Genome-wide comparative analysis reveals human- mouse regulatory landscape and evolution

Background: Because species-specific gene expression is driven by species-specific regulation, understanding the relationship between sequence and function of the regulatory regions in different species will help elucidate how differences among species arise. Despite active experimental and computational research, the relationships among sequence, conservation, and function are still poorly understood. Results: We compared transcription factor occupied segments (TFos) for 116 human and 35 mouse TFs in 546 human and 125 mouse cell types and tissues from the Human and the Mouse ENCODE projects. We based the map between human and mouse TFos on a one-to-one nucleotide cross-species mapper, bnMapper, that utilizes whole genome alignments (WGA). Our analysis shows that TFos are under evolutionary constraint, but a substantial portion (25.1% of mouse and 25.85% of human on average) of the TFos does not have a homologous sequence on the other species; this portion varies among cell types and TFs. Furthermore, 47.67% and 57.01% of the homologous TFos sequence shows binding activity on the other species for human and mouse respectively. However, 79.87% and 69.22% is repurposed such that it binds the same TF in different cells or different TFs in the same cells. Remarkably, within the set of TFos not showing conservation of occupancy, the corresponding genome regions in the other species are preferred locations of novel TFos. These events suggest that a substantial amount of functional regulatory sequences is exapted from other biochemically active genomic material. Despite substantial repurposing of TFos, we did not find substantial changes in their predicted target genes, suggesting that CRMs buffer evolutionary events allowing little or no change in the TF – target gene associations. Thus, the small portion of TFos with strictly conserved occupancy underestimates the degree of conservation of regulatory interactions. Conclusion: We mapped regulatory sequences from an extensive number of TFs and cell types between human and mouse. A comparative analysis of this correspondence unveiled the extent of the shared regulatory sequence across TFs and cell types under study. Importantly, a large part of the shared regulatory sequence repurposed on the other species. This sequence, fueled by turnover events, provides a strong case for exaptation in regulatory elements.

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Ancestral regulatory mechanisms specify conserved midbrain circuitry in arthropods and vertebrates

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1918797117 ◽

2020 ◽

Vol 117 (32) ◽

pp. 19544-19555 ◽

Cited By ~ 2

Author(s):

Jessika C. Bridi ◽

Zoe N. Ludlow ◽

Benjamin Kottler ◽

Beate Hartmann ◽

Lies Vanden Broeck ◽

...

Keyword(s):

Neural Development ◽

Gene Networks ◽

Motor Coordination ◽

Regulatory Elements ◽

Regulatory Mechanisms ◽

Cell Protein ◽

Specific Gene ◽

Regulatory Sequences ◽

Embryonic Mouse ◽

And Function

Corresponding attributes of neural development and function suggest arthropod and vertebrate brains may have an evolutionarily conserved organization. However, the underlying mechanisms have remained elusive. Here, we identify a gene regulatory and character identity network defining the deutocerebral–tritocerebral boundary (DTB) inDrosophila. This network comprises genes homologous to those directing midbrain-hindbrain boundary (MHB) formation in vertebrates and their closest chordate relatives. Genetic tracing reveals that the embryonic DTB gives rise to adult midbrain circuits that in flies control auditory and vestibular information processing and motor coordination, as do MHB-derived circuits in vertebrates. DTB-specific gene expression and function are directed bycis-regulatory elements of developmental control genes that include homologs of mammalianZinc finger of the cerebellumandPurkinje cell protein 4.DrosophilaDTB-specificcis-regulatory elements correspond to regulatory sequences of humanENGRAILED-2, PAX-2, andDACHSHUND-1that direct MHB-specific expression in the embryonic mouse brain. We show thatcis-regulatory elements and the gene networks they regulate direct the formation and function of midbrain circuits for balance and motor coordination in insects and mammals. Regulatory mechanisms mediating the genetic specification of cephalic neural circuits in arthropods correspond to those in chordates, thereby implying their origin before the divergence of deuterostomes and ecdysozoans.

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Comparative Transcriptomic Analysis of the Hematopoietic System between Human and Mouse by Single Cell RNA Sequencing

Cells ◽

10.3390/cells10050973 ◽

2021 ◽

Vol 10 (5) ◽

pp. 973

Author(s):

Shouguo Gao ◽

Zhijie Wu ◽

Jeerthi Kannan ◽

Liza Mathews ◽

Xingmin Feng ◽

...

