Chromatin loop anchors contain core structural components of the gene expression machinery in maize

Abstract Background Three-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heterochromatic regions marked by higher repeat content, but little is known on their spatial organization and genome-wide occurrence in relation to transcriptional activity. Results Here, ultra-deep Hi-C sequencing of maize B73 leaf tissue was combined with gene expression and open chromatin sequencing for chromatin loop discovery and correlation with hierarchical topologically-associating domains (TADs) and transcriptional activity. A majority of all anchors are shared between multiple loops from previous public maize high-resolution interactome datasets, suggesting a highly dynamic environment, with a conserved set of anchors involved in multiple interaction networks. Chromatin loop interiors are marked by higher repeat contents than the anchors flanking them. A small fraction of high-resolution interaction anchors, fully embedded in larger chromatin loops, co-locate with active genes and putative protein-binding sites. Combinatorial analyses indicate that all anchors studied here co-locate with at least 81.5% of expressed genes and 74% of open chromatin regions. Approximately 38% of all Hi-C chromatin loops are fully embedded within hierarchical TAD-like domains, while the remaining ones share anchors with domain boundaries or with distinct domains. Those various loop types exhibit specific patterns of overlap for open chromatin regions and expressed genes, but no apparent pattern of gene expression. In addition, up to 63% of all unique variants derived from a prior public maize eQTL dataset overlap with Hi-C loop anchors. Anchor annotation suggests that < 7% of all loops detected here are potentially devoid of any genes or regulatory elements. The overall organization of chromatin loop anchors in the maize genome suggest a loop modeling system hypothesized to resemble phase separation of repeat-rich regions. Conclusions Sets of conserved chromatin loop anchors mapping to hierarchical domains contains core structural components of the gene expression machinery in maize. The data presented here will be a useful reference to further investigate their function in regard to the formation of transcriptional complexes and the regulation of transcriptional activity in the maize genome.

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Chromatin loop anchors contain core structural components of the gene expression machinery in maize

10.21203/rs.3.rs-50688/v2 ◽

2020 ◽

Author(s):

Stephane Deschamps ◽

John A Crow ◽

Nadia Chaidir ◽

Brooke Peterson-Burch ◽

Sunil Kumar ◽

...

Keyword(s):

Gene Expression ◽

High Resolution ◽

Transcriptional Activity ◽

Spatial Organization ◽

Regulatory Elements ◽

Open Chromatin ◽

Maize Genome ◽

Chromatin Loop ◽

Structural Components ◽

Chromatin Loops

Abstract BackgroundThree-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heterochromatic regions marked by higher repeat content, but little is known on their spatial organization and genome-wide occurrence in relation to transcriptional activity. ResultsHere, ultra-deep Hi-C sequencing of maize B73 leaf tissue was combined with gene expression and open chromatin sequencing for chromatin loop discovery and correlation with hierarchical topologically-associating domains (TADs) and transcriptional activity. A majority of all anchors are shared between multiple loops from previous public maize high-resolution interactome datasets, suggesting a highly dynamic environment, with a conserved set of anchors involved in multiple interaction networks. Chromatin loop interiors are marked by higher repeat contents than the anchors flanking them. A small fraction of high-resolution interaction anchors, fully embedded in larger chromatin loops, co-locate with active genes and putative protein-binding sites. Combinatorial analyses indicate that all anchors studied here co-locate with at least 81.5% of expressed genes and 74% of open chromatin regions. Approximately 38% of all Hi-C chromatin loops are fully embedded within hierarchical TAD-like domains, while the remaining ones share anchors with domain boundaries or with distinct domains. Those various loop types exhibit specific patterns of overlap for open chromatin regions and expressed genes, but no apparent pattern of gene expression. In addition, up to 63% of all unique variants derived from a prior public maize eQTL dataset overlap with Hi-C loop anchors. Anchor annotation suggests that <7% of all loops detected here are potentially devoid of any genes or regulatory elements. The overall organization of chromatin loop anchors in the maize genome suggest a loop modeling system hypothesized to resemble phase separation of repeat-rich regions. ConclusionsSets of conserved chromatin loop anchors mapping to hierarchical domains contains core structural components of the gene expression machinery in maize. The data presented here will be a useful reference to further investigate their function in regard to the formation of transcriptional complexes and the regulation of transcriptional activity in the maize genome.

