Journal of Genetics and Genomics

Molecular insights into the transgenerational inheritance of stress memory

Qian Zhang, Ye Tian

2022, 49(2): 89-95. doi: 10.1016/j.jgg.2021.11.015

Abstract (304) PDF (28)

Abstract:
There is accumulating evidence to show that environmental stressors can regulate a variety of phenotypes in descendants through germline-mediated epigenetic inheritance. Studies of model organisms exposed to environmental cues (e.g., diet, heat stress, toxins) indicate that altered DNA methylations, histone modifications, or non-coding RNAs in the germ cells are responsible for the transgenerational effects. In addition, it has also become evident that maternal provision could provide a mechanism for the transgenerational inheritance of stress adaptations that result from ancestral environmental cues. However, how the signal of environmentally-induced stress response transmits from the soma to the germline, which may influence offspring fitness, remains largely elusive. Small RNAs could serve as signaling molecules that transmit between tissues and even across generations. Furthermore, a recent study revealed that neuronal mitochondrial perturbations induce a transgenerational induction of the mitochondrial unfolded protein response mediated by a Wnt-dependent increase in mitochondrial DNA levels. Here, we review recent work on the molecular mechanism by which parental experience can affect future generations and the importance of soma-to-germline signaling for transgenerational inheritance.

The quantitative proteome atlas of a model cyanobacterium

Jinlong Wang, Xiahe Huang, Haitao Ge, Yan Wang, Weiyang Chen, Limin Zheng, Chengcheng Huang, Haomeng Yang, Lingyu Li, Na Sui, Yu Wang, Yuanya Zhang, Dandan Lu, Longfa Fang, Wu Xu, Yuqiang Jiang, Fang Huang, Yingchun Wang

2022, 49(2): 96-108. doi: 10.1016/j.jgg.2021.09.007

Abstract (203) PDF (27)

Abstract:
Cyanobacteria are a group of oxygenic photosynthetic bacteria with great potentials in biotechnological applications and advantages as models for photosynthesis research. The subcellular localizations of the majority of proteins in any cyanobacteria remain undetermined, representing a major challenge in using cyanobacteria for both basic and industrial researches. Here, using label-free quantitative proteomics, we map 2027 proteins of Synechocystis sp. PCC6803, a model cyanobacterium, to different subcellular compartments and generate a proteome atlas with such information. The atlas leads to numerous unexpected but important findings, including the predominant localization of the histidine kinases Hik33 and Hik27 on the thylakoid but not the plasma membrane. Such information completely changes the concept regarding how the two kinases are activated. Together, the atlas provides subcellular localization information for nearly 60% proteome of a model cyanobacterium, and will serve as an important resource for the cyanobacterial research community.

Phylogeny and sex chromosome evolution of Palaeognathae

Zongji Wang, Jilin Zhang, Xiaoman Xu, Christopher Witt, Yuan Deng, Guangji Chen, Guanliang Meng, Shaohong Feng, Luohao Xu, Tamas Szekely, Guojie Zhang, Qi Zhou

2022, 49(2): 109-119. doi: 10.1016/j.jgg.2021.06.013

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Abstract:
Many paleognaths (ratites and tinamous) have a pair of homomorphic ZW sex chromosomes in contrast to the highly differentiated sex chromosomes of most other birds. To understand the evolutionary causes for the different tempos of sex chromosome evolution, we produced female genomes of 12 paleognathous species and reconstructed the phylogeny and the evolutionary history of paleognathous sex chromosomes. We uncovered that Palaeognathae sex chromosomes had undergone stepwise recombination suppression and formed a pattern of “evolutionary strata”. Nine of the 15 studied species' sex chromosomes have maintained homologous recombination in their long pseudoautosomal regions extending more than half of the entire chromosome length. We found that in the older strata, the W chromosome suffered more serious functional gene loss. Their homologous Z-linked regions, compared with other genomic regions, have produced an excess of species-specific autosomal duplicated genes that evolved female-specific expression, in contrast to their broadly expressed progenitors. We speculate such “defeminization” of Z chromosome with underrepresentation of female-biased genes and slow divergence of sex chromosomes of paleognaths might be related to their distinctive mode of sexual selection targeting females rather than males, which evolved in their common ancestors.