Keyword(s):

Single Cell ◽

Gene Networks ◽

Single Cells ◽

Cell Types ◽

Regulatory Elements ◽

Regulatory Sequence ◽

Sequence Motifs ◽

Hematopoietic Stem ◽

Stem And Progenitor Cells ◽

Human And Mouse

(1) Background: mouse models are fundamental to the study of hematopoiesis, but comparisons between mouse and human in single cells have been limited in depth. (2) Methods: we constructed a single-cell resolution transcriptomic atlas of hematopoietic stem and progenitor cells (HSPCs) of human and mouse, from a total of 32,805 single cells. We used Monocle to examine the trajectories of hematopoietic differentiation, and SCENIC to analyze gene networks underlying hematopoiesis. (3) Results: After alignment with Seurat 2, the cells of mouse and human could be separated by same cell type categories. Cells were grouped into 17 subpopulations; cluster-specific genes were species-conserved and shared functional themes. The clustering dendrogram indicated that cell types were highly conserved between human and mouse. A visualization of the Monocle results provided an intuitive representation of HSPC differentiation to three dominant branches (Erythroid/megakaryocytic, Myeloid, and Lymphoid), derived directly from the hematopoietic stem cell and the long-term hematopoietic stem cells in both human and mouse. Gene regulation was similarly conserved, reflected by comparable transcriptional factors and regulatory sequence motifs in subpopulations of cells. (4) Conclusions: our analysis has confirmed evolutionary conservation in the hematopoietic systems of mouse and human, extending to cell types, gene expression and regulatory elements.

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Ancestral Regulatory Mechanisms Specify Conserved Midbrain Circuitry in Arthropods and Vertebrates

10.1101/820555 ◽

2019 ◽

Author(s):

Jessika C. Bridi ◽

Zoe N. Ludlow ◽

Benjamin Kottler ◽

Beate Hartmann ◽

Lies Vanden Broeck ◽

...

Keyword(s):

Neural Development ◽

Motor Coordination ◽

Regulatory Elements ◽

Regulatory Mechanisms ◽

Cell Protein ◽

Specific Gene ◽

Regulatory Sequences ◽

Specific Expression ◽

Embryonic Mouse ◽

And Function

ABSTRACTCorresponding attributes of neural development and function suggest arthropod and vertebrate brains may have an evolutionarily conserved organization. However, the underlying mechanisms have remained elusive. Here we identify a gene regulatory and character identity network defining the deutocerebral-tritocerebral boundary (DTB) in Drosophila. We show this network comprises genes homologous to those directing midbrain-hindbrain boundary (MHB) formation in vertebrates and their closest chordate relatives. Genetic tracing reveals that the embryonic DTB gives rise to adult midbrain circuits that in flies control auditory and vestibular information processing and motor coordination, as do MHB-derived circuits in vertebrates. DTB-specific gene expression and function is directed by cis-regulatory elements (CREs) of developmental control genes that include homologs of mammalian Zinc finger of the cerebellum and Purkinje cell protein 4. Moreover, Drosophila DTB-specific CREs correspond to regulatory sequences of human ENGRAILED-2, PAX-2 and DACHSHUND-1 that direct MHB-specific expression in the embryonic mouse brain. Together, these findings imply ancestral regulatory mechanisms mediating the genetic specification of midbrain-cerebellar circuitry for balance and motor control that may predated the radiation of cephalic nervous systems across the animal kingdom.

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Origins and Function of VL30 lncRNA Packaging in Small Extracellular Vesicles: Implications for Cellular Physiology and Pathology

Biomedicines ◽

10.3390/biomedicines9111742 ◽

2021 ◽

Vol 9 (11) ◽

pp. 1742

Author(s):

Stefania Mantziou ◽

Georgios S. Markopoulos

Keyword(s):

