Functional interplay between histone H1 and HMG proteins in chromatin

Postnikov, Yuri V.; Bustin, Michael

doi:10.1016/j.bbagrm.2015.10.006

Cited by 62 publications

(62 citation statements)

References 83 publications

(120 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…[63][64] Our findings indicate that HMGN1 can also bind directly to K120 of H2B, and HMGN2 can bind directly to K206 of H1.2 in the context of native chromatin in situ, which may provide the sought-after mechanism to explain its structural effects on 20 chromatin configuration directly. [65][66] Likewise, we observed new protein-protein interactions involving ADARB1 with histone H2B, and centriolin/CNTRL with histone H3. This suggests that these two proteins may have unanticipated functions on DNA and/or chromatin.…”

Section: Analysis Of the Cross-linked Chromatin Fraction Identified 1mentioning

confidence: 64%

Optimized cross-linking mass spectrometry for in situ interaction proteomics

Ser¹,

Cifani²,

Kentsis³

2018

Preprint

View full text Add to dashboard Cite

Recent development of mass spectrometer cleavable protein cross-linkers and algorithms for their spectral identification now permits large-scale cross-linking mass spectrometry (XL-MS).Here, we optimized the use of cleavable disuccinimidyl sulfoxide (DSSO) cross-linker for labeling native protein complexes in live human cells. We applied a generalized linear mixture model to calibrate cross-link peptide-spectra matching (CSM) scores to control the sensitivity and specificity of large-scale XL-MS. Using specific CSM score thresholds to control the false discovery rate, we found that higher-energy collisional dissociation (HCD) and electron transfer dissociation (ETD) can both be effective for large-scale XL-MS protein interaction mapping. We found that the density and coverage of protein-protein interaction maps can be significantly improved through the use of multiple proteases. In addition, the use of sample-specific search databases can be used to improve the specificity of cross-linked peptide spectral matching.Application of this approach to human chromatin labeled in live cells recapitulated known and revealed new protein interactions of nucleosomes and other chromatin-associated complexes in situ. This optimized approach for mapping native protein interactions should be useful for a wide range of biological problems. 5 Experimental Section Reagents. Disuccinimidyl sulfoxide (DSSO), formic acid, dimethyl sulfoxide (DMSO), and LC-MS grade solvents were obtained from Thermo Scientific. Bovine serum albumin (BSA), (4-(2hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), sodium chloride, magnesium chloride, potassium chloride, sucrose, ethylenediaminetetraacetic acid (EDTA), dithiothreitol, guanidinium hydrochloride, Staphylococcus aureus micrococcal nuclease, iodoacetamide, ammonium bