{"title":"CTCF优先支持短层相关结构域。","authors":"Lukasz Stanislaw Kaczmarczyk,Nehora Levi,Tamar Segal,Mali Salmon-Divon,Gabi Gerlitz","doi":"10.1007/s10577-022-09686-5","DOIUrl":null,"url":null,"abstract":"More than one third of the mammalian genome is in a close association with the nuclear lamina, thus these genomic regions were termed lamina-associated domains (LADs). This association is fundamental for many aspects of chromatin biology including transcription, replication, and DNA damage repair. LADs association with the nuclear envelope is thought to be dependent on two major mechanisms: The first mechanism is the interaction between nuclear membrane proteins such as LBR with heterochromatin modifications that are enriched in LADs chromatin. The second mechanism is based on proteins that bind the borders of the LADs and support the association of the LADs with the nuclear envelope. Two factors were suggested to support the second mechanism: CCCTC-binding factor (CTCF) and YY1 based on their enriched binding to LADs borders. However, this mechanism has not been proven yet at a whole genome level. Here, to test if CTCF supports the LADs landscape, we generated melanoma cells with a partial loss of function (pLoF) of CTCF by the CRISPR-Cas9 system and determined the LADs landscape by lamin B ChIP-seq analysis. We found that under regular growth conditions, CTCF pLoF led to modest changes in the LADs landscape that included an increase in the signal of 2% of the LADs and a decrease in the signal of 8% of the LADs. However, CTCF importance for the LADs landscape was much higher upon induction of a chromatin stress. We induced chromatin stress by inhibiting RNA polymerase II, an intervention that is known to alter chromatin compaction and supercoiling. Notably, only in CTCF pLoF cells, the chromatin stress led to the dissociation of 7% of the LADs from the lamina. The CTCF-dependent LADs had almost three times shorter median length than the non-affected LADs, were enriched in CTCF binding at their borders, and were higher in their facultative-status (cell-type specific). Thus, it appears that CTCF is a key factor in facilitating the association of short facultative LADs with the nuclear lamina upon chromatin stress.","PeriodicalId":50698,"journal":{"name":"Chromosome Research","volume":"308 ","pages":"123-136"},"PeriodicalIF":2.4000,"publicationDate":"2022-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"CTCF supports preferentially short lamina-associated domains.\",\"authors\":\"Lukasz Stanislaw Kaczmarczyk,Nehora Levi,Tamar Segal,Mali Salmon-Divon,Gabi Gerlitz\",\"doi\":\"10.1007/s10577-022-09686-5\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"More than one third of the mammalian genome is in a close association with the nuclear lamina, thus these genomic regions were termed lamina-associated domains (LADs). This association is fundamental for many aspects of chromatin biology including transcription, replication, and DNA damage repair. LADs association with the nuclear envelope is thought to be dependent on two major mechanisms: The first mechanism is the interaction between nuclear membrane proteins such as LBR with heterochromatin modifications that are enriched in LADs chromatin. The second mechanism is based on proteins that bind the borders of the LADs and support the association of the LADs with the nuclear envelope. Two factors were suggested to support the second mechanism: CCCTC-binding factor (CTCF) and YY1 based on their enriched binding to LADs borders. However, this mechanism has not been proven yet at a whole genome level. Here, to test if CTCF supports the LADs landscape, we generated melanoma cells with a partial loss of function (pLoF) of CTCF by the CRISPR-Cas9 system and determined the LADs landscape by lamin B ChIP-seq analysis. We found that under regular growth conditions, CTCF pLoF led to modest changes in the LADs landscape that included an increase in the signal of 2% of the LADs and a decrease in the signal of 8% of the LADs. However, CTCF importance for the LADs landscape was much higher upon induction of a chromatin stress. We induced chromatin stress by inhibiting RNA polymerase II, an intervention that is known to alter chromatin compaction and supercoiling. Notably, only in CTCF pLoF cells, the chromatin stress led to the dissociation of 7% of the LADs from the lamina. The CTCF-dependent LADs had almost three times shorter median length than the non-affected LADs, were enriched in CTCF binding at their borders, and were higher in their facultative-status (cell-type specific). 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引用次数: 0