Extracellular Vesicles ◽

Active Regions ◽

Regulatory Elements ◽

Binding Motif ◽

Regulatory Sequences ◽

Chromosomal Distribution ◽

Non Coding Rna ◽

Rna Biology ◽

And Function

Long non-coding RNAs (lncRNAs) have emerged during the post-genomic era as significant epigenetic regulators. Viral-like 30 elements (VL30s) are a family of mouse retrotransposons that are transcribed into functional lncRNAs. Recent data suggest that VL30 RNAs are efficiently packaged in small extracellular vesicles (SEVs) through an SEV enrichment sequence. We analysed VL30 elements for the presence of the distinct 26 nt SEV enrichment motif and found that SEV enrichment is an inherent hallmark of the VL30 family, contained in 36 full-length elements, with a widespread chromosomal distribution. Among them, 25 elements represent active, present-day integrations and contain an abundance of regulatory sequences. Phylogenetic analysis revealed a recent spread of SEV-VL30s from 4.4 million years ago till today. Importantly, 39 elements contain an SFPQ-binding motif, associated with the transcriptional induction of oncogenes. Most SEV-VL30s reside in transcriptionally active regions, as characterised by their distribution adjacent to candidate cis-regulatory elements (cCREs). Network analysis of SEV-VL30-associated genes suggests a distinct transcriptional footprint associated with embryonal abnormalities and neoplasia. Given the established role of VL30s in oncogenesis, we conclude that their potential to spread through SEVs represents a novel mechanism for non-coding RNA biology with numerous implications for cellular homeostasis and disease.

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Cardiac Cell Type-Specific Gene Regulatory Programs and Disease Risk Association

10.1101/2020.09.11.291724 ◽

2020 ◽

Author(s):

James D. Hocker ◽

Olivier B. Poirion ◽

Fugui Zhu ◽

Justin Buchanan ◽

Kai Zhang ◽

...

Keyword(s):

Cardiovascular Disease ◽

Disease Risk ◽

Cardiovascular Disease Risk ◽

Cell Types ◽

Regulatory Elements ◽

Specific Gene ◽

Dependent Manner ◽

Cardiac Cell ◽

Risk Variants ◽

Gene Regulatory

ABSTRACTBackgroundCis-regulatory elements such as enhancers and promoters are crucial for directing gene expression in the human heart. Dysregulation of these elements can result in many cardiovascular diseases that are major leading causes of morbidity and mortality worldwide. In addition, genetic variants associated with cardiovascular disease risk are enriched within cis-regulatory elements. However, the location and activity of these cis-regulatory elements in individual cardiac cell types remains to be fully defined.MethodsWe performed single nucleus ATAC-seq and single nucleus RNA-seq to define a comprehensive catalogue of candidate cis-regulatory elements (cCREs) and gene expression patterns for the distinct cell types comprising each chamber of four non-failing human hearts. We used this catalogue to computationally deconvolute dynamic enhancers in failing hearts and to assign cardiovascular disease risk variants to cCREs in individual cardiac cell types. Finally, we applied reporter assays, genome editing and electrophysiogical measurements in in vitro differentiated human cardiomyocytes to validate the molecular mechanisms of cardiovascular disease risk variants.ResultsWe defined >287,000 candidate cis-regulatory elements (cCREs) in human hearts at single-cell resolution, which notably revealed gene regulatory programs controlling specific cell types in a cardiac region/structure-dependent manner and during heart failure. We further report enrichment of cardiovascular disease risk variants in cCREs of distinct cardiac cell types, including a strong enrichment of atrial fibrillation variants in cardiomyocyte cCREs, and reveal 38 candidate causal atrial fibrillation variants localized to cardiomyocyte cCREs. Two such risk variants residing within a cardiomyocyte-specific cCRE at the KCNH2/HERG locus resulted in reduced enhancer activity compared to the non-risk allele. Finally, we found that deletion of the cCRE containing these variants decreased KCNH2 expression and prolonged action potential repolarization in an enhancer dosage-dependent manner.ConclusionsThis comprehensive atlas of human cardiac cCREs provides the foundation for not only illuminating cell type-specific gene regulatory programs controlling human hearts during health and disease, but also interpreting genetic risk loci for a wide spectrum of cardiovascular diseases.

