Chromatin Conformation Capture Research Articles

Transcriptional Hubs Within Cliques in Ensemble Hi-C Chromatin Interaction Networks.

Chromatin conformation capture technologies permit the study of chromatin spatial organization on a genome-wide scale at a variety of resolutions. Despite the increasing precision and resolution of high-throughput chromatin conformation capture (Hi-C) methods, it remains challenging to conclusively link transcriptional activity to spatial organizational phenomena. We have developed a clique-based approach for analyzing Hi-C data that helps identify chromosomal hotspots that feature considerable enrichment of chromatin annotations for transcriptional start sites and, building on previously published work, show that these chromosomal hotspots are not only significantly enriched in RNA polymerase II binding sites as identified by the ENCODE project, but also identify a noticeable increase in FANTOM5 and GTEx transcription within our identified cliques across a variety of tissue types. From the obtained data, we surmise that our cliques are a suitable method for identifying transcription factories in Hi-C data, and outline further extensions to the method that may make it useful for locating regions of increased transcriptional activity in datasets where in-depth expression or polymerase data may not be available.

Whole-genome sequencing of Ganoderma boninense, the causal agent of basal stem rot disease in oil palm, via combined short- and long-read sequencing

The hemibiotrophic Basidiomycete pathogen Ganoderma boninense (Gb) is the dominant causal agent of oil palm basal stem rot disease. Here, we report a complete chromosomal genome map of Gb using a combination of short-read Illumina and long-read Pacific Biosciences (PacBio) sequencing platforms combined with chromatin conformation capture data from the Chicago and Hi-C platforms. The genome was 55.87 Mb in length and assembled to a high contiguity (N50: 304.34 kb) of 12 chromosomes built from 112 scaffolds, with a total of only 4.34 Mb (~ 7.77%) remaining unplaced. The final assemblies were evaluated for completeness of the genome by using Benchmarking Universal Single Copy Orthologs (BUSCO) v4.1.4, and based on 4464 total BUSCO polyporales group searches, the assemblies yielded 4264 (95.52%) of the conserved orthologs as complete and only a few fragmented BUSCO of 42 (0.94%) as well as a missing BUSCO of 158 (3.53%). Genome annotation predicted a total of 21,074 coding genes, with a GC content ratio of 59.2%. The genome features were analyzed with different databases, which revealed 2471 Gene Ontology/GO (11.72%), 5418 KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthologous/KO (25.71%), 13,913 Cluster of Orthologous Groups of proteins/COG (66.02%), 60 ABC transporter (0.28%), 1049 Carbohydrate-Active Enzymes/CAZy (4.98%), 4005 pathogen–host interactions/PHI (19%), and 515 fungal transcription factor/FTFD (2.44%) genes. The results obtained in this study provide deep insight for further studies in the future.

Probabilistic association of differentially expressed genes with cis-regulatory elements.

Differential gene expression in response to perturbations is mediated at least in part by changes in binding of transcription factors (TFs) and other proteins at specific genomic regions. Association of these cis-regulatory elements (CREs) with their target genes is a challenging task that is essential to address many biological and mechanistic questions. Many current approaches rely on chromatin conformation capture techniques or single-cell correlational methods to establish CRE-to-gene associations. These methods can be effective but have limitations, including resolution, gaps in detectable association distances, and cost. As an alternative, we have developed DegCre, a nonparametric method that evaluates correlations between measurements of perturbation-induced differential gene expression and differential regulatory signal at CREs to score possible CRE-to-gene associations. It has several unique features, including the ability to use any type of CRE activity measurement, yield probabilistic scores for CRE-to-gene pairs, and assess CRE-to-gene pairings across a wide range of sequence distances. We apply DegCre to six data sets, each using different perturbations and containing a variety of regulatory signal measurements, including chromatin openness, histone modifications, and TF occupancy. To test their efficacy, we compare DegCre associations to Hi-C loop calls and CRISPR-validated CRE-to-gene associations, establishing good performance by DegCre that is comparable or superior to competing methods. DegCre is a novel approach to the association of CREs to genes from a perturbation-differential perspective, with strengths that are complementary to existing approaches and allow for new insights into gene regulation.

