results demonstrate that cell lineage has the largest effect on RT, whereas switching from a mitotic to an endoreplicative cell cycle has little to no effect on RT. Additionally, we demonstrate that the RT differences we observed in all cases are largely independent of transcriptional differences. We also employed a genetic approach in these same cell types to understand the relative contribution the eukaryotic RT control factor, Rif1, has on RT control. Our results demonstrate that Rif1 can function in a tissue-specific manner to control RT. Importantly, the Protein Phosphatase 1 (PP1) binding motif of Rif1 is essential for Rif1 to regulate RT. Together, our data support a model in which the RT program is primarily driven by cell lineage and is further refined by Rif1/PP1 to ultimately generate tissue-specific RT programs.

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Identification of tissue-specific cell death using methylation patterns of circulating DNA

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1519286113 ◽

2016 ◽

Vol 113 (13) ◽

pp. E1826-E1834 ◽

Cited By ~ 251

Author(s):

Roni Lehmann-Werman ◽

Daniel Neiman ◽

Hai Zemmour ◽

Joshua Moss ◽

Judith Magenheim ◽

...

Keyword(s):

Cell Death ◽

Minimally Invasive ◽

Dna Sequences ◽

Cell Types ◽

The Body ◽

Specific Cell ◽

Circulating Dna ◽

Cell Type ◽

Tissue Specific ◽

Methylation Patterns

Minimally invasive detection of cell death could prove an invaluable resource in many physiologic and pathologic situations. Cell-free circulating DNA (cfDNA) released from dying cells is emerging as a diagnostic tool for monitoring cancer dynamics and graft failure. However, existing methods rely on differences in DNA sequences in source tissues, so that cell death cannot be identified in tissues with a normal genome. We developed a method of detecting tissue-specific cell death in humans based on tissue-specific methylation patterns in cfDNA. We interrogated tissue-specific methylome databases to identify cell type-specific DNA methylation signatures and developed a method to detect these signatures in mixed DNA samples. We isolated cfDNA from plasma or serum of donors, treated the cfDNA with bisulfite, PCR-amplified the cfDNA, and sequenced it to quantify cfDNA carrying the methylation markers of the cell type of interest. Pancreatic β-cell DNA was identified in the circulation of patients with recently diagnosed type-1 diabetes and islet-graft recipients; oligodendrocyte DNA was identified in patients with relapsing multiple sclerosis; neuronal/glial DNA was identified in patients after traumatic brain injury or cardiac arrest; and exocrine pancreas DNA was identified in patients with pancreatic cancer or pancreatitis. This proof-of-concept study demonstrates that the tissue origins of cfDNA and thus the rate of death of specific cell types can be determined in humans. The approach can be adapted to identify cfDNA derived from any cell type in the body, offering a minimally invasive window for diagnosing and monitoring a broad spectrum of human pathologies as well as providing a better understanding of normal tissue dynamics.

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Rif1 Functions in a Tissue-Specific Manner To Control Replication Timing Through Its PP1-Binding Motif

Genetics ◽

10.1534/genetics.120.303155 ◽

2020 ◽

Vol 215 (1) ◽

pp. 75-87 ◽

Cited By ~ 2

Author(s):

Robin L. Armstrong ◽

Souradip Das ◽

Christina A. Hill ◽

Robert J. Duronio ◽

Jared T. Nordman

Keyword(s):

Cell Cycle ◽

Genome Stability ◽

Cell Lineage ◽

Replication Timing ◽

Cell Types ◽

Replication Initiation ◽

Control Factor ◽

Binding Motif ◽

Tissue Specific ◽

Specific Manner

Replication initiation in eukaryotic cells occurs asynchronously throughout S phase, yielding early- and late-replicating regions of the genome, a process known as replication timing (RT). RT changes during development to ensure accurate genome duplication and maintain genome stability. To understand the relative contributions that cell lineage, cell cycle, and replication initiation regulators have on RT, we utilized the powerful developmental systems available in Drosophila melanogaster. We generated and compared RT profiles from mitotic cells of different tissues and from mitotic and endocycling cells of the same tissue. Our results demonstrate that cell lineage has the largest effect on RT, whereas switching from a mitotic to an endoreplicative cell cycle has little to no effect on RT. Additionally, we demonstrate that the RT differences we observed in all cases are largely independent of transcriptional differences. We also employed a genetic approach in these same cell types to understand the relative contribution the eukaryotic RT control factor, Rif1, has on RT control. Our results demonstrate that Rif1 can function in a tissue-specific manner to control RT. Importantly, the Protein Phosphatase 1 (PP1) binding motif of Rif1 is essential for Rif1 to regulate RT. Together, our data support a model in which the RT program is primarily driven by cell lineage and is further refined by Rif1/PP1 to ultimately generate tissue-specific RT programs.

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Differential Expression of the ARF GAP Genes GIT1 and GIT2 in Mouse Tissues

Journal of Histochemistry & Cytochemistry ◽

10.1369/jhc.7a7207.2007 ◽

2007 ◽

Vol 55 (10) ◽

pp. 1039-1048 ◽

Cited By ~ 32

Author(s):

Robert Schmalzigaug ◽

Hyewon Phee ◽

Collin E. Davidson ◽

Arthur Weiss ◽

Richard T. Premont

Keyword(s):

T Cell Activation ◽

Cell Activation ◽

Cell Types ◽

The Body ◽

Developmental Expression ◽

Specific Cell ◽

Gtpase Activating Proteins ◽

Gap Genes ◽

Mouse Tissues ◽

G Protein Coupled

GIT1 and GIT2 belong to the family of ADP-ribosylation factor GTPase-activating proteins (ARF-GAP) and have been implicated in the regulation of G protein-coupled receptor sequestration, cell migration, T-cell activation, neuronal spine formation, and aggregate formation in Huntington's disease. Examination of endogenous GIT protein expression in tissues, however, has been hampered by the lack of GIT2-specific antibodies. To visualize GIT1 and GIT2 gene expression in mouse tissues, we created mice with β-galactosidase (β-Gal) reporters inserted into the two GIT genes. β-Gal staining confirmed the broad tissue distribution of GIT1 and GIT2 in the mouse but also revealed striking differences. GIT2 is expressed in most cells of the body, whereas GIT1 is restricted to only a subset of cells. For example, GIT2 is uniformly expressed throughout lung and liver, whereas GIT1 is restricted to cells lining blood vessels, bronchi, and bile ducts. Expression of GIT1 and GIT2 is mutually exclusive in the testes, where a developmental expression shift occurs, with GIT2 present in spermatogonia but GIT1 in mature spermatids. In conclusion, analysis of endogenous GIT expression revealed a nearly ubiquitous distribution of GIT2, whereas GIT1 is restricted to specific cell types even in tissues with apparently high GIT1 expression and is entirely absent from some tissues. (J Histochem Cytochem 55: 1039–1048, 2007)

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

BMC Genomics ◽

10.1186/s12864-020-07078-9 ◽

2020 ◽

Vol 21 (1) ◽

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

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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