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Chromatin Loop Anchors Are Core Structural Components of the Gene Expression Machinery in Maize

10.21203/rs.3.rs-50688/v1 ◽

2020 ◽

Author(s):

Stephane Deschamps ◽

John A Crow ◽

Nadia Chaidir ◽

Brooke Peterson-Burch ◽

Sunil Kumar ◽

...

Keyword(s):

Gene Expression ◽

High Resolution ◽

Transcriptional Activity ◽

Spatial Organization ◽

Target Genes ◽

Regulation Of Gene Expression ◽

Regulatory Elements ◽

Open Chromatin ◽

Chromatin Loop ◽

Chromatin Loops

Abstract Background Three-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heterochromatic regions marked by higher repeat content, but little is known on their spatial organization and genome-wide occurrence in relation to transcriptional activity. Results Here, ultra-deep Hi-C sequencing of maize B73 leaf tissue was combined with gene expression and open chromatin sequencing for chromatin loop discovery and correlation with transcriptional activity. Chromatin loops, made of two “anchors” flanking a loop “interior”, overlap with up to 90% of high-resolution interaction domains from a previous public maize interactome dataset. A majority of all anchors are shared between multiple loops, suggesting a highly dynamic environment, with a conserved set of anchors involved in multiple interaction networks. Chromatin loop interiors are marked by higher repeat contents than the anchors flanking them. A small fraction of high-resolution interaction anchors, fully embedded in larger chromatin loops, co-locate with active genes and putative protein-binding sites. Combinatorial analysis indicate that all anchors studied here co-locate with at least 81.5% of expressed genes and 74% of open chromatin regions. Up to 63% of all unique variants derived from a prior public maize eQTL datasets overlap with Hi-C loop anchors. Anchor annotation suggests that <7% of all loops detected from one Hi-C library are potentially devoid of any genes or regulatory elements. The overall conservation and organization of chromatin loop anchors in the maize genome suggest a loop modeling system hypothesized to resemble phase separation of repeat-rich regions. Conclusions A majority of expressed genes and open chromatin regions co-locate with a conserved set of chromatin loop anchors. The results presented here will be a useful reference to further investigate the function of chromatin loop anchors and of the formation of interaction regions in the regulation of gene expression in maize.

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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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Enhancer variants associated with Alzheimer’s disease affect gene expression via chromatin looping

BMC Medical Genomics ◽

10.1186/s12920-019-0574-8 ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 7

Author(s):

Masataka Kikuchi ◽

Norikazu Hara ◽

Mai Hasegawa ◽

Akinori Miyashita ◽

Ryozo Kuwano ◽

...

Keyword(s):

Gene Expression ◽

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Regulatory Elements ◽

Genome Wide Association Studies ◽

Expression Levels ◽

Chromatin Loops ◽

Coding Regions ◽

Affect Gene Expression ◽

Gene Expression Levels

Abstract Background Genome-wide association studies (GWASs) have identified single-nucleotide polymorphisms (SNPs) that may be genetic factors underlying Alzheimer’s disease (AD). However, how these AD-associated SNPs (AD SNPs) contribute to the pathogenesis of this disease is poorly understood because most of them are located in non-coding regions, such as introns and intergenic regions. Previous studies reported that some disease-associated SNPs affect regulatory elements including enhancers. We hypothesized that non-coding AD SNPs are located in enhancers and affect gene expression levels via chromatin loops. Methods To characterize AD SNPs within non-coding regions, we extracted 406 AD SNPs with GWAS p-values of less than 1.00 × 10− 6 from the GWAS catalog database. Of these, we selected 392 SNPs within non-coding regions. Next, we checked whether those non-coding AD SNPs were located in enhancers that typically regulate gene expression levels using publicly available data for enhancers that were predicted in 127 human tissues or cell types. We sought expression quantitative trait locus (eQTL) genes affected by non-coding AD SNPs within enhancers because enhancers are regulatory elements that influence the gene expression levels. To elucidate how the non-coding AD SNPs within enhancers affect the gene expression levels, we identified chromatin-chromatin interactions by Hi-C experiments. Results We report the following findings: (1) nearly 30% of non-coding AD SNPs are located in enhancers; (2) eQTL genes affected by non-coding AD SNPs within enhancers are associated with amyloid beta clearance, synaptic transmission, and immune responses; (3) 95% of the AD SNPs located in enhancers co-localize with their eQTL genes in topologically associating domains suggesting that regulation may occur through chromatin higher-order structures; (4) rs1476679 spatially contacts the promoters of eQTL genes via CTCF-CTCF interactions; (5) the effect of other AD SNPs such as rs7364180 is likely to be, at least in part, indirect through regulation of transcription factors that in turn regulate AD associated genes. Conclusion Our results suggest that non-coding AD SNPs may affect the function of enhancers thereby influencing the expression levels of surrounding or distant genes via chromatin loops. This result may explain how some non-coding AD SNPs contribute to AD pathogenesis.