First telomere-to-telomere gapless assembly of the rice blast fungus Pyricularia oryzae

Rice blast caused by Pyricularia oryzae (syn., Magnaporthe oryzae) was one of the most destructive diseases of rice throughout the world. Genome assembly was fundamental to genetic variation identification and critically impacted the understanding of its ability to overcome host resistance. Here, we report a gapless genome assembly of rice blast fungus P. oryzae strain P131 using PacBio, Illumina and high throughput chromatin conformation capture (Hi-C) sequencing data. This assembly contained seven complete chromosomes (43,237,743 bp) and a circular mitochondrial genome (34,866 bp). Approximately 14.31% of this assembly carried repeat sequences, significantly greater than its previous assembled version. This assembly had a 99.9% complement in BUSCO evaluation. A total of 14,982 genes protein-coding genes were predicted. In summary, we assembled the first telomere-to-telomere gapless genome of P. oryzae, which would be a valuable genome resource for future research on the genome evolution and host adaptation.

Allele-Specific Regulation of the Candidate Autism Liability Gene RAI1 by the Enhancer Variant rs4925102 (C/G).

Retinoic acid-induced 1 (RAI1) is a dosage-sensitive gene that causes autistic phenotypes when deleted or duplicated. Observations from clinical cases and animal models also suggest that changes of RAI1 expression levels contribute to autism. Previously, we used a bioinformatic approach to identify several single nucleotide polymorphisms (SNPs) located within the 5'-region of RAI1 that correlate with RAI1 mRNA expression in the human brain. In particular, the SNP rs4925102 was identified as a candidate cis-acting regulatory variant, the genotype of which may affect the binding of transcription factors that influence RAI1 mRNA expression. In this study, we provide experimental evidence based on reporter gene, chromatin immunoprecipitation (ChIP), and chromatin conformation capture (3C) assays that rs4925102 regulates RAI1 mRNA expression in an allele-specific manner in human cell lines, including the neuroblastoma-derived cell line SH-SY5Y. We also describe a statistically significant association between rs4925102 genotype and autism spectrum disorder (ASD) diagnosis in a case-control study and near-statistically significant association in an Autism Genome Project (AGP) transmission disequilibrium (TDT) study using Caucasian subjects.

A chromosome-level genome assembly of the spider mite Tetranychus piercei McGregor

Despite the rapid advances in sequencing technology, limited genomic resources are currently available for phytophagous spider mites, which include many important agricultural pests. One of these pests is Tetranychus piercei (McGregor), a serious banana pest in East Asia exhibiting remarkable tolerance to high temperature. In this study, we assembled a high-quality genome of T. piercei using a combination of PacBio long reads and Illumina short reads sequencing. With the assistance of chromatin conformation capture technology, 99.9% of the contigs were anchored into three pseudochromosomes with a total size of 86.02 Mb. Repetitive elements, accounting for 14.16% of this genome (12.20 Mb), are predominantly composed of long-terminal repeats (30.7%). By combining evidence of ab initio prediction, transcripts, and homologous proteins, we annotated 11,881 protein-coding genes. Both the genome and proteins have high BUSCO completeness scores (>94%). This high-quality genome, along with reliable annotation, provides a valuable resource for investigating the high-temperature tolerance of this species and exploring the genomic basis that underlies the host range evolution of spider mites.

Chromosome-level genome assembly of the European green woodpecker Picus viridis.

The European green woodpecker, Picus viridis, is a widely distributed species found in the Western Palearctic region. Here, we assembled a highly contiguous genome assembly for this species using a combination of short- and long-read sequencing and scaffolded with chromatin conformation capture (Hi-C). The final genome assembly was 1.28 Gb and features a scaffold N50 of 37 Mb and a scaffold L50 of 39.165 Mb. The assembly incorporates 89.4% of the genes identified in birds in OrthoDB. Gene and repetitive content annotation on the assembly detected 15,805 genes and a ∼30.1% occurrence of repetitive elements, respectively. Analysis of synteny demonstrates the fragmented nature of the P. viridis genome when compared to the chicken (Gallus gallus). The assembly and annotations produced in this study will certainly help for further research into the genomics of P. viridis and the comparative evolution of woodpeckers. Five historical and seven contemporary samples have been resequenced and may give insights on the population history of this species.