The Melastoma dodecandrum genome and the evolution of Myrtales

Yang Hao, Yu-Zhen Zhou, Bin Chen, Gui-Zhen Chen, Zhen-Ying Wen, Diyang Zhang, Wei-Hong Sun, Ding-Kun Liu, Jie Huang, Jin-Liao Chen, Xiao-Qin Zhou, Wan-Lin Fan, Wen-Chun Zhang, Lin Luo, Wen-Chao Han, Yan Zheng, Long Li, Peng-Cheng Lu, Yue Xing, Shu-Ya Liu, Jia-Ting Sun, Ying-Hui Cao, Yan-Ping Zhang, Xiao-Ling Shi, Sha-Sha Wu, Ye Ai, Jun-Wen Zhai, Si-Ren Lan, Zhong-Jian Liu, Dong-Hui Peng

2022, 49(2): 120-131. doi: 10.1016/j.jgg.2021.10.004

Abstract (394) PDF (51)

Abstract:
Melastomataceae has abundant morphological diversity with high economic and ornamental merit in Myrtales. The phylogenetic position of Myrtales is still contested. Here, we report the chromosome-level genome assembly of Melastoma dodecandrum in Melastomataceae. The assembled genome size is 299.81 Mb with a contig N50 value of 3.00 Mb. Genome evolution analysis indicated that M. dodecandrum, Eucalyptus grandis, and Punica granatum were clustered into a clade of Myrtales and formed a sister group with the ancestor of fabids and malvids. We found that M. dodecandrum experienced four whole-genome polyploidization events: the ancient event was shared with most eudicots, one event was shared with Myrtales, and the other two events were unique to M. dodecandrum. Moreover, we identified MADS-box genes and found that the AP1-like genes expanded, and AP3-like genes might have undergone subfunctionalization. The SUAR63-like genes and AG-like genes showed different expression patterns in stamens, which may be associated with heteranthery. In addition, we found that LAZY1-like genes were involved in the negative regulation of stem branching development, which may be related to its creeping features. Our study sheds new light on the evolution of Melastomataceae and Myrtales, which provides a comprehensive genetic resource for future research.

Aberrant nuclear lamina contributes to the malignancy of human gliomas

Shunqi Pei, Xuehui Wang, Xuan Wang, Hao Huang, Huaping Tao, Binghua Xie, Aifen Yang, Mengsheng Qiu, Zhou Tan

2022, 49(2): 132-144. doi: 10.1016/j.jgg.2021.08.013

Abstract (208) PDF (12)

Abstract:
Glioma is the most common type of tumor in the central nervous system, accounting for around 80% of all malignant brain tumors. Previous studies showed a significant association between nuclear morphology and the malignant progress of gliomas. By virtue of integrated proteomics and genomics analyses as well as experimental validations, we identify three nuclear lamin genes (LMNA, LMNB1, and LMNB2) that are significantly upregulated in glioma tissues compared with normal brain tissues. We show that elevated expressions of LMNB1, LMNB2, and LMNA in glioma cells are highly associated with the rapid progression of the disease and the knockdown of LMNB1, LMNB2, and LMNA dramatically suppresses glioma progression in both in vitro and in vivo mouse models. Moreover, the repression of glioma cell growth by lamin knockdown is mediated by the pRb-mediated G1-S inhibition. On the contrary, overexpression of lamins in normal human astrocytes dramatically induced nuclear morphological aberrations and accelerated cell growth. Together, our multi-omics-based analysis has revealed a previously unrecognized role of lamin genes in gliomagenesis, providing a strong support for the key link between aberrant tumor nuclear shape and the survival of glioma patients. Based on these findings, lamins are proposed to be potential oncogene targets for therapeutic treatments of brain tumors.

Mapping of de novo mutations in primary biliary cholangitis to a disease-specific co-expression network underlying homeostasis and metabolism

Lu Wang, Jinchen Li, Chan Wang, Ruqi Tang, Jialong Liang, Yuhua Gong, Yaping Dai, Ningling Ding, Jian Wu, Na Dai, Lei Liu, Yi Zhao, Youlin Shao, Weifeng Zhao, Peng Jiang, Xingjuan Shi, Weichang Chen, Ye Tian, Xiangdong Liu, Xiong Ma, Zhongsheng Sun

2022, 49(2): 145-154. doi: 10.1016/j.jgg.2021.07.019

Abstract (216) PDF (16)

