Knock-out screening of somatic linker histones reveals non-redundant roles in hESCs

  • Fernanda Vargas Romero

Student thesis: Doctoral Thesis


H1 linker histones are structural components of chromatin, generally implicated in the formation of “higher order” chromatin states. With eleven non-allelic subtypes in mammals, the H1 family is highly diverse. While they are commonly associated with chromatin compaction and transcription repression, these histones also play crucial roles in mouse development and stem cell differentiation. Although the prevailing belief is that H1 subtypes have redundant functions, their distinct amino acid composition and differential expression throughout development suggest subtype-specific roles. Previous studies have explored the roles and interactions of linker histones, but limitations in model systems, cell types, and subtypes studied have hindered our comprehensive understanding of the implications and synergy of multiple H1 linker histones. To gain insight into the individual and combined roles of linker histones in human embryonic stem cells (hESCs), we conducted an extensive study in which we systematically removed each somatic linker histone and looked at all potential combinations. Using RNA-seq and in-depth bioinformatic analysis, we discovered that linker histones in hESCs exhibit partial non-redundancy. We classified them into three main groups associated with distinct biological processes, particularly related to development and stem cell differentiation. We observed that depleting H1.1 or H1.5 influenced the proportion of mesodermal progenitor cells, with further impact when combined with specific H1 subtypes, resulting in changes in ectodermal progenitor cells. Additionally, we demonstrated that linker histones synergistically regulate interconnected biological pathways, potentially affecting early stem cell differentiation. Based on our findings, we propose that H1 subtypes regulate specific transcriptional programs, which in conjunction, are fundamental in the coordination of essential cellular processes involved in early human embryonic development, both in the ground state of hESCs and during stem cell differentiation. We anticipate that the generation of the H1 KO library described in our study will provide a novel tool for studying the role of linker histones in later stages of human development and will facilitate the comprehension of specific roles of these chromatin proteins in other relevant cellular processes.
Date of AwardMar 2023
Original languageEnglish (US)
Awarding Institution
  • Biological, Environmental Sciences and Engineering
SupervisorWolfgang Fischle (Supervisor)


  • Genome editing
  • hESCs
  • Linker histones
  • Cell differentiation

Cite this