Abstract 405: Translocation detection in cancer using low-pass pore-c sequencing

Abstract Complex chromosomal rearrangements, including translocations, play a critical role in oncogenesis and are often identified as recurrent genetic aberrations in hematologic malignancies and solid tumors[1]. Translocation detection by karyotyping of an individual’s metaphase chromosomes remains challenging for detection of balanced rearrangements, which have no gain or loss of genetic material. Rearrangement detection using whole-genome sequencing is a viable alternative, but it relies on breakpoint-spanning reads and requires high sequencing depth (30-60x) with long reads to achieve high sensitivity, especially in repetitive regions of the genome[2]. Here, we describe a workflow for translocation detection at low sequencing depth with Oxford Nanopore’s long read chromatin conformation capture technique, Pore-C[3]. Importantly, for translocation calling, Pore-C does not rely on breakpoint-spanning reads but rather the high intrachromosomal interaction frequency of genomic regions around the breakpoint, thus largely lowering sequencing depth requirements and reducing mapping issues in low complexity regions. We prepared, barcoded, and sequenced Pore-C libraries of 3 cancer cell lines including lung cancer (A549), Acute Monocytic Leukemia (THP-1), melanoma (COLO 829) and its matching normal (COLO 829 BL) on a single Q20+ MinION flow cell (FLO-MIN114). Genome-wide contact maps of low-pass data (<1.5 Gbps per sample) were compared against higher depth (>30 Gbps per sample) Hi-C maps [4], revealing that low-pass Pore-C successfully captured large-scale genomic rearrangement. For example, chromosomal pairs chr8-chr11 and chr15-chr19 in A549, chr9-chr11 and chr1-chr20 in THP1, and chr7-chr15 in Colo829 were detected at <0.5X depth of sequencing coverage. These translocation events were further validated by breakpoint analysis using adaptive sampling, where targeted regions were previously confirmed by independent studies[4],[5]. Low-pass Pore-C detects translocations in an unbiased manner and does not require prior knowledge of the translocation structure. Combined with its simple sample-preparation workflow and the capability to provide genome-wide copy-number information in a single experiment, it can serve as a cost-effective and comprehensive tool for cancer genomic studies. [1] Chromosomal translocations in human cancer, Nature, 372, 143 (1994) [2] Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumors, Genome Biology, 18, 125 (2017) [3] Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing, Nature Biotechnology, 40, 1488(2022) [4] Chromosomal translocations detection in cancer cells using chromosomal conformation capture data, Genes (Basel), 13, 7 (2022) [5] A multi-platform reference for somatic structural variation detection, Cell Genomics, 2, 6 (2022) Citation Format: Scott Hickey, Xiaoguang Dai, Sergey Aganezov, John Beaulaurier, Eoghan Harrington, Sissel Juul. Translocation detection in cancer using low-pass pore-c sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 405.

Abstract 2860: High-resolution mapping of oncogenic structural changes in osteosarcoma