Abstract:
Primary biliary cholangitis (PBC) is an autoimmune disease involving dysregulation of a broad array of homeostatic and metabolic processes. Although considerable single-nucleotide polymorphisms have been unveiled, a large fraction of risk factors remains enigmatic. Candidate genes with rare mutations that tend to confer more deleterious effects need to be identified. To help pinpoint cellular and developmental mechanisms beyond common noncoding variants, we integrate whole exome sequencing with integrative network analysis to investigate genes harboring de novo mutations. Prominent convergence has been revealed on a network of disease-specific co-expression comprised of 55 genes associated with homeostasis and metabolism. The transcription factor gene MEF2D and the DNA repair gene PARP2 are highlighted as hub genes and identified to be up- and down-regulated, respectively, in peripheral blood data set. Enrichment analysis demonstrates that altered expression of MEF2D and PARP2 may trigger a series of molecular and cellular processes with pivotal roles in PBC pathophysiology. Our study identifies genes with de novo mutations in PBC and suggests that a subset of genes in homeostasis and metabolism tend to act in synergy through converging on co-expression network, providing novel insights into the etiology of PBC and expanding the pool of molecular candidates for discovering clinically actionable biomarkers.

The role of genotype and diet in shaping gut microbiome in a genetic vitamin A deficient mouse model

Jun Xu, Jie-Ni Zhang, Bo-Hui Sun, Qing Liu, Juan Ma, Qian Zhang, Yong-Xin Liu, Ning Chen, Feng Chen

2022, 49(2): 155-164. doi: 10.1016/j.jgg.2021.08.015

Abstract (248) PDF (23)

Abstract:
Multifactors have been reported to affect the gut microbiome, including genotype, age, diet, and nutrition. However, few reports have investigated the relative capacity of different factors to shape the gut microbiome in a single study. Our design used a genetic vitamin A-deficient mouse model, the Rbp4 mouse, feeding with the low vitamin A diets at different ages of initiation (4 or 7 weeks) for 28 days. Fecal samples were collected for bacterial profiling at seven time points after diet controlling. With Rbp4 depletion, Akkermansia decreased and Bacteroides increased, whereas Desulfovibrio, Barnesiella, Clostridium_XlVa, and Lactobacillus fluctuated. The bacterial community swiftly adjusted with the vitamin A-deficient diet administration and gradually changed (e.g., decrease of Barnesiella and increase of Desulfovibrio). Age exerted a relatively weaker but long-last influence. At an earlier age to feed a vitamin A-deficient diet, a higher microbial dysbiosis index will be valued. Of note, the shaping effects of diet and age on the bacterial community varied with the difference of genotype, which might indicate a greater role of genotype than diet and age in shaping the gut microbiome.

The sex determination gene doublesex is required during adulthood to maintain sexual orientation

Qionglin Peng, Jiangtao Chen, Xiangbin Su, Rong Wang, Caihong Han, Yufeng Pan

2022, 49(2): 165-168. doi: 10.1016/j.jgg.2021.08.006

Abstract (308) PDF (30)

Abstract:

Identification of CHMP4C as a new risk gene for inherited dilated cardiomyopathy

Nianwei Zhou, Lu Tang, Yingying Jiang, Xuejie Li, Shifang Shan, Bo Yuan, Shengmei Qin, Cuizhen Pan, Xiaolin Wang, Xianhong Shu, Zilong Qiu, Junbo Ge

2022, 49(2): 169-172. doi: 10.1016/j.jgg.2021.08.014

Abstract (180) PDF (25)

Abstract:

Transcriptional memory of different types of genes is generally maintained under various environmental conditions in Saccharomyces cerevisiae

Ru-Xin Wang, Yu-Min Li, Runfa Chen, Hai-Ning Du

2022, 49(2): 173-176. doi: 10.1016/j.jgg.2021.10.007

Abstract (300) PDF (48)

Abstract:

Genome-wide meta-analysis identifies ten new psoriasis susceptibility loci in the Chinese population

Weiwei Chen, Wenjun Wang, Liang Yong, Qi Zhen, Yafen Yu, Huiyao Ge, Yiwen Mao, Lu Cao, Ruixue Zhang, Xia Hu, Zhuo Li, Yirui Wang, Wencheng Fan, Qiongqiong Xu, Hui Zhang, Shirui Chen, Jing Wu, Liangdan Sun

2022, 49(2): 177-180. doi: 10.1016/j.jgg.2021.10.001

Abstract (118) PDF (20)

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2022 Vol. 49, No. 2