Alternative super-enhancers result in similar gene expression in different tissues

Alternatively Constructed Estrogen Receptor Alpha-Driven Super-Enhancers Result in Similar Gene Expression in Breast and Endometrial Cell Lines

International Journal of Molecular Sciences ◽

10.3390/ijms21051630 ◽

2020 ◽

Vol 21 (5) ◽

pp. 1630 ◽

Cited By ~ 1

Author(s):

Dóra Bojcsuk ◽

Gergely Nagy ◽

Bálint László Bálint

Keyword(s):

Estrogen Receptor ◽

Cell Lines ◽

Estrogen Receptor Alpha ◽

Receptor Alpha ◽

Highly Active ◽

Ishikawa Cells ◽

Cell Type Specific ◽

The Individual ◽

Similar Gene ◽

Mcf 7

Super-enhancers (SEs) are clusters of highly active enhancers, regulating cell type-specific and disease-related genes, including oncogenes. The individual regulatory regions within SEs might be simultaneously bound by different transcription factors (TFs) and co-regulators, which together establish a chromatin environment conducting to effective transcription. While cells with distinct TF profiles can have different functions, how different cells control overlapping genetic programs remains a question. In this paper, we show that the construction of estrogen receptor alpha-driven SEs is tissue-specific, both collaborating TFs and the active SE components greatly differ between human breast cancer-derived MCF-7 and endometrial cancer-derived Ishikawa cells; nonetheless, SEs common to both cell lines have similar transcriptional outputs. These results delineate that despite the existence of a combinatorial code allowing alternative SE construction, a single master regulator might be able to determine the overall activity of SEs.

An atlas of human proximal epididymis reveals cell-specific functions and distinct roles for CFTR

Life Science Alliance ◽

10.26508/lsa.202000744 ◽

2020 ◽

Vol 3 (11) ◽

pp. e202000744

Author(s):

Shih-Hsing Leir ◽

Shiyi Yin ◽

Jenny L Kerschner ◽

Wilmel Cosme ◽

Ann Harris

Keyword(s):

Fluid Transport ◽

Cell Types ◽

Efferent Ducts ◽

Molecular Events ◽

Specific Distribution ◽

Multiple Cell ◽

Cell Type Specific ◽

Marked Cell ◽

The Individual ◽

Male Genital

Spermatozoa released from the testis are unable to fertilize an egg without a coordinated process of maturation in the lumen of the epididymis. Relatively little is known about the molecular events that integrate this critical progression along the male genital ducts in man. Here, we use single cell RNA-sequencing to construct an atlas of the human proximal epididymis. We find that the CFTR, which is pivotal in normal epididymis fluid transport, is most abundant in surface epithelial cells in the efferent ducts and in rare clear cells in the caput epididymis, suggesting region-specific functional properties. We reveal transcriptional signatures for multiple cell clusters, which identify the individual roles of principal, apical, narrow, basal, clear, halo, and stromal cells in the epididymis. A marked cell type–specific distribution of function is seen along the duct with local specialization of individual cell types integrating processes of sperm maturation.

P004 Critical paralog proteins has a cell-type specific rewiring role in Ulcerative Colitis associated signalling processes

Journal of Crohn s and Colitis ◽

10.1093/ecco-jcc/jjab076.133 ◽

2021 ◽

Vol 15 (Supplement_1) ◽

pp. S126-S127

Author(s):

P Kornilova ◽

L Potari-Gul ◽

D Modos ◽

M Madgwick ◽

W Haerty ◽

...