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P-element-mediated enhancer detection applied to the study of oogenesis in Drosophila

Development ◽

10.1242/dev.107.2.189 ◽

1989 ◽

Vol 107 (2) ◽

pp. 189-200 ◽

Cited By ~ 11

Author(s):

U. Grossniklaus ◽

H.J. Bellen ◽

C. Wilson ◽

W.J. Gehring

Keyword(s):

Germ Line ◽

Expression Patterns ◽

Cell Types ◽

Regulatory Elements ◽

P Element ◽

Regulatory Sequences ◽

Transcriptional Regulatory ◽

Morphological Criteria ◽

Enhancer Detection ◽

New Strategies

We have stained the ovaries of nearly 600 different Drosophila strains carrying single copies of a P-element enhancer detector. This transposon detects neighbouring genomic transcriptional regulatory sequences by means of a beta-galactosidase reporter gene. Numerous strains are stained in specific cells and at specific stages of oogenesis and provide useful ovarian markers for cell types that in some cases have not previously been recognized by morphological criteria. Since recent data have suggested that a substantial number of the regulatory elements detected by enhancer detection control neighbouring genes, we discuss the implications of our results concerning ovarian gene expression patterns in Drosophila. We have also identified a small number of insertion-linked recessive mutants that are sterile or lead to ovarian defects. We observe a strong correlation with specific germ line staining patterns in these strains, suggesting that certain patterns are more likely to be associated with female sterile genes than others. On the basis of our results, we suggest new strategies, which are not primarily based on the generation of mutants, to screen for and isolated female sterile genes.

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Development of a CRISPR-SaCas9 system for projection- and function-specific gene editing in the rat brain

Science Advances ◽

10.1126/sciadv.aay6687 ◽

2020 ◽

Vol 6 (12) ◽

pp. eaay6687 ◽

Cited By ~ 4

Author(s):

Haojie Sun ◽

Su Fu ◽

Shuang Cui ◽

Xiangsha Yin ◽

Xiaoyan Sun ◽

...

Keyword(s):

Rat Brain ◽

Gene Editing ◽

High Efficiency ◽

Protein A ◽

Cell Types ◽

Cell Labeling ◽

Specific Gene ◽

Creb Binding Protein ◽

A Genome ◽

And Function

A genome editing technique based on the clustered regularly interspaced short palindromic repeats (CRISPR)–associated endonuclease Cas9 enables efficient modification of genes in various cell types, including neurons. However, neuronal ensembles even in the same brain region are not anatomically or functionally uniform but divide into distinct subpopulations. Such heterogeneity requires gene editing in specific neuronal populations. We developed a CRISPR-SaCas9 system–based technique, and its combined application with anterograde/retrograde AAV vectors and activity-dependent cell-labeling techniques achieved projection- and function-specific gene editing in the rat brain. As a proof-of-principle application, we knocked down the cbp (CREB-binding protein), a sample target gene, in specific neuronal subpopulations in the medial prefrontal cortex, and demonstrated the significance of the projection- and function-specific CRISPR-SaCas9 system in revealing neuronal and circuit basis of memory. The high efficiency and specificity of our projection- and function-specific CRISPR-SaCas9 system could be widely applied in neural circuitry studies.

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Differential evolution in 3′UTRs leads to specific gene expression in Staphylococcus

Nucleic Acids Research ◽

10.1093/nar/gkaa047 ◽

2020 ◽

Vol 48 (5) ◽

pp. 2544-2563 ◽

Cited By ~ 2

Author(s):

Pilar Menendez-Gil ◽

Carlos J Caballero ◽

Arancha Catalan-Moreno ◽

Naiara Irurzun ◽

Inigo Barrio-Hernandez ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Regulation ◽

Bacterial Species ◽

Regulatory Elements ◽

Specific Gene ◽

Species Differentiation ◽

Orthologous Genes ◽

Genome Wide ◽

Sequence Variations ◽

Species Specific

Abstract The evolution of gene expression regulation has contributed to species differentiation. The 3′ untranslated regions (3′UTRs) of mRNAs include regulatory elements that modulate gene expression; however, our knowledge of their implications in the divergence of bacterial species is currently limited. In this study, we performed genome-wide comparative analyses of mRNAs encoding orthologous proteins from the genus Staphylococcus and found that mRNA conservation was lost mostly downstream of the coding sequence (CDS), indicating the presence of high sequence diversity in the 3′UTRs of orthologous genes. Transcriptomic mapping of different staphylococcal species confirmed that 3′UTRs were also variable in length. We constructed chimeric mRNAs carrying the 3′UTR of orthologous genes and demonstrated that 3′UTR sequence variations affect protein production. This suggested that species-specific functional 3′UTRs might be specifically selected during evolution. 3′UTR variations may occur through different processes, including gene rearrangements, local nucleotide changes, and the transposition of insertion sequences. By extending the conservation analyses to specific 3′UTRs, as well as the entire set of Escherichia coli and Bacillus subtilis mRNAs, we showed that 3′UTR variability is widespread in bacteria. In summary, our work unveils an evolutionary bias within 3′UTRs that results in species-specific non-coding sequences that may contribute to bacterial diversity.