Abstract We have leveraged long-read and spatial sequencing modalities to identify cancer-specific oncogenic alterations for treatment of osteosarcomas. Osteosarcoma is archetypal of cancers driven by aneuploidy and structural rearrangement rather than point mutations. The functional consequences of many SVs stem from their effect on multidimensional genome organization. SVs can enable enhancer hijacking, alter boundaries of topologically associated domains (TADs), and move gene loci to different regulatory compartments to affect gene expression. SVs can also lead to the formation of extrachromosomal DNA amplicons (ecDNA), which can be megabases in size and can incorporate both genes and regulatory elements to result in substantial increases in gene transcription and intratumor heterogeneity. Complex SVs may have profound implications for prognosis and treatment in OS and other cancers yet they remain poorly understood. By incorporating long-read optical genome mapping (OGM) and chromatin conformation capture sequencing (HiC), we studied SVs in osteosarcoma with the goal of elucidating their contribution to cancer development. We used a unique panel of 11 OS patient-derived xenograft (PDX) cell lines which have been previously characterized regarding response to targeted therapies as well as genomically via whole genome (WGS), RNA (RNA-seq), and chromatin accessibility (ATAC-seq) sequencing. To understand the complex genomic reorganization that occurs in osteosarcoma, we integrated OGM and WGS data for all 11 cell lines to describe detailed genome-wide SVs including ecDNA formation. PDX lines assayed using OGM exhibited between 106 and 704 translocations each (versus zero detected in germline controls) and we identified dozens of potential ecDNA amplicons, including one amplicon which may explain exceptionally high expression of YAP1 and BIRC3 transcripts. Further, we used HiC to describe the topological environment resulting from these SVs and observed potential enhancer hijacking events affecting dozens of known oncogenes including MYC and CDK4. HiC interaction maps among six cell lines reveal genomic compartments and TAD boundaries in detail, with 4,167 unique TAD boundaries identified among six cell lines using 50kb genomic bins. Despite the observed complexity of these genomes, we note that 71% of TAD boundaries are consistent in at least four of the six HiC assayed cell lines, and 44% are present in all six lines. Changing TAD boundaries are associated with numerous SVs and/or copy number discrepancies, and are associated with genomic regions that contain genes with dysregulated RNA transcript levels. Overall, OGM and HiC modalities add considerably to our ability to detect oncogenic SVs and the genes they affect. Citation Format: Andrew Scott Clugston, Stan Leung, Eunice Fuentes, Leanne Sayles, Megan Ostrowski, Coco Wu, Christina Curtis, Zhicheng Ma, Yanding Zhao, Georgi K. Marinov, Vijay Ramani, Marcus Breese, Alejandro Sweet-Cordero. High-resolution mapping of oncogenic structural changes in osteosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2860.

Hi-C, a chromatin 3D structure technique advancing the functional genomics of immune cells.

The functional performance of immune cells relies on a complex transcriptional regulatory network. The three-dimensional structure of chromatin can affect chromatin status and gene expression patterns, and plays an important regulatory role in gene transcription. Currently available techniques for studying chromatin spatial structure include chromatin conformation capture techniques and their derivatives, chromatin accessibility sequencing techniques, and others. Additionally, the recently emerged deep learning technology can be utilized as a tool to enhance the analysis of data. In this review, we elucidate the definition and significance of the three-dimensional chromatin structure, summarize the technologies available for studying it, and describe the research progress on the chromatin spatial structure of dendritic cells, macrophages, T cells, B cells, and neutrophils.

A chromosome-level genome of mango exclusively from long-read sequence data.

Improvements in long-read sequencing techniques have greatly accelerated plant genome sequencing. Current de novo assemblies are routinely achieved by assembling long-read sequence data into contigs that are assembled to chromosome level by chromatin conformation capture. We report here a chromosome-level mango genome using only PacBio high-fidelity (HiFi) long reads. HiFi reads at high coverage (204x) resulted in the assembly of 17 chromosomes, each as a single contig with telomeres at both ends. The remaining three chromosomes were represented each by two contigs, with telomeres at one end and ribosomal repeats at the other end. Analyzing contig ends allowed them to be paired and linked to generate the remaining three complete chromosomes, telomere-to-telomere but with ribosomal repeats of uncertain length. The assembled genome was 365 Mb with 100% completeness as assessed by Benchmarking Universal Single-Copy Orthologs analysis. The haplotypes assembled demonstrated extensive structural differences. This approach using very high genome coverage may be useful for assembling high-quality genomes for many other plants.

Identification of a distal enhancer regulating hedgehog interacting protein gene in human lung epithelial cells

An intergenic region at chromosome 4q31 is one of the most significant regions associated with COPD susceptibility and lung function in GWAS. In this region, the implicated causal gene HHIP has a unique epithelial expression pattern in adult human lungs, in contrast to dominant expression in fibroblasts in murine lungs. However, the mechanism underlying the species-dependent cell type-specific regulation of HHIP remains largely unknown. We employed snATAC-seq analysis to identify open chromatin regions within the COPD GWAS region in various human lung cell types. ChIP-quantitative PCR, reporter assays, chromatin conformation capture assays and Hi-C assays were conducted to characterize the regulatory element in this region. CRISPR/Cas9-editing was performed in BEAS-2B cells to generate single colonies with stable knockout of the regulatory element. RT-PCR and Western blot assays were used to evaluate expression of HHIP and epithelial-mesenchymal transition (EMT)-related marker genes. We identified a distal enhancer within the COPD 4q31 GWAS locus that regulates HHIP transcription at baseline and after TGFβ treatment in a SMAD3-dependent, but Hedgehog-independent manner in human bronchial epithelial cells. The distal enhancer also maintains chromatin topological domains near 4q31 locus and HHIP gene. Reduced HHIP expression led to increased EMT induced by TGFβ in human bronchial epithelial cells. A distal enhancer regulates HHIP expression both under homeostatic condition and upon TGFβ treatment in human bronchial epithelial cells. The interaction between HHIP and TGFβ signalling possibly contributes to COPD pathogenesis. Supported by NIH grants R01HL127200, R01HL148667 and R01HL162783 (to X. Z).