Keyword(s):

Ulcerative Colitis ◽

Notch Pathway ◽

Cell Types ◽

Goblet Cells ◽

Signalling Pathways ◽

Cell Type ◽

Altered Expression ◽

Hypoxia Response ◽

Cell Functions ◽

Cell Type Specific

Abstract Background Cell functions are regulated by signalling pathways that often cross-talk with each other. These cross-talks are usually cell-type specific and, as we showed earlier, often mediated by so called critical paralog proteins (proteins resulted due to gene duplication but then diverged both in terms of their regulation and their functions). As dysregulation of cell functions is a hallmark of chronic inflammatory diseases, including Ulcerative Colitis (UC), here we investigated the role of such critical paralog proteins in the regulation of some key functions, in UC-associated cell types. Methods In this study, we compared healthy and diseased (non-inflamed UC) conditions. Using network biology approaches combined with single-cell RNAseq data, we identified critical paralog groups in myofibroblasts, regulatory T cells and goblet cells that show cell and/or condition specificity in the process of autophagy, Notch and T-cell receptor signalling. Results We focused our analysis on the Notch pathway-related processes, in particular the EGLN paralogs (EGLN1-3). The EGLN enzymes are prolyl hydroxylases and EGLN1, EGLN3 can directly inhibit the HIF1A transcription factor, while HIF1A induces the expression of all the three EGLN gene upon hypoxia. This negative feedback loop tends to control the amount of EGLNs and the activation status of the HIF1A proteins, therefore maintaining an adequate hypoxia response. In the intestine, EGLN2 and EGLN3 are described as potential regulators of inflammation, and both are downregulated in UC patients. Importantly, we found that the expression of EGLN paralogs shows cell-type and condition specificity. While goblet cells express all three paralogs in both healthy and UC conditions, myofibroblasts express EGLN3 only in the healthy condition. As EGLN3 is responsible for tight junction integrity, and it can regulate hypoxia response, the lack of EGLN3 in UC could contribute to the disrupted epithelial barrier function and dysregulation of myofibroblasts. Accordingly, in mice, depletion of Egln3 causes an increased susceptibility to colitis. Conclusion We have developed a bioinformatic pipeline to reconstruct cell-type specific signalling networks to identify the key differences among critical regulators of the signalling flow (ie., critical paralog proteins) in UC-associated cell types and in comparison of healthy and non-inflamed UC conditions. We analysed the altered expression of paralog genes in signalling pathways in UC-associated cell-types, and demonstrated their role with the condition and cell-type specific expression of EGLN3.

A cis-regulatory atlas in maize at single-cell resolution

10.1101/2020.09.27.315499 ◽

2020 ◽

Author(s):

Alexandre P. Marand ◽

Zongliang Chen ◽

Andrea Gallavotti ◽

Robert J. Schmitz

Keyword(s):

Single Cell ◽

Cell Types ◽

Regulatory Elements ◽

Cellular Heterogeneity ◽

Cell Type ◽

Crop Species ◽

Cell Functions ◽

Cell Type Specific ◽

Type Specification ◽

Accessible Chromatin

ABSTRACTCis-regulatory elements (CREs) encode the genomic blueprints for coordinating spatiotemporal gene expression programs underlying highly specialized cell functions. To identify CREs underlying cell-type specification and developmental transitions, we implemented single-cell sequencing of Assay for Transposase Accessible Chromatin in an atlas of Zea mays organs. We describe 92 distinct states of chromatin accessibility across more than 165,913 putative CREs, 56,575 cells, and 52 known cell-types in maize using a novel implementation of regularized quasibinomial logistic regression. Cell states were largely determined by combinatorial accessibility of transcription factors (TFs) and their binding sites. A neural network revealed that cell identity could be accurately predicted (>0.94) solely based on TF binding site accessibility. Co-accessible chromatin recapitulated higher-order chromatin interactions, with distinct sets of TFs coordinating cell type-specific regulatory dynamics. Pseudotime reconstruction and alignment with Arabidopsis thaliana trajectories identified conserved TFs, associated motifs, and cis-regulatory regions specifying sequential developmental progressions. Cell-type specific accessible chromatin regions were enriched with phenotype-associated genetic variants and signatures of selection, revealing the major cell-types and putative CREs targeted by modern maize breeding. Collectively, our analysis affords a comprehensive framework for understanding cellular heterogeneity, evolution, and cis-regulatory grammar of cell-type specification in a major crop species.