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Insight into GATA1 transcriptional activity through interrogation of cis elements disrupted in human erythroid disorders

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1521754113 ◽

2016 ◽

Vol 113 (16) ◽

pp. 4434-4439 ◽

Cited By ~ 40

Author(s):

Aoi Wakabayashi ◽

Jacob C. Ulirsch ◽

Leif S. Ludwig ◽

Claudia Fiorini ◽

Makiko Yasuda ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Transcriptional Activity ◽

Regulatory Elements ◽

Binding Motif ◽

Targeted Disruption ◽

Altered Gene Expression ◽

Whole Exome ◽

Altered Gene ◽

Insight Into

Whole-exome sequencing has been incredibly successful in identifying causal genetic variants and has revealed a number of novel genes associated with blood and other diseases. One limitation of this approach is that it overlooks mutations in noncoding regulatory elements. Furthermore, the mechanisms by which mutations in transcriptional cis-regulatory elements result in disease remain poorly understood. Here we used CRISPR/Cas9 genome editing to interrogate three such elements harboring mutations in human erythroid disorders, which in all cases are predicted to disrupt a canonical binding motif for the hematopoietic transcription factor GATA1. Deletions of as few as two to four nucleotides resulted in a substantial decrease (>80%) in target gene expression. Isolated deletions of the canonical GATA1 binding motif completely abrogated binding of the cofactor TAL1, which binds to a separate motif. Having verified the functionality of these three GATA1 motifs, we demonstrate strong evolutionary conservation of GATA1 motifs in regulatory elements proximal to other genes implicated in erythroid disorders, and show that targeted disruption of such elements results in altered gene expression. By modeling transcription factor binding patterns, we show that multiple transcription factors are associated with erythroid gene expression, and have created predictive maps modeling putative disruptions of their binding sites at key regulatory elements. Our study provides insight into GATA1 transcriptional activity and may prove a useful resource for investigating the pathogenicity of noncoding variants in human erythroid disorders.

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The Causes and Consequences of Spatial Organization of the Genome in Regulation of Gene Expression

Frontiers in Immunology ◽

10.3389/fimmu.2021.682397 ◽

2021 ◽

Vol 12 ◽

Author(s):

Marios Agelopoulos ◽

Spyros Foutadakis ◽

Dimitris Thanos

Keyword(s):

Gene Expression ◽

Spatial Organization ◽

Protein Complexes ◽

Regulation Of Gene Expression ◽

Regulatory Elements ◽

Current View ◽

Regulation Of Expression ◽

Time Space ◽

Transcriptional Regulatory ◽

Immune Related Genes

Regulation of gene expression in time, space and quantity is orchestrated by the functional interplay of cis-acting elements and trans-acting factors. Our current view postulates that transcription factors recognize enhancer DNA and read the transcriptional regulatory code by cooperative DNA binding to specific DNA motifs, thus instructing the recruitment of transcriptional regulatory complexes forming a plethora of higher-ordered multi-protein-DNA and protein-protein complexes. Here, we reviewed the formation of multi-dimensional chromatin assemblies implicated in gene expression with emphasis on the regulatory role of enhancer hubs as coordinators of stochastic gene expression. Enhancer hubs contain many interacting regulatory elements and represent a remarkably dynamic and heterogeneous network of multivalent interactions. A functional consequence of such complex interaction networks could be that individual enhancers function synergistically to ensure coordination, tight control and robustness in regulation of expression of spatially connected genes. In this review, we discuss fundamental paradigms of such inter- and intra- chromosomal associations both in the context of immune-related genes and beyond.

