Biology subjects

Nir Friedman

Publications and source records attributed to Nir Friedman.

3 recordsLinked to original sources

bioRxiv2016

Elucidating Combinatorial Chromatin States by Co-ImmunoPrecipitation (comb-ChIP)

Chromatin ImmunoPrecipitation followed by massively parallel sequencing (ChIP-Seq) has been instrumental to our current view of chromatin structure and function, and identifies correlating histone marks, which together demarcate biologically-relevant domains. However, as with most genome-wide assays, ChIP-seq is an ensemble measurement that reports on the average occupancy of individual modifications in a population of cells. Consequently, our understanding of the combinatorial nature of chromatin states relies almost exclusively on spatial correlations. Here, we report the development of a novel protocol, called indexed Combinatorial ChIP (comb-ChIP), which has the power to determine the genome-wide co-occurrence of histone marks at single nucleosome resolution. We show that at regions of overlapping ChIP signals, certain combinations of marks (H3K36me3 and H3K79me3) tend to co-occur on the same nucleosome, while other combinations (H3K4me3 and H3K36me3) do not, reflecting differences in the underlying chromatin pathways. We further use comb-ChIP to detect changes in histone mark co-occurrence upon genetic perturbation, illuminating new aspects of the Set2-RPD3S pathway. Overall, comb-ChIP promises to greatly improve our understanding of the structural and functional complexity of chromatin.

Genomics↗

bioRxiv2016

Genome-wide histone modification patterns in Kluyveromyces Lactis reveal evolutionary adaptation of a heterochromatin-associated mark

The packaging of eukaryotic genomes into nucleosomes plays critical roles in all DNA-templated processes, and chromatin structure has been implicated as a key factor in the evolution of gene regulatory programs. While the functions of many histone modifications appear to be highly conserved throughout evolution, some well-studied modifications such as H3K9 and H3K27 methylation are not found in major model organisms such as Saccharomyces cerevisiae, while other modifications gain/lose regulatory functions during evolution. To study such a transition we focused on H3K9 methylation, a heterochromatin mark found in metazoans and in the fission yeast S. pombe, but which has been lost in the lineage leading to the model budding yeast S. cerevisiae. We show that this mark is present in the relatively understudied yeast Kluyveromyces lactis, a Hemiascomycete that diverged from S. cerevisiae prior to the whole-genome duplication event that played a key role in the evolution of a primarily fermentative lifestyle. We mapped genome-wide patterns of H3K9 methylation as well as several conserved modifications. We find that well-studied modifications such as H3K4me3, H3K36me3, and H3S10ph exhibit generally conserved localization patterns. Interestingly, we show H3K9 methylation in K. lactis primarily occurs over highly-transcribed regions, including both Pol2 and Pol3 transcription units. We identified the H3K9 methylase as the ortholog of Set6, whose function in S. cerevisiae is obscure. Functionally, we show that deletion of KlSet6 does not affect highly H3K9me3-marked genes, providing another example of a major disconnect between histone mark localization and function. Together, these results shed light on surprising plasticity in the function of a widespread chromatin mark.

Genomics↗

bioRxiv2014

Tracking global changes induced in the CD4 T cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence.

The clonal theory of adaptive immunity proposes that immunological responses are encoded by increases in the frequency of lymphocytes carrying antigen-specific receptors. In this study, we measure the frequency of different TcRs in CD4+ T cell populations of mice immunized with a complex antigen, killed Mycobacterium tuberculosis, using high throughput parallel sequencing of the TcR beta chain. In order to track the changes induced by immunisation within this very heterogeneous repertoire, the sequence data were classified by counting the frequency of different clusters of short (3 or 4) continuous stretches of amino acids within the CDR3 repertoire of different mice. Both unsupervised (hierarchical clustering) and supervised (support vector machine) analysis of these different distributions of sequence clusters differentiated between immunised and unimmunised mice with 100% efficiency. The CD4+ T cell receptor repertoires of mice 5 and 14 days post immunisation were clearly different from that of unimmunised mice, but were not distinguishable from each other. However, the repertoires of mice 60 days post immunisation were distinct both from unimmunised mice, and the day 5/14 animals. Our results reinforce the remarkable diversity of the T cell receptor repertoire, resulting in many diverse private TcRs contributing to the T cell response even in genetically identical mice responding to the same antigen. Finally, specific motifs defined by short sequences of amino acids within the CDR3 region may have a major effect on TcR specificity. The results of this study provide new insights into the properties of the CD4+ adaptive T cell response.

Immunology↗