Seven linker histone H1 variants are present in human somatic cells with distinct prevalence across cell types. Despite being key structural components of chromatin, it is not known whether the different variants have specific roles in the regulation of nuclear processes or are differentially distributed throughout the genome. Using variant-specific antibodies to H1 and hemagglutinin (HA)-tagged recombinant H1 variants expressed in breast cancer cells, we have investigated the distribution of six H1 variants in promoters and genome-wide. H1 is depleted at promoters depending on its transcriptional status and differs between variants. Notably, H1.2 is less abundant than other variants at the transcription start sites of inactive genes, and promoters enriched in H1.2 are different from those enriched in other variants and tend to be repressed. Additionally, H1.2 is enriched at chromosomal domains characterized by low guanine–cytosine (GC) content and is associated with lamina-associated domains. Meanwhile, other variants are associated with higher GC content, CpG islands and gene-rich domains. For instance, H1.0 and H1X are enriched at gene-rich chromosomes, whereas H1.2 is depleted. In short, histone H1 is not uniformly distributed along the genome and there are differences between variants, H1.2 being the one showing the most specific pattern and strongest correlation with low gene expression.

Background: There are seven histone H1 variants in somatic mammalian cells, two of which are replication-independent, H1.0 and H1X. Results: In breast cancer cells, H1.0 is enriched at nucleolus-associated domains, whereas H1X is associated with RNA polymerase II-enriched regions. Conclusion: Most H1 variants show great redundancy across the genome, but there is also some specificity. Significance: Some H1 variants may have specific functions.Unlike core histones, the linker histone H1 family is more evolutionarily diverse, and many organisms have multiple H1 variants or subtypes. In mammals, the H1 family includes seven somatic H1 variants; H1.1 to H1.5 are expressed in a replicationdependent manner, whereas H1.0 and H1X are replication-independent. Using ChIP-sequencing data and cell fractionation, we have compared the genomic distribution of H1.0 and H1X in human breast cancer cells, in which we previously observed differential distribution of H1.2 compared with the other subtypes. We have found H1.0 to be enriched at nucleolus-associated DNA repeats and chromatin domains, whereas H1X is associated with coding regions, RNA polymerase II-enriched regions, and hypomethylated CpG islands. Further, H1X accumulates within constitutive or included exons and retained introns and toward the 3 end of expressed genes. Inducible H1X knockdown does not affect cell proliferation but dysregulates a subset of genes related to cell movement and transport. In H1X-depleted cells, the promoters of up-regulated genes are not occupied specifically by this variant, have a lower than average H1 content, and, unexpectedly, do not form an H1 valley upon induction. We conclude that H1 variants are not distributed evenly across the genome and may participate with some specificity in chromatin domain organization or gene regulation.There are five major classes of histones that participate in the correct folding of eukaryotic DNA into chromatin: the core histones H2A, H2B, H3, and H4, which form an octamer and constitute the nucleosome core particle, and the linker histone H1, which binds to the nucleosomes near the entry/exit sites of linker DNA. Stabilization of the condensed states of chromatin is the function most commonly attributed to the linker histone (1, 2), in addition to its inhibitory effect in vitro on nucleosome mobility (3) and transcription (4).Histone H1 in humans is a family of closely related, single gene-encoded proteins, including seven somatic subtypes (H1.1 to H1.5, H1.0, and H1X), three testis-specific variants (H1t, H1T2, and HILS1), and one restricted to oocytes (H1oo) (5, 6). Among the somatic histone H1 variants, H1.1 to H1.5 are expressed in a replication-dependent manner, whereas H1.0 and H1X are replication-independent. The H1.1 to H1.5-encoding genes are clustered in a region of chromosome 6 together with the core histone genes, whereas the H1X and H1.0 genes are on chromosomes 3 and 22, respectively. H1.2 to H1.5 and H1X are ubiquitously expressed, H1.1 is restricted to certain tissues, and H1.0 accumulat...