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Analysis of putative cis-regulatory elements regulating blood pressure variation

10.1101/820522 ◽

2019 ◽

Author(s):

Priyanka Nandakumar ◽

Dongwon Lee ◽

Thomas J. Hoffmann ◽

Georg B. Ehret ◽

Dan Arking ◽

...

Keyword(s):

Gene Expression ◽

Blood Pressure ◽

Cell Types ◽

Regulatory Elements ◽

Open Chromatin ◽

Genome Wide Association Studies ◽

Cell Type ◽

Functional Scores ◽

Cell Type Specific ◽

Different Tissues

AbstractHundreds of loci have been associated with blood pressure traits from many genome-wide association studies. We identified an enrichment of these loci in aorta and tibial artery expression quantitative trait loci in our previous work in ∼100,000 Genetic Epidemiology Research on Aging (GERA) study participants. In the present study, we subsequently focused on determining putative regulatory regions for these and other tissues of relevance to blood pressure, to both fine-map these loci by pinpointing genes and variants of functional interest within them, and to identify any novel genes.We constructed maps of putative cis-regulatory elements using publicly available open chromatin data for the heart, aorta and tibial arteries, and multiple kidney cell types. Sequence variants within these regions may be evaluated quantitatively for their tissue- or cell-type-specific regulatory impact using deltaSVM functional scores, as described in our previous work. In order to identify genes of interest, we aggregate these variants in these putative cis-regulatory elements within 50Kb of the start or end of genes considered as “expressed” in these tissues or cell types using publicly available gene expression data, and use the deltaSVM scores as weights in the well-known group-wise sequence kernel association test (SKAT). We test for association with both blood pressure traits as well as expression within these tissues or cell types of interest, and identify several genes, including MTHFR, C10orf32, CSK, NOV, ULK4, SDCCAG8, SCAMP5, RPP25, HDGFRP3, VPS37B, and PPCDC. Although our study centers on blood pressure traits, we additionally examined two known genes, SCN5A and NOS1AP involved in the cardiac trait QT interval, in the Atherosclerosis Risk in Communities Study (ARIC), as a positive control, and observed an expected heart-specific effect. Thus, our method may be used to identify variants and genes for further functional testing using tissue- or cell-type-specific putative regulatory information.Author SummarySequence change in genes (“variants”) are linked to the presence and severity of different traits or diseases. However, as genes may be expressed in different tissues and at different times and degrees, using this information is expected to more accurately identify genes of interest. Variants within the genes are essential, but also in the sequences (“regulatory elements”) that control the genes’ expression in different tissues or cell types. In this study, we aim to use this information about expression and variants potentially involved in gene expression regulation to better pinpoint genes and variants in regulatory elements of interest for blood pressure regulation. We do so by taking advantage of such data that are publicly available, and use methods to combine information about variants in aggregate within a gene’s putative regulatory elements in tissues thought to be relevant for blood pressure, and identify several genes, meant to enable experimental follow-up.

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The High-resolution Timeline of Expression of Ribosomal Protein Genes in Yeast

10.1101/170399 ◽

2017 ◽

Author(s):

Xueling Li ◽

Gang Chen ◽

Bernard Fongang ◽

Dirar Homouz ◽

Maga Rowicka ◽

...

Keyword(s):

