Journal of Genetics and Genomics

Many facades of CTCF unified by its coding for three-dimensional genome architecture

Qiang Wu, Peifeng Liu, Leyang Wang

2020, 47(8): 407-424. doi: 10.1016/j.jgg.2020.06.008

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Abstract:
CCCTC-binding factor (CTCF) is a multifunctional zinc finger protein that is conserved in metazoan species. CTCF is consistently found to play an important role in many diverse biological processes. CTCF/cohesin-mediated active chromatin ‘loop extrusion’ architects three-dimensional (3D) genome folding. The 3D architectural role of CTCF underlies its multifarious functions, including developmental regulation of gene expression, protocadherin (Pcdh) promoter choice in the nervous system, immunoglobulin (Ig) and T-cell receptor (Tcr) V(D)J recombination in the immune system, homeobox (Hox) gene control during limb development, as well as many other aspects of biology. Here, we review the pleiotropic functions of CTCF from the perspective of its essential role in 3D genome architecture and topological promoter/enhancer selection. We envision the 3D genome as an enormous complex architecture, with tens of thousands of CTCF sites as connecting nodes and CTCF proteins as mysterious bonds that glue together genomic building parts with distinct articulation joints. In particular, we focus on the internal mechanisms by which CTCF controls higher order chromatin structures that manifest its many façades of physiological and pathological functions. We also discuss the dichotomic role of CTCF sites as intriguing 3D genome nodes for seemingly contradictory ‘looping bridges’ and ‘topological insulators’ to frame a beautiful magnificent house for a cell's nuclear home.

Decoding the plant genome: From epigenome to 3D organization

Weizhi Ouyang, Zhilin Cao, Dan Xiong, Guoliang Li, Xingwang Li

2020, 47(8): 425-435. doi: 10.1016/j.jgg.2020.06.007

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Abstract:
The linear genome of eukaryotes is partitioned into diverse chromatin states and packaged into a three-dimensional (3D) structure, which has functional implications in DNA replication, DNA repair, and transcriptional regulation. Over the past decades, research on plant functional genomics and epigenomics has made great progress, with thousands of genes cloned and molecular mechanisms of diverse biological processes elucidated. Recently, 3D genome research has gradually attracted great attention of many plant researchers. Herein, we briefly review the progress in genomic and epigenomic research in plants, with a focus on Arabidopsis and rice, and summarize the currently used technologies and advances in plant 3D genome organization studies. We also discuss the relationships between one-dimensional linear genome sequences, epigenomic states, and the 3D chromatin architecture. This review provides basis for future research on plant 3D genomics.

HPV-CCDC106 integration alters local chromosome architecture and hijacks an enhancer by three-dimensional genome structure remodeling in cervical cancer

Canhui Cao, Ping Hong, Xingyu Huang, Da Lin, Gang Cao, Liming Wang, Bei Feng, Ping Wu, Hui Shen, Qian Xu, Ci Ren, Yifan Meng, Wenhua Zhi, Ruidi Yu, Juncheng Wei, Wencheng Ding, Xun Tian, Qinghua Zhang, Wei Li, Qinglei Gao, Gang Chen, Kezhen Li, Wing-Kin Sung, Zheng Hu, Hui Wang, Guoliang Li, Peng Wu

2020, 47(8): 437-450. doi: 10.1016/j.jgg.2020.05.006

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Abstract:
Integration of human papillomavirus (HPV) DNA into the human genome is a reputed key driver of cervical cancer. However, the effects of HPV integration on chromatin structural organization and gene expression are largely unknown. We studied a cohort of 61 samples and identified an integration hot spot in the CCDC106 gene on chromosome 19. We then selected fresh cancer tissue that contained the unique integration loci at CCDC106 with no HPV episomal DNA and performed whole-genome, RNA, chromatin immunoprecipitation and high-throughput chromosome conformation capture (Hi-C) sequencing to identify the mechanisms of HPV integration in cervical carcinogenesis. Molecular analyses indicated that chromosome 19 exhibited significant genomic variation and differential expression densities, with correlation found between three-dimensional (3D) structural change and gene expression. Importantly, HPV integration divided one topologically associated domain (TAD) into two smaller TADs and hijacked an enhancer from PEG3 to CCDC106, with a decrease in PEG3 expression and an increase in CCDC106 expression. This expression dysregulation was further confirmed using 10 samples from our cohort, which exhibited the same HPV-CCDC106 integration. In summary, we found that HPV-CCDC106 integration altered local chromosome architecture and hijacked an enhancer via 3D genome structure remodeling. Thus, this study provides insight into the 3D structural mechanism underlying HPV integration in cervical carcinogenesis.

