Restricted chromosomal silencing in nucleolar dominance

Failure of one parent's chromosomes to organize nucleoli in an interspecific hybrid is an epigenetic phenomenon known as nucleolar dominance. Selective gene silencing on a scale of millions of bp is known to be involved, but the full extent to which nucleolus organizer region (NOR)-bearing chromosomes are inactivated beyond the NORs is unknown. Aided by genome sequence data for Arabidopsis thaliana, we have mapped the extent of nucleolar dominance-induced silencing in Arabidopsis suecica, the allotetraploid hybrid of A. thaliana and Arabidopsis arenosa. Using a sensitive reverse transcription PCR assay, we show that the four A. thaliana NORs, each ≈4 Mbp in size, are ≈99.5% silenced in A. suecica vegetative leaves, whereas the NORs inherited from A. arenosa remain fully active. The two A. thaliana NORs, NOR2 and NOR4, abut the telomeres on chromosomes 2 and 4, thus there are no genes distal to the NORs. The three protein-coding genes nearest NOR4 on its centromere-proximal side, the closest of which is only 3.1 kb from rRNA gene sequences, are shown to be transcribed in the hybrid despite the silencing of the adjacent ≈4-Mbp NOR. These data argue against hypotheses in which NOR inactivation is attributed to the spread of silencing from adjacent chromosomal regions, but favor models in which NORs or rRNA genes are the targets of regulation.

种间杂种中，某一亲本的染色体无法组织核仁形成，该现象被称为核仁显性（nucleolar dominance），属于表观遗传事件。已知该过程涉及百万碱基对级别的选择性基因沉默，但目前仍不清楚核仁组织区（nucleolus organizer region, NOR）所在染色体在NOR区域之外的失活范围。借助拟南芥（Arabidopsis thaliana）的基因组序列数据，我们对瑞典拟南芥（Arabidopsis suecica）——一种由拟南芥与砂生拟南芥（Arabidopsis arenosa）形成的异源四倍体杂种——中核仁显性诱导的基因沉默范围进行了定位。通过灵敏的逆转录PCR（reverse transcription PCR）检测，我们发现瑞典拟南芥营养叶内，源自拟南芥的4个核仁组织区（每个大小约4 Mbp）的沉默率高达99.5%，而源自砂生拟南芥的核仁组织区则完全保持活性。拟南芥的两个核仁组织区NOR2和NOR4分别紧邻2号、4号染色体的端粒，因此NOR区域的远端不存在其他基因。在NOR4的着丝粒近端一侧，距离最近的三个蛋白质编码基因（其中最接近的与核糖体RNA（ribosomal RNA，rRNA）基因序列仅相距3.1 kb），即便相邻的约4 Mbp的核仁组织区处于沉默状态，仍可在该杂种中被转录。上述数据反驳了“核仁组织区失活由沉默信号从相邻染色体区域扩散所导致”的假说，转而支持以核仁组织区或核糖体RNA基因为调控靶点的模型。