摘要
超过三分之一的哺乳动物基因组与核层密切相关,因此这些基因组区域被称为层相关结构域(lamina-associated domains, LADs)。这种关联是染色质生物学许多方面的基础,包括转录、复制和DNA损伤修复。LADs与核膜的关联被认为依赖于两种主要机制:第一种机制是核膜蛋白(如LBR)与富含LADs染色质的异染色质修饰之间的相互作用。第二种机制是基于结合LADs边界并支持LADs与核膜结合的蛋白质。两个因子被认为支持第二种机制:ccctc结合因子(CTCF)和YY1,基于它们与LADs边界的丰富结合。然而,这种机制尚未在全基因组水平上得到证实。在这里,为了测试CTCF是否支持LADs景观,我们通过CRISPR-Cas9系统生成了CTCF部分功能丧失(pLoF)的黑色素瘤细胞,并通过lamin B ChIP-seq分析确定了LADs景观。我们发现,在正常生长条件下,CTCF pLoF导致LADs景观的适度变化,包括2%的LADs信号增加和8%的LADs信号减少。然而,在染色质胁迫诱导下,CTCF对LADs景观的重要性要高得多。我们通过抑制RNA聚合酶II来诱导染色质应激,这是一种已知的改变染色质压实和超卷曲的干预。值得注意的是,只有在CTCF pLoF细胞中,染色质应激导致7%的LADs从层中分离。CTCF依赖性lad的中位长度几乎比未受影响的lad短三倍,其边界富含CTCF结合,并且其兼性状态(细胞类型特异性)更高。因此,CTCF似乎是在染色质胁迫下促进短兼性LADs与核层关联的关键因素。
CTCF supports preferentially short lamina-associated domains.
More than one third of the mammalian genome is in a close association with the nuclear lamina, thus these genomic regions were termed lamina-associated domains (LADs). This association is fundamental for many aspects of chromatin biology including transcription, replication, and DNA damage repair. LADs association with the nuclear envelope is thought to be dependent on two major mechanisms: The first mechanism is the interaction between nuclear membrane proteins such as LBR with heterochromatin modifications that are enriched in LADs chromatin. The second mechanism is based on proteins that bind the borders of the LADs and support the association of the LADs with the nuclear envelope. Two factors were suggested to support the second mechanism: CCCTC-binding factor (CTCF) and YY1 based on their enriched binding to LADs borders. However, this mechanism has not been proven yet at a whole genome level. Here, to test if CTCF supports the LADs landscape, we generated melanoma cells with a partial loss of function (pLoF) of CTCF by the CRISPR-Cas9 system and determined the LADs landscape by lamin B ChIP-seq analysis. We found that under regular growth conditions, CTCF pLoF led to modest changes in the LADs landscape that included an increase in the signal of 2% of the LADs and a decrease in the signal of 8% of the LADs. However, CTCF importance for the LADs landscape was much higher upon induction of a chromatin stress. We induced chromatin stress by inhibiting RNA polymerase II, an intervention that is known to alter chromatin compaction and supercoiling. Notably, only in CTCF pLoF cells, the chromatin stress led to the dissociation of 7% of the LADs from the lamina. The CTCF-dependent LADs had almost three times shorter median length than the non-affected LADs, were enriched in CTCF binding at their borders, and were higher in their facultative-status (cell-type specific). Thus, it appears that CTCF is a key factor in facilitating the association of short facultative LADs with the nuclear lamina upon chromatin stress.
期刊介绍:
Chromosome Research publishes manuscripts from work based on all organisms and encourages submissions in the following areas including, but not limited, to:
· Chromosomes and their linkage to diseases;
· Chromosome organization within the nucleus;
· Chromatin biology (transcription, non-coding RNA, etc);
· Chromosome structure, function and mechanics;
· Chromosome and DNA repair;
· Epigenetic chromosomal functions (centromeres, telomeres, replication, imprinting,
dosage compensation, sex determination, chromosome remodeling);
· Architectural/epigenomic organization of the genome;
· Functional annotation of the genome;
· Functional and comparative genomics in plants and animals;
· Karyology studies that help resolve difficult taxonomic problems or that provide
clues to fundamental mechanisms of genome and karyotype evolution in plants and animals;
· Mitosis and Meiosis;
· Cancer cytogenomics.