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Transposable elements as a potent source of diverse cis -regulatory sequences in mammalian genomes

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2019.0347 ◽

2020 ◽

Vol 375 (1795) ◽

pp. 20190347 ◽

Cited By ~ 14

Author(s):

Vasavi Sundaram ◽

Joanna Wysocka

Keyword(s):

Gene Regulation ◽

Transposable Elements ◽

Regulatory Networks ◽

Regulatory Elements ◽

Regulatory Function ◽

Specific Gene ◽

Regulatory Sequences ◽

Dependent Manner ◽

Unique Contribution ◽

Regulatory Potential

Eukaryotic gene regulation is mediated by cis -regulatory elements, which are embedded within the vast non-coding genomic space and recognized by the transcription factors in a sequence- and context-dependent manner. A large proportion of eukaryotic genomes, including at least half of the human genome, are composed of transposable elements (TEs), which in their ancestral form carried their own cis -regulatory sequences able to exploit the host trans environment to promote TE transcription and facilitate transposition. Although not all present-day TE copies have retained this regulatory function, the preexisting regulatory potential of TEs can provide a rich source of cis -regulatory innovation for the host. Here, we review recent evidence documenting diverse contributions of TE sequences to gene regulation by functioning as enhancers, promoters, silencers and boundary elements. We discuss how TE-derived enhancer sequences can rapidly facilitate changes in existing gene regulatory networks and mediate species- and cell-type-specific regulatory innovations, and we postulate a unique contribution of TEs to species-specific gene expression divergence in pluripotency and early embryogenesis. With advances in genome-wide technologies and analyses, systematic investigation of TEs' cis -regulatory potential is now possible and our understanding of the biological impact of genomic TEs is increasing. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.

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ImmuneRegulation: a web-based tool for identifying human immune regulatory elements

Nucleic Acids Research ◽

10.1093/nar/gkz450 ◽

2019 ◽

Vol 47 (W1) ◽

pp. W142-W150 ◽

Cited By ~ 2

Author(s):

Selim Kalayci ◽

Myvizhi Esai Selvan ◽

Irene Ramos ◽

Chris Cotsapas ◽

Eva Harris ◽

...

Keyword(s):

Gene Expression ◽

Cell Types ◽

Regulatory Elements ◽

Specific Gene ◽

Web Based ◽

Transcriptome Regulation ◽

Rich Data ◽

User Friendly ◽

Gene Expression Levels

Abstract Humans vary considerably both in their baseline and activated immune phenotypes. We developed a user-friendly open-access web portal, ImmuneRegulation, that enables users to interactively explore immune regulatory elements that drive cell-type or cohort-specific gene expression levels. ImmuneRegulation currently provides the largest centrally integrated resource on human transcriptome regulation across whole blood and blood cell types, including (i) ∼43,000 genotyped individuals with associated gene expression data from ∼51,000 experiments, yielding genetic variant-gene expression associations on ∼220 million eQTLs; (ii) 14 million transcription factor (TF)-binding region hits extracted from 1945 ChIP-seq studies; and (iii) the latest GWAS catalog with 67,230 published variant-trait associations. Users can interactively explore associations between queried gene(s) and their regulators (cis-eQTLs, trans-eQTLs or TFs) across multiple cohorts and studies. These regulators may explain genotype-dependent gene expression variations and be critical in selecting the ideal cohorts or cell types for follow-up studies or in developing predictive models. Overall, ImmuneRegulation significantly lowers the barriers between complex immune regulation data and researchers who want rapid, intuitive and high-quality access to the effects of regulatory elements on gene expression in multiple studies to empower investigators in translating these rich data into biological insights and clinical applications, and is freely available at https://immuneregulation.mssm.edu.

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