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APOE4 is the strongest genetic risk factor for Alzheimer’s disease (AD)(1–3). Yet, the effects of APOE4 on the human brain are not fully understood, limiting opportunities to develop targeted therapeutics for APOE4 and other AD risk factors(4–8). To gain more comprehensive insight into the impact of APOE4 on the human brain, we performed single-cell transcriptomics profiling of post-mortem human brains from APOE4-carriers compared to non-carriers. This revealed that APOE4 is associated with widespread gene expression changes across all cell types of the human brain. Consistent with APOE’s biological function(2–6), APOE4 significantly altered signaling pathways associated with cholesterol homeostasis and transport. Confirming these findings with histological and lipidomic analysis of the post-mortem human brain, iPSC-derived cells, and targeted-replacement mice, we further discovered that cholesterol is aberrantly deposited in oligodendrocytes, myelinating cells responsible for insulating and promoting electrical activity of neurons. We discovered altered cholesterol localization in the APOE4 brain coincides with reduced myelination. Pharmacologically facilitating cholesterol transport increases axonal myelination and improves learning and memory in APOE4 mice. Our study delivers a single-cell atlas detailing the transcriptional effects of APOE4 on the aged human brain and establishes a functional link between APOE4, cholesterol, myelination, and memory; opening paths to new therapeutic opportunities for AD.

Histone modifiers play essential roles in controlling transcription and organizing eukaryotic genomes into functional domains. Here, we show that Set1, the catalytic subunit of the highly conserved Set1C/COMPASS complex responsible for histone H3K4 methylation (H3K4me), behaves as a repressor of the transcriptome largely independent of Set1C and H3K4me in the fission yeast Schizosaccharomyces pombe. Intriguingly, while Set1 is enriched at highly expressed and repressed loci, Set1 binding levels do not generally correlate with the levels of transcription. We show that Set1 is recruited by the ATF/CREB homolog Atf1 to heterochromatic loci and promoters of stress-response genes. Moreover, we demonstrate that Set1 coordinates with the class II histone deacetylase Clr3 in heterochromatin assembly at prominent chromosomal landmarks and repression of the transcriptome that includes Tf2 retrotransposons, noncoding RNAs, and regulators of development and stress-responses. Our study delineates a molecular framework for elucidating the functional links between transcriptome control and chromatin organization. DOI: http://dx.doi.org/10.7554/eLife.04506.001, eLife digest Genes can be turned on or off at different times in an organism's life. In humans, yeast and other eukaryotes, this is mainly controlled by the way DNA is packaged with proteins—known as histones—in a structure called chromatin. Genes that are switched on, or only temporarily switched off, are associated with areas of the genome where the chromatin is loosely packed. In contrast, genes that remain switched off for long periods of time are found in regions—known as heterochromatin—where the chromatin is tightly packed. There are many enzymes that can modify histones to change the structure of chromatin. One enzyme—called Set1—adds a methyl tag to chromatin, which is known to be associated with genes being switched on. However, Lorenz et al. found that Set1 also has other roles in modifying chromatin in the yeast Schizosaccharomyces pombe. The experiments found that Set1 helps to keep genes switched off and that this role is largely independent of its ability to add the methyl tag to chromatin. Set1 is recruited to many sites across the genome by another protein called Atf1, which is involved in the cell's response to environmental stresses. Lorenz et al. believe that this helps to put these genes in a ‘poised’ off state so that they are ready to be switched on rapidly if needed. Set1 also works with another protein that removes acetyl tags—which encourage chromatin to be less tightly packed—from histones. Together, both proteins contribute to the assembly of heterochromatin and keep genes involved in development and stress responses switched off when they are not required. Collectively, these experiments reveal unexpected and important insights into how Set1—which plays critical roles in many aspects of human health including aging and cancer—works in cells. DOI: http://dx.doi.org/10.7554/eLife.04506.002

In fission yeast, factors involved in the RNA interference (RNAi) pathway including Argonaute, Dicer, and RNA-dependent RNA polymerase are required for heterochromatin assembly at centromeric repeats and the silent mating-type region. Previously, we have shown that RNA-induced initiation of transcriptional gene silencing (RITS) complex containing the Argonaute protein and small interfering RNAs (siRNAs) localizes to heterochromatic loci and collaborates with heterochromatin assembly factors via a self-enforcing RNAi loop mechanism to couple siRNA generation with heterochromatin formation. Here, we investigate the role of RNA-dependent RNA polymerase (Rdp1) and its polymerase activity in the assembly of heterochromatin. We find that Rdp1, similar to RITS, localizes to all known heterochromatic loci, and its localization at centromeric repeats depends on components of RITS and Dicer as well as heterochromatin assembly factors including Clr4/Suv39h and Swi6/HP1 proteins. We show that a point mutation within the catalytic domain of Rdp1 abolished its RNA-dependent RNA polymerase activity and resulted in the loss of transcriptional silencing and heterochromatin at centromeres, together with defects in mitotic chromosome segregation and telomere clustering. Moreover, the RITS complex in the rdp1 mutant does not contain siRNAs, and is delocalized from centromeres. These results not only implicate Rdp1 as an essential component of a self-enforcing RNAi loop but also ascribe a critical role for its RNA-dependent RNA polymerase activity in siRNA production necessary for heterochromatin formation.

Summary Transcriptional gene silencing (TGS) is the mechanism generally thought by which heterochromatin effects silencing. However, recent discovery in fission yeast of a cis -acting posttranscriptional gene-silencing ( cis -PTGS) pathway operated by the RNAi machinery at heterochromatin challenges the role of TGS in heterochromatic silencing. Here, we describe a multienzyme effector complex (termed SHREC) that mediates heterochromatic TGS in fission yeast. SHREC consists of a core quartet of proteins—Clr1, Clr2, Clr3, and Mit1—which distribute throughout all major heterochromatin domains to effect TGS via distinct activities associated with the histone deacetylase Clr3 and the SNF2 chromatin-remodeling factor homolog Mit1. SHREC is also recruited to the telomeres by multiple independent mechanisms involving telomere binding protein Ccq1 cooperating with Taz1 and the RNAi machinery, and to euchromatic sites, via mechanism(s) distinct from its heterochromatin localization aided by Swi6/HP1. Our analyses suggest that SHREC regulates nucleosome positioning to assemble higher-order chromatin structures critical for heterochromatin functions.

Chromatin modifiers impose regulatory controls over diverse chromosomal processes including transcription, nuclear organization, and genome stability. Here we reveal an unexpected role for the histone methyltransferase Set1 (KMT2) as a general transcriptional repressor of the fission yeast Schizosaccharomyces pombe genome. Set1 localizes to repetitive elements and represses both forward and reverse transcripts associated with centromeric and subtelomeric heterochromatin and Tf2 long terminal repeats (LTRs) retrotransposons distinct from its H3K4 methylation (H3K4me) activity. Set1 cooperates with Abp1, the S. pombe homolog of the mammalian centromere binding protein B (CENP-B), to mediate its repression of Tf2s. Intriguingly, Set1 helps organize dispersed Tf2s into distinct nuclear foci termed Tf bodies, the integrity of which requires class I/II histone deacetylases (HDACs) and Sirtuin. Our study uncovers dual roles for Set1 in the maintenance of euchromatin and heterochromatin, and its cooperation with a functional transposase-containing transcription factor to mediate repression and genome organization of dispersed retrotransposons.