Combinatorial single-cell profiling of all major chromatin types with MAbID

Abstract

Gene expression programs result from the collective activity of many regulatory factors. To obtain insight into the mechanisms that govern gene regulation, it is imperative to study their combined mode of action and interconnectivity. However, it has been challenging to simultaneously measure a combination of these factors within one sample. Here, we introduce MAbID, a method that combines genomic profiling of many histone modifications and chromatin-binding proteins in a single reaction. MAbID employs antibody-DNA conjugates to enable genomic barcoding of chromatin at sites of epitope occupancy. This barcoding strategy allows for the combined incubation of multiple antibodies in a single sample to reveal the genomic distributions of many epigenetic states simultaneously. We used MAbID to profile both active and inactive chromatin types in human cell lines and multiplexed measurements in the same sample without loss of data quality. Moreover, we obtained joint measurements of six epitopes covering all major chromatin types in single cells during mouse in vitro neural differentiation and captured associated changes in multifactorial chromatin states. Thus, MAbID holds the potential to gain unique insights into the interplay between gene regulatory mechanisms, especially in settings with limited sample material and in single cells.

Time-resolved and multifactorial profiling in single cells resolves the order of heterochromatin formation events during X-chromosome inactivation

“…As a non-Tn5-based approach, Dam&ChIC bypasses the intrinsic bias of other technologies towards more efficient recovery of euchromatic features (Buenrostro et al, 2013; Kaya-Okur et al, 2020), and is therefore also suitable to probe the interplay between features of the constitutive heterochromatin landscape. Despite that some technologies have circumvented the Tn5-intrinsic bias by using Tn5 fusions targeting constitutive heterochromatin (Tedesco et al, 2022) or non-Tn5-dependent genome tagging strategies (Lochs et al, 2023), their sensitivity remains comparatively low. Thus, Dam&ChIC is a suitable approach to examine combinations of chromatin features that range from euchromatic to constitutively heterochromatic, and interrogate their coordinated regulatory function on chromatin, from large domains to individual genes and promoters.…”

“…In addition, the co-occurrence of detachment from the nuclear lamina and entry into the G1 cell-cycle phase, identify that genomelamina interactions of the Xi are likely lost upon mitotic exit. fusions targeting constitutive heterochromatin (Tedesco et al, 2022) or non-Tn5-dependent genome tagging strategies (Lochs et al, 2023), their sensitivity remains comparatively low. Thus, Dam&ChIC is a suitable approach to examine combinations of chromatin features that range from euchromatic to constitutively heterochromatic, and interrogate their coordinated regulatory function on chromatin, from large domains to individual genes and promoters.…”

“…To address this, recently several methods were developed to measure multiple chromatin features from the same cell. Experimental approaches such as multi-CUT&Tag (Gopalan et al, 2021), MulTI-Tag (Meers et al, 2022), nano-CT (Bartosovic & Castelo-Branco, 2022), NTT-seq (Stuart et al, 2022) and scMAbID (Lochs et al, 2023) all recover multifactorial chromatin information by using mixtures of target-specific antibodies and in situ tagging of the chromatin. The information provided by these methods hold the promise to study cooperativity and the order of gene-regulatory events in the same cell.…”

Single-nuclei histone modification profiling of the adult human central nervous system unveils epigenetic memory of developmental programs

“…The rise of powerful single-cell epigenomic technologies has now made this level of profiling attainable. Single-cell studies covering DNA methylation 25 and individual histone modifications [26][27][28][29][30][31][32][33][34][35][36] have started elucidating these epigenetic landscapes in the mouse adult CNS; however the exploration of the adult human CNS remains limited and currently only DNA methylation and chromatin architecture have been analysed at the single cell level 37 . Regarding histone modifications, current datasets are restricted to single cell analysis of H3K27me3 of a glioblastoma tumour from one patient 30 and bulk characterization of glioblastoma tumours 18 , or specific fluorescent-activated nuclei sorted subpopulations in the human cortex 38 , while multi-modal single-cell profiling of the different cell states in the adult human CNS is still lacking.…”