Orchestrating chromosome conformation capture analysis with Bioconductor.

Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data structures, computational methods and visualization tools available in Bioconductor to investigate Hi-C, micro-C and other 3C-related data, in R. An online book ( https://bioconductor.org/books/OHCA/ ) further provides prospective end users with a number of workflows to process, import, analyze and visualize any type of chromosome conformation capture data.

MMCT-Loop: a mix model-based pipeline for calling targeted 3D chromatin loops.

Protein-specific Chromatin Conformation Capture (3C)-based technologies have become essential for identifying distal genomic interactions with critical roles in gene regulation. The standard techniques include Chromatin Interaction Analysis by Paired-End Tag (ChIA-PET), in situ Hi-C followed by chromatin immunoprecipitation (HiChIP) also known as PLAC-seq. To identify chromatin interactions from these data, a variety of computational methods have emerged. Although these state-of-art methods address many issues with loop calling, only few methods can fit different data types simultaneously, and the accuracy as well as the efficiency these approaches remains limited. Here we have generated a pipeline, MMCT-Loop, which ensures the accurate identification of strong loops as well as dynamic or weak loops through a mixed model. MMCT-Loop outperforms existing methods in accuracy, and the detected loops show higher activation functionality. To highlight the utility of MMCT-Loop, we applied it to conformational data derived from neural stem cell (NSCs) and uncovered several previously unidentified regulatory regions for key master regulators of stem cell identity. MMCT-Loop is an accurate and efficient loop caller for targeted conformation capture data, which supports raw data or pre-processed valid pairs as input, the output interactions are formatted and easily uploaded to a genome browser for visualization.

Assessing 2D visual encoding of 3D spatial connectivity.

Introduction: When visualizing complex data, the layout method chosen can greatly affect the ability to identify outliers, spot incorrect modeling assumptions, or recognize unexpected patterns. Additionally, visual layout can play a crucial role in communicating results to peers. Methods: In this paper, we compared the effectiveness of three visual layouts-the adjacency matrix, a half-matrix layout, and a circular layout-for visualizing spatial connectivity data, e.g., contacts derived from chromatin conformation capture experiments. To assess these visual layouts, we conducted a study comprising 150 participants from Amazon's Mechanical Turk, as well as a second expert study comprising 30 biomedical research scientists. Results: The Mechanical Turk study found that the circular layout was the most accurate and intuitive, while the expert study found that the circular and half-matrix layouts were more accurate than the matrix layout. Discussion: We concluded that the circular layout may be a good default choice for visualizing smaller datasets with relatively few spatial contacts, while, for larger datasets, the half- matrix layout may be a better choice. Our results also demonstrated how crowdsourcing methods could be used to determine which visual layouts are best for addressing specific data challenges in bioinformatics.

Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.

BL-Hi-C reveals the 3D genome structure of Brassica crops with high sensitivity.

High-throughput Chromatin Conformation Capture (Hi-C) technologies can be used to investigate the three-dimensional genomic structure of plants. However, the practical utility of these technologies is impeded by significant background noise, hindering their capability in detecting fine 3D genomic structures. In this study, we optimized the Bridge Linker Hi-C technology (BL-Hi-C) to comprehensively investigate the 3D chromatin landscape of Brassica rapa and Brassica oleracea. The Bouquet configuration of both B. rapa and B. oleracea was elucidated through the construction of a 3D genome simulation. The optimized BL-Hi-C exhibited lower background noise compared to conventional Hi-C methods. Taking this advantage, we used BL-Hi-C to identify FLC gene loops in Arabidopsis, B. rapa, and B. oleracea. We observed that gene loops of FLC2 exhibited conservation across Arabidopsis, B. rapa, and B. oleracea. While gene loops of syntenic FLCs exhibited conservation across B. rapa and B. oleracea, variations in gene loops were evident among multiple paralogs FLCs within the same species. Collectively, our findings highlight the high sensitivity of optimized BL-Hi-C as a powerful tool for investigating the fine 3D genomic organization.