The novel male meiosis recombination regulator coordinates the progression of meiosis prophase I

Miao Li, Haiwei Feng, Zexiong Lin, Jiahuan Zheng, Dongteng Liu, Rui Guo, Junshi Li, Raymond H.W. Li, Ernest H.Y. Ng, Michael S.Y. Huen, P. Jeremy Wang, William S.B. Yeung, Kui Liu

2020, 47(8): 451-465. doi: 10.1016/j.jgg.2020.08.001

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Abstract:
Meiosis is a specialized cell division for producing haploid gametes in sexually reproducing organisms. In this study, we have independently identified a novel meiosis protein male meiosis recombination regulator (MAMERR)/4930432K21Rik and showed that it is indispensable for meiosis prophase I progression in male mice. Using super-resolution structured illumination microscopy, we found that MAMERR functions at the same double-strand breaks as the replication protein A and meiosis-specific with OB domains/spermatogenesis associated 22 complex. We generated a Mamerr-deficient mouse model by deleting exons 3–6 and found that most of Mamerr spermatocytes were arrested at pachynema and failed to progress to diplonema, although they exhibited almost intact synapsis and progression to the pachytene stage along with XY body formation. Further mechanistic studies revealed that the recruitment of DMC1/RAD51 and heat shock factor 2–binding protein in Mamerr spermatocytes was only mildly impaired with a partial reduction in double-strand break repair, whereas a substantial reduction in ubiquitination on the autosomal axes and on the XY body appeared as a major phenotype in Mamerr spermatocytes. We propose that MAMERR may participate in meiotic prophase I progression by regulating the ubiquitination of key meiotic proteins on autosomes and XY chromosomes, and in the absence of MAMERR, the repressed ubiquitination of key meiotic proteins leads to pachytene arrest and cell death.

Longitudinal epitranscriptome profiling reveals the crucial role of N6-methyladenosine methylation in porcine prenatal skeletal muscle development

Xinxin Zhang, Yilong Yao, Jinghua Han, Yalan Yang, Yun Chen, Zhonglin Tang, Fei Gao

2020, 47(8): 466-476. doi: 10.1016/j.jgg.2020.07.003

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Abstract:
N⁶-methyladenosine (m⁶A) represents the most abundantly occurring mRNA modification and is involved in the regulation of skeletal muscle development. However, the status and function of m⁶A methylation in prenatal myogenesis remains unclear. In this study, we first demonstrated that knockdown of METTL14, an m⁶A methyltransferase, inhibited the differentiation and promoted the proliferation of C2C12 myoblast cells. Then, using a refined m⁶A-specific methylated RNA immunoprecipitation (RIP) with next generation sequencing (MeRIP-seq) method that is optimal for use with samples containing small amounts of RNA, we performed transcriptome-wide m⁶A profiling for six prenatal skeletal muscle developmental stages spanning two important waves of porcine myogenesis. The results revealed that, along with a continuous decrease in the mRNA expression of the m⁶A reader protein insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), the m⁶A methylome underwent highly dynamic changes across different development stages, with most of the affected genes being enriched in pathways related to skeletal muscle development. RNA immunoprecipitation confirmed that IGF2BP1 targets 76 genes involved in pathways associated with muscle development, including the key marker genes MYH2 and MyoG. Moreover, small interfering RNA (siRNA)-mediated knockdown of IGF2BP1 induced phenotypic changes in C2C12 myoblasts similar to those observed with knockdown of METTL14. In conclusion, we clarified the dynamics of m⁶A methylation and identified key genes involved in the regulatory network of porcine skeletal muscle development.

Analyses of functional conservation and divergence reveal requirement of bHLH010/089/091 for pollen development at elevated temperature in Arabidopsis

Ying Fu, Mengyu Li, Shiting Zhang, Qi Yang, Engao Zhu, Chenjiang You, Ji Qi, Hong Ma, Fang Chang

2020, 47(8): 477-492. doi: 10.1016/j.jgg.2020.09.001

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Abstract:
The Arabidopsis bHLH010/089/091 (basic helix-loop-helix) genes are functionally redundant and are required for both anther development and normal expression of DYT1-activated anther-related genes. These three genes are conserved in Brassicaceae, suggesting that each of them is under selection pressure; however, little is known about the possible functional differences among these bHLH genes and between the bHLH and DYT1 genes. Here, we compared novel anther transcriptomic data sets from bHLH010/089/091 single and double mutants, with an anther transcriptomic data set from the wild type (WT) and a previously obtained anther transcriptomic data set from the bhlh010 bhlh089 bhlh091 triple mutant. The results revealed molecular phenotypes that support the functional redundancy and divergence of bHLH010, bHLH089, and bHLH091, as well as the functional overlap and difference between them and DYT1. DNA-binding analyses revealed that DYT1 and bHLH089 specifically recognize the TCATGTGC box to activate the expression of target genes, including ATA20, EXL4, and MEE48. In addition, among genes whose expression was affected in the bhlh010 bhlh089 double and bhlh010 bhlh089 bhlh091 triple mutants, genes that are involved in the stress response and cell signaling were enriched, which included 256 genes whose expression was preferentially induced by heat during early flower development. Moreover, the bhlh double mutants exhibited defective pollen development when the plants were grown under elevated temperature, suggesting that bHLH genes are important for anther gene expression under such conditions. These results are consistent with the observation that the heat-induced expression of several genes is less in thebhlh mutants than that in the WT. Therefore, our results provide important insights into the molecular mechanism underlying the activation of direct targets by DYT1-bHLH089 heterodimers and demonstrate the protective roles of bHLH010/089/091 in maintaining fertility upon heat stress.

Critical role of zebrafish dnajb5 in myocardial proliferation and regeneration

Meijun Pang, Connie Xiong, Chenglu Xiao, Jianyong Du, Lixia Zheng, Linlu Bai, Xiaojun Zhu, Jing-Wei Xiong

2020, 47(8): 493-496. doi: 10.1016/j.jgg.2020.07.005

Abstract (110) HTML PDF (1)

Abstract:

2020 Vol. 47, No. 8