OTME-6. Deep sequencing reveals heterogeneity of brain metastasis-associated macrophages and microglia and uncovers their cell type-specific functions within the tumor microenvironment

Neuro-Oncology Advances ◽

10.1093/noajnl/vdab070.057 ◽

2021 ◽

Vol 3 (Supplement_2) ◽

pp. ii14-ii14

Author(s):

Michael Schulz ◽

Tijna Alekseeva ◽

Julian Anthes ◽

Jandranka Macas ◽

Birgitta Michels ◽

...

Keyword(s):

Brain Tumors ◽

Immune Cell ◽

Inflammatory Responses ◽

Whole Brain Radiotherapy ◽

Cell Types ◽

Therapy Resistance ◽

Cell Type ◽

Cell Functions ◽

Brain Radiotherapy ◽

Cell Type Specific

Abstract Macrophages represent a highly plastic cell type,indispensable for tissue and organ homeostasis, as well as innate immunity. Basic and translational research attributed tumor-promoting functions to macrophages, and their presence is often associated to poor patient prognosis and therapy resistance. While brain-resident macrophages, the so-called microglia (MG), represent the major immune cell type in the parenchyma under normal conditions, primary and metastatic brain tumors induce the recruitment of different immune cell types from the periphery, including monocyte-derived macrophages (MDM). Controversy remained about the redundancy of disease-associated molecular signatures and functions. The identification of markers that reliably distinguish brain-resident from blood-borne tumor-associated macrophages (TAMs) allowed the interrogation of molecular traits of different TAM populations in mouse and human brain tumors. Using RNA-Seq, we demonstrated that TAMs rapidly acquire disease-associated transcriptional programs upon initial tumor infiltration, while gene expression remained stable during different stages of BrM progression. Across different BrM models, disease-associated transcriptional changes revealed lineage-specific, non-redundant functions of TAM populations, which was further reflected by cell type-specific occupation of different niches within the BrM microenvironment. Furthermore, we observed dose- and cell type-specific immune modulatory effects of whole brain radiotherapy on myeloid cells in BrM leading to a transient loss of disease-associated transcriptional programs predominately in blood-borne myeloid populations. This effect can at least in part be attributed to a replenishment of the recruited macrophage pool. This observation was further supported by scRNA-Seq analyses revealing higher heterogeneity of TAM-MDM compared to TAM-MG under treatment-naïve conditions and in response to radiotherapy. Together, our results point towards the phenotypic plasticity of TAMs, especially MDMs, and the contribution of each compartment in instigating cancer-associated inflammation or the establishment of an immuno-suppressive TME. While TAM-MG exert functions related to pro-inflammatory responses, TAM-MDM are rather involved in tissue repair and regulation of adaptive immune cell functions.

Subcellular sequencing of single neurons reveals the dendritic transcriptome of GABAergic interneurons

10.1101/2020.10.17.341651 ◽

2020 ◽

Author(s):

Julio D. Perez ◽

Susanne tom Dieck ◽

Beatriz Alvarez-Castelao ◽

Ivy C.W. Chan ◽

Erin M. Schuman

Keyword(s):