CD-Loop: a chromatin loop detection method based on the diffusion model.

In recent years, there have been significant advances in various chromatin conformation capture techniques, and annotating the topological structure from Hi-C contact maps has become crucial for studying the three-dimensional structure of chromosomes. However, the structure and function of chromatin loops are highly dynamic and diverse, influenced by multiple factors. Therefore, obtaining the three-dimensional structure of the genome remains a challenging task. Among many chromatin loop prediction methods, it is difficult to fully extract features from the contact map and make accurate predictions at low sequencing depths. In this study, we put forward a deep learning framework based on the diffusion model called CD-Loop for predicting accurate chromatin loops. First, by pre-training the input data, we obtain prior probabilities for predicting the classification of the Hi-C contact map. Then, by combining the denoising process based on the diffusion model and the prior probability obtained by pre-training, candidate loops were predicted from the input Hi-C contact map. Finally, CD-Loop uses a density-based clustering algorithm to cluster the candidate chromatin loops and predict the final chromatin loops. We compared CD-Loop with the currently popular methods, such as Peakachu, Chromosight, and Mustache, and found that in different cell types, species, and sequencing depths, CD-Loop outperforms other methods in loop annotation. We conclude that CD-Loop can accurately predict chromatin loops and reveal cell-type specificity. The code is available at https://github.com/wangyang199897/CD-Loop.

Shaping gene expression and its evolution by chromatin architecture and enhancer activity.

Transcriptional regulation plays a pivotal role in orchestrating the intricate genetic programs governing embryonic development. The expression of developmental genes relies on the combined activity of several cis-regulatory elements (CREs), such as enhancers and silencers, which can be located at long linear distances from the genes that they regulate and that interact with them through establishment of chromatin loops. Mutations affecting their activity or interaction with their target genes can lead to developmental disorders and are thought to have importantly contributed to the evolution of the animal body plan. The income of next-generation-sequencing approaches has allowed identifying over a million of sequences with putative regulatory potential in the human genome. Characterizing their function and establishing gene-CREs maps is essential to decode the logic governing developmental gene expression and is one of the major challenges of the post-genomic era. Chromatin 3D organization plays an essential role in determining how CREs specifically contact their target genes while avoiding deleterious off-target interactions. Our understanding of these aspects has greatly advanced with the income of chromatin conformation capture techniques and fluorescence microscopy approaches to visualize the organization of DNA elements in the nucleus. Here we will summarize relevant aspects of how the interplay between CRE activity and chromatin 3D organization regulates developmental gene expression and how it relates to pathological conditions and the evolution of animal body plan.

Chromosome-level genome assembly of the Stoliczka’s Asian trident bat (Aselliscus stoliczkanus)

Stoliczka’s Asian trident bat (Aselliscus stoliczkanus) is a small-bodied species and very sensitive to climate change. Here, we presented a chromosome-level genome assembly of A. stoliczkanus by combining Illumina sequencing, Nanopore sequencing and high-throughput chromatin conformation capture (Hi-C) sequencing technology. The genome assembly was 2.18 Gb in size with 98.26% of the genome sequences anchored onto 14 autosomes and two sex chromosomes (X and Y). The quality of the genome assembly is very high with a contig and scaffold N50 of 72.98 and 162 Mb, respectively, Benchmarking Universal Single-Copy Orthologs (BUSCO) score of 96.6%, and the consensus quality value (QV) of 47.44. A total of 20,567 genes were predicted and 98.8% of these genes were functionally annotated. Syntenic blocks between A. stoliczkanus and Homo sapiens, together with previous comparative cytogenetic studies, provide valuable foundations for further comparative genomic and cytogenetic studies in mammals. The reference-quality genome of A. stoliczkanus contributes an important resource for conservative genomics and landscape genomics in predicting adaptation and vulnerability to climate change.