GSE128675
Rhythmic chromatin interactions with lamin B1 in liver reflect stochasticity in variable lamina-associated domains during the circadian cycle
Purpose: Many mammalian genes exhibit circadian expression patterns concordant with periodic binding of transcription factors, chromatin modifications and chromosomal interactions. We determined whether lamina-associated domains (LADs) display oscillatory circadian patterns of interaction with nuclear lamin B1 during hte circadian cycle, and identified any relationship to changes in gene expression patterns in oscillatory LADs or in their vinicity. Methods: To this end, we mapped LADs by  chromatin immunoprecipitation-sequencing (ChIP-seq) of lamin B1 (LMNB1) (antibody ab16048, Abcam) from mouse livers colected every 6 h, for 30 h, after entrainment of the circadian clock by 24-h fasting and refeeding.  Gene expression profiles were also analyzed by RNA-sequencing (RNA-seq) at the same time points. Results and Conclusions: We report periodic interactions of chromatin domains with nuclear lamin B1, suggesting rhythmic associations of fractions of the genome with the nuclear lamina. Entrainment of the circadian clock by fasting and refeeding is accompanied in mouse liver by a gain of lamin-chromatin interactions followed by oscillations in these interactions at hundreds of lamina-associated domains (LADs). A subset of these oscillations exhibit periodicity and affect one or both LAD borders or entire stand-alone LADs. Periodic LADs are however not a dominant feature of these variable LADs, as most LADs are conserved during the circadian cycle. LAD oscillations are for the most part asynchronous between the 5' and 3' ends of LADs. Periodic LADs also uncoupled from gene expression patterns, periodic or not, within or in vicinity of these LADs. Accordingly, periodic genes, including central clock-control genes, are located megabases away from LADs, suggesting their residence in a transcriptionally permissive environment throughout the circadian cycle. Our data suggest autonomous oscillatory associations of fractions of the genome with the nuclear lamina, providing new evidence for rhythmic spatial configurations of chromatin. However, our data also argue that periodic LADs constitute a minor fraction of variable LADs, and reflect stochasticity in variable lamin-chromatin interactions during the circadian cycle. Overall design: Lamin B1 ChIP-seq analysis (2 biological replicates, i.e. 2 mice) and RNA-seq analysis (3 biological replicates; 3 mice) of the livers collected from wild-type C57Bl/6 male mice as follows: non-synchronized (NS) mice,  18 h before entrainment of the circadian clock, and mice at the following time points after entrainment of the clock by 24-h fasting and refeeding ad lib: circadian time zero (CT0), CT12, CT18, CT24 and CT30. Seven mice were sacrified aat each time point, livers were collected, partitioned and snap-frozen in liquid nitrogen. For LMNB1 ChIL-seq, ChIP DNA was purified by phenolchloroform extraction and ethanol precipitation, before Illumina library preparation at our sequencing facility on an Illumina HiSeq2500. For RNA-seq, total RNA was isolated from 3 replicates using the RNeasy Mini Kit (Qiagen). DNase treatment was done with RQ1 RNase-Free DNase (M101, Promega) and libraries were prepared and sequenced on an Illumina HiSeq2500.