Hippocampal Neurons ◽

Large Population ◽

Cell Types ◽

Gabaergic Neurons ◽

Gabaergic Interneurons ◽

Local Translation ◽

Cell Type ◽

Cell Type Specific ◽

The Individual

AbstractThe localization and translation of mRNAs to dendrites and axons maintains and modifies the local proteome of neurons, and is essential for synaptic plasticity. Although significant efforts have allowed the identification of localized mRNAs in excitatory neurons, it is still unclear whether interneurons also localize a large population of mRNAs. In addition, the variability in the population of localized mRNAs within and between cell-types is unknown. Here we developed a method for the transcriptomic characterization of a single neuron’s subcellular compartments, which combines laser capture microdissection with scRNA-seq. This allowed us to separately profile the dendritic and somatic transcriptomes of individual rat hippocampal neurons and investigate the relation in mRNA abundances between the soma and dendrites of single glutamatergic and GABAergic neurons. We identified two types of glutamatergic and three types of GABAergic interneurons and we found that, like their excitatory counterparts, interneurons contain a rich repertoire of ~4000 mRNAs. The individual somatic transcriptomes exhibited more cell type-specific features than their associated dendritic transcriptomes. The detection and abundance of dendritic mRNAs was not always simply predicted by their somatic counterparts. Finally, using cell-type specific metabolic labelling of isolated neurites, we demonstrated that the processes not only of Glutamatergic but also of GABAergic neurons are capable of local translation, suggesting mRNA localization and local translation is a general property of neurons.

Cell-Type Targeted NF-kappaB Inhibition for the Treatment of Inflammatory Diseases

Cells ◽

10.3390/cells9071627 ◽

2020 ◽

Vol 9 (7) ◽

pp. 1627

Author(s):

Bettina Sehnert ◽

Harald Burkhardt ◽

Stefan Dübel ◽

Reinhard E. Voll

Keyword(s):

Adverse Effects ◽

Inflammatory Diseases ◽

Cell Types ◽

Cell Type ◽

Modular Architecture ◽

Biological Targets ◽

Cell Functions ◽

Cell Type Specific ◽

Nf Kappab

Deregulated NF-k activation is not only involved in cancer but also contributes to the pathogenesis of chronic inflammatory diseases like rheumatoid arthritis (RA) and multiple sclerosis (MS). Ideally, therapeutic NF-KappaB inhibition should only take place in those cell types that are involved in disease pathogenesis to maintain physiological cell functions in all other cells. In contrast, unselective NF-kappaB inhibition in all cells results in multiple adverse effects, a major hindrance in drug development. Hitherto, various substances exist to inhibit different steps of NF-kappaB signaling. However, powerful tools for cell-type specific NF-kappaB inhibition are not yet established. Here, we review the role of NF-kappaB in inflammatory diseases, current strategies for drug delivery and NF-kappaB inhibition and point out the “sneaking ligand” approach. Sneaking ligand fusion proteins (SLFPs) are recombinant proteins with modular architecture consisting of three domains. The prototype SLC1 binds specifically to the activated endothelium and blocks canonical NF-kappaB activation. In vivo, SLC1 attenuated clinical and histological signs of experimental arthritides. The SLFP architecture allows an easy exchange of binding and effector domains and represents an attractive approach to study disease-relevant biological targets in a broad range of diseases. In vivo, SLFP treatment might increase therapeutic efficacy while minimizing adverse effects.

H/ACA snoRNA levels are regulated during stem cell differentiation

Nucleic Acids Research ◽

10.1093/nar/gkaa612 ◽

2020 ◽

Vol 48 (15) ◽

pp. 8686-8703

Author(s):

Kathleen L McCann ◽

Sanam L Kavari ◽

Adam B Burkholder ◽

Bart T Phillips ◽

Traci M Tanaka Hall

Keyword(s):

