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In meiotic prophase, chromosomes are organized into compacted loop arrays to promote homolog pairing and recombination. Here, we probe the architecture of the mouse spermatocyte genome in early and late meiotic prophase using chromosome conformation capture (Hi-C). Our data support the established loop array model of meiotic chromosomes, and infer loops averaging 0.8–1.0 megabase pairs (Mb) in early prophase and extending to 1.5–2.0 Mb in late prophase as chromosomes compact and homologs undergo synapsis. Topologically associating domains (TADs) are lost in meiotic prophase, suggesting that assembly of the meiotic chromosome axis alters the activity of chromosome-associated cohesin complexes. While TADs are lost, physically separated A and B compartments are maintained in meiotic prophase. Moreover, meiotic DNA breaks and interhomolog crossovers preferentially form in the gene-dense A compartment, revealing a role for chromatin organization in meiotic recombination. Finally, direct detection of interhomolog contacts genome-wide reveals the structural basis for homolog alignment and juxtaposition by the synaptonemal complex.Comparative Hi-C analysis of synchronized mouse spermatocyte populations reveals dynamic changes in chromosome organization during meiotic prophase that permit homolog pairing while sustaining gene expression.

A large number of putative cis -regulatory sequences have been annotated in the human genome, but the genes they control remain poorly defined. To bridge this gap, we generate maps of long-range chromatin interactions centered on 18,943 well-annotated promoters for protein-coding genes in 27 human cell/tissue types. We use this information to infer the target genes of 70,329 candidate regulatory elements and suggest potential regulatory function for 27,325 noncoding sequence variants associated with 2,117 physiological traits and diseases. Integrative analysis of these promoter-centered interactome maps reveals widespread enhancer-like promoters involved in gene regulation and common molecular pathways underlying distinct groups of human traits and diseases. Mapping long-range chromatin interactions in 27 human cell/tissue types identifies candidate target genes of 70,329 putative regulatory elements. Further analysis suggests potential regulatory function for 27,325 noncoding variants associated with 2,117 traits and diseases.

Chromatin architecture has been implicated in cell type-specific gene regulatory programs, yet how chromatin remodels during development remains to be fully elucidated. Here, by interrogating chromatin reorganization during human pluripotent stem cell (hPSC) differentiation, we discover a role for the primate-specific endogenous retrotransposon human endogenous retrovirus subfamily H (HERV-H) in creating topologically associating domains (TADs) in hPSCs. Deleting these HERV-H elements eliminates their corresponding TAD boundaries and reduces the transcription of upstream genes, while de novo insertion of HERV-H elements can introduce new TAD boundaries. The ability of HERV-H to create TAD boundaries depends on high transcription, as transcriptional repression of HERV-H elements prevents the formation of boundaries. This ability is not limited to hPSCs, as these actively transcribed HERV-H elements and their corresponding TAD boundaries also appear in pluripotent stem cells from other hominids but not in more distantly related species lacking HERV-H elements. Overall, our results provide direct evidence for retrotransposons in actively shaping cell type- and species-specific chromatin architecture. Genetic deletion or transcriptional silencing of HERV-H elements in human pluripotent stem cells (hPSCs) eliminates nearby topologically associating domain boundaries, while de novo insertion of HERV-H elements can introduce new ones. Mutations of specific HERV-H elements can impact hPSC differentiation.

Pituitary apoplexy is a rare but potentially life-threatening complication of androgen deprivation therapy for prostate cancer. We present a case of a 70-year-old African American male with prostate cancer who developed symptoms of pituitary apoplexy, including hot flashes, nausea, vomiting, and cranial nerve III palsy, following the initiation of leuprolide therapy. Imaging revealed a pituitary adenoma with hemorrhage, and prompt multidisciplinary management was initiated. The patient was managed conservatively with improvement in symptoms. This case highlights the importance of recognizing the potential for pituitary apoplexy in patients receiving GnRH agonist therapy. We discuss the clinical presentation of GnRH agonist induced pituitary apoplexy, emphasizing that clinicians should maintain a high index of suspicion and promptly investigate any new neuro- ophthalmic symptoms in this group of patients. Ultimately, prompt diagnosis and treatment are crucial to mitigate the severity of this complication in patients with prostate cancer undergoing androgen deprivation therapy.

Pituitary apoplexy is a rare but potentially life-threatening complication of androgen deprivation therapy for prostate cancer. We present a case of a 70-year-old African American male with prostate cancer who developed symptoms of pituitary apoplexy, including hot flashes, nausea, vomiting, and cranial nerve III palsy, following the initiation of leuprolide therapy. Imaging revealed a pituitary adenoma with hemorrhage, and prompt multi-disciplinary management was initiated. The patient was managed conservatively with improvement in symptoms. This case highlights the importance of recognizing the potential for pituitary apoplexy in patients receiving GnRH agonist therapy. We discuss the clinical presentation of GnRH agonist induced pituitary apoplexy, emphasizing that clinicians should maintain a high index of suspicion and promptly investigate any new neuro-ophthalmic symptoms in this group of patients. Ultimately, prompt diagnosis and treatment are crucial to mitigate the severity of this complication in patients with prostate cancer undergoing androgen deprivation therapy.

Dear Editor, Formation of long-range chromatin loops is a crucial step in transcriptional activation of target genes by dis- tal enhancers [1-2]. Mapping such structural features can help define target genes for enhancers and annotate non-coding sequence variants linked to human diseases [1-3]. Study of the higher-order chromatin organization has been facilitated by the development of chromosome conformation capture （3C）-based technologies [4, 5]. Among the commonly used high-throughput 3C approaches are Hi-C [6] and chromatin interaction analysis by paired-end tag sequencing （ChlA-PET） [7]. Global analysis of long-range chromatin interactions using Hi-C has been achieved at kilobase resolution but requires billions of sequencing reads [8]. High-resolution analysis of long-range chromatin interactions at selected genomic regions can be attained cost-effectively through either ChIA-PET [7, 9] or targeted capture and sequencing of Hi-C libraries [10]. ChIA-PET has been used to identify long-range interactions at promoters and enhancers at high resolution in various cell types and species [11]. However, this procedure requires hundreds of million cells as starting materials, likely because chromatin im- munoprecipitation and proximity ligation are performed after chromatin shearing, which potentially leads to great disruption of protein/DNA complexes. To reduce the amount of input materials and improve the sensitivity and robustness of the assay, we developed Proximity Ligation-Assisted ChIP-seq （PLAC-seq）, in which proximity ligation is conducted in nuclei prior to chromatin shearing and immunoprecipitation （Figure 1A, Supplementary information, Figure S1A and Data S1）. We demonstrated that by switching the order of proximity ligation and chromatin shearing steps, PLAC-seq greatly improves the efficiency and accuracy over ChIA-PET [7, 9] in detection of long-range chromatin interactions in mammalian cells.

A Correction to this paper has been published: https://doi.org/10.1038/s41586-020-03089-4.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.An amendment to this paper has been published and can be accessed via a link at the top of the paper.

We report a highly sensitive and cost-effective method for genome-wide identification of chromatin interactions in eukaryotic cells. Combining proximity ligation with chromatin immunoprecipitation and sequencing, the method outperforms the state of art approach in sensitivity, accuracy and ease of operation. Application of the method to mouse embryonic stem cells improves mapping of enhancer-promoter interactions.