Gene Expression ◽

High Resolution ◽

Ribosomal Proteins ◽

Ribosome Biogenesis ◽

Center Of Mass ◽

Regulatory Elements ◽

Ribosomal Protein Genes ◽

Translational Initiation ◽

Expression Of Genes ◽

Expression Time

AbstractThe yeast ribosome is a complex molecular machine built from four rRNAs and over 70 r-proteins. Ribosome biogenesis involves ordered incorporation of ribosomal proteins, accompanied by and association and dissociation of other proteins specific to different stages of the process. By model-based analysis of temporal profiles of gene expression in a metabolically regulated system, we obtained an accurate, high-resolution estimation of the time of expression of genes coding for proteins involved in ribosome biogenesis. The ribosomal proteins are expressed in a sequence that spans approximately 25-minutes under metabolically regulated conditions. The genes coding for proteins incorporated into the mature ribosome are expressed significantly later than those that are not incorporated, but are otherwise involved in ribosome biogenesis, localization and assembly, rRNA processing and translational initiation. The relative expression time of proteins localized within specified neighborhood is significantly correlated with the distance to the centroid of the mature ribosome: protein localized closer to the center of mass of the entire complex tend to be expressed earlier than the protein localized further from the center. The timeline of gene expression also agrees with the known dependencies between recruitment of specific proteins into the mature ribosome. These findings are consistent in two independent experiments. We have further identified regulatory elements correlated with the time of regulation, including a possible dependence of expression time on the position of the RAP1 binding site within the 5’UTR.

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DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution

10.1101/2020.04.30.069377 ◽

2020 ◽

Cited By ~ 1

Author(s):

Hanqing Liu ◽

Jingtian Zhou ◽

Wei Tian ◽

Chongyuan Luo ◽

Anna Bartlett ◽

...

Keyword(s):

Dna Methylation ◽

Mouse Brain ◽

Spatial Organization ◽

Brain Area ◽

Cell Types ◽

Regulatory Elements ◽

Mammalian Brain ◽

Open Chromatin ◽

Cell Type ◽

Single Nucleus

SummaryMammalian brain cells are remarkably diverse in gene expression, anatomy, and function, yet the regulatory DNA landscape underlying this extensive heterogeneity is poorly understood. We carried out a comprehensive assessment of the epigenomes of mouse brain cell types by applying single nucleus DNA methylation sequencing to profile 110,294 nuclei from 45 regions of the mouse cortex, hippocampus, striatum, pallidum, and olfactory areas. We identified 161 cell clusters with distinct spatial locations and projection targets. We constructed taxonomies of these epigenetic types, annotated with signature genes, regulatory elements, and transcription factors. These features indicate the potential regulatory landscape supporting the assignment of putative cell types, and reveal repetitive usage of regulators in excitatory and inhibitory cells for determining subtypes. The DNA methylation landscape of excitatory neurons in the cortex and hippocampus varied continuously along spatial gradients. Using this deep dataset, an artificial neural network model was constructed that precisely predicts single neuron cell-type identity and brain area spatial location. Integration of high-resolution DNA methylomes with single-nucleus chromatin accessibility data allowed prediction of high-confidence enhancer-gene interactions for all identified cell types, which were subsequently validated by cell-type-specific chromatin conformation capture experiments. By combining multi-omic datasets (DNA methylation, chromatin contacts, and open chromatin) from single nuclei and annotating the regulatory genome of hundreds of cell types in the mouse brain, our DNA methylation atlas establishes the epigenetic basis for neuronal diversity and spatial organization throughout the mouse brain.

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Single cell resolution regulatory landscape of the mouse kidney highlights cellular differentiation programs and renal disease targets

10.1101/2020.05.24.113910 ◽

2020 ◽

Cited By ~ 1

Author(s):

Zhen Miao ◽

Michael S. Balzer ◽

Ziyuan Ma ◽

Hongbo Liu ◽

Junnan Wu ◽

...

Keyword(s):

Gene Expression ◽

Single Cell ◽

Kidney Development ◽

Developmental Stages ◽

Major Gene ◽

Cell Types ◽

Regulatory Elements ◽

Open Chromatin ◽

Cell Type ◽

Single Nucleotide Variants

AbstractDetermining the epigenetic program that generates unique cell types in the kidney is critical for understanding cell-type heterogeneity during tissue homeostasis and injury response.Here, we profiled open chromatin and gene expression in developing and adult mouse kidneys at single cell resolution. We show critical reliance of gene expression on distal regulatory elements (enhancers). We define key cell type-specific transcription factors and major gene-regulatory circuits for kidney cells. Dynamic chromatin and expression changes during nephron progenitor differentiation demonstrated that podocyte commitment occurs early and is associated with sustained Foxl1 expression. Renal tubule cells followed a more complex differentiation, where Hfn4a was associated with proximal and Tfap2b with distal fate. Mapping single nucleotide variants associated with human kidney disease identified critical cell types, developmental stages, genes, and regulatory mechanisms.We provide a global single cell resolution view of chromatin accessibility of kidney development. The dataset is available via interactive public websites.

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