Stem Cells ◽

Embryonic Stem ◽

Ribosomal Subunit ◽

Stem Cell Differentiation ◽

Cell Types ◽

Cellular Models ◽

Cell Type Specific ◽

Nucleolar Rnas ◽

Fine Tune ◽

Trna Binding

Abstract H/ACA small nucleolar RNAs (snoRNAs) guide pseudouridylation as part of a small nucleolar ribonucleoprotein complex (snoRNP). Disruption of H/ACA snoRNA levels in stem cells impairs pluripotency, yet it remains unclear how H/ACA snoRNAs contribute to differentiation. To determine if H/ACA snoRNA levels are dynamic during differentiation, we comprehensively profiled H/ACA snoRNA abundance in multiple murine cell types and during differentiation in three cellular models, including mouse embryonic stem cells and mouse myoblasts. We determined that the profiles of H/ACA snoRNA abundance are cell-type specific, and we identified a subset of snoRNAs that are specifically regulated during differentiation. Additionally, we demonstrated that a decrease in Snora27 abundance upon differentiation corresponds to a decrease in pseudouridylation of its target site within the E-site transfer RNA (tRNA) binding region of the 28S ribosomal RNA (rRNA) in the large ribosomal subunit. Together, these data point toward a potential model in which H/ACA snoRNAs are specifically regulated during differentiation to alter pseudouridylation and fine tune ribosome function.

Comprehensive Cell Type Specific Transcriptomics of the Human Kidney

10.1101/238063 ◽

2017 ◽

Cited By ~ 7

Author(s):

V Sivakamasundari ◽

Mohan Bolisetty ◽

Santhosh Sivajothi ◽

Shannon Bessonett ◽

Diane Ruan ◽

...

Keyword(s):

Human Kidney ◽

Cell Types ◽

Cell Type ◽

Vascular Integrity ◽

Normal Human Kidney ◽

Normal Human ◽

Cell Type Specific ◽

Disease Associated Genes ◽

Transcriptome Resource ◽

The Individual

AbstractThe human kidney is a complex organ composed of specialized cell types. To better define this cellular complexity, we profiled the individual transcriptomes of 22,469 normal human kidney cells, identifying 27 cell types. We describe three distinct endothelial cell populations, a novel subset of intercalated cells, interstitial macrophage and dendritic cells, and identify numerous novel cell-type-specific markers, many validated using imaging mass cytometry and immunohistochemistry. Receptor-ligand analysis revealed previously unknown intercalated-endothelial and intercalated-distal nephron interactions, suggesting a role in maintenance of vascular integrity and intercalated cell survival. Notably, kidney disease-associated genes were largely expressed in proximal tubules, podocytes, endothelial and myeloid cells, highlighting an underappreciated role for endothelial cells in kidney pathologies. Our analysis also provides a resource of cell type enriched markers, solute carriers, channels and lncRNAs. In summary, this cell-type-specific transcriptome resource provides the foundation for a comprehensive understanding of kidney function and dysfunction at single cell resolution.

Role of Transcriptional Read-Through in PRE Activity in Drosophila melanogaster

Acta Naturae ◽

10.32607/20758251-2016-8-2-79-86 ◽

2016 ◽

Vol 8 (2) ◽

pp. 79-86 ◽

Cited By ~ 3

Author(s):

P. V. Elizar’ev ◽

D. V. Lomaev ◽

D. A. Chetverina ◽

P. G. Georgiev ◽

M. M. Erokhin

Keyword(s):

Dna Sequences ◽

Cell Types ◽

Transcription Terminator ◽

Response Elements ◽

Polycomb Response Elements ◽

The Individual ◽

Multicellular Organisms ◽

Different Cell Types ◽

Main Factor

Maintenance of the individual patterns of gene expression in different cell types is required for the differentiation and development of multicellular organisms. Expression of many genes is controlled by Polycomb (PcG) and Trithorax (TrxG) group proteins that act through association with chromatin. PcG/TrxG are assembled on the DNA sequences termed PREs (Polycomb Response Elements), the activity of which can be modulated and switched from repression to activation. In this study, we analyzed the influence of transcriptional read-through on PRE activity switch mediated by the yeast activator GAL4. We show that a transcription terminator inserted between the promoter and PRE doesnt prevent switching of PRE activity from repression to activation. We demonstrate that, independently of PRE orientation, high levels of transcription fail to dislodge PcG/TrxG proteins from PRE in the absence of a terminator. Thus, transcription is not the main factor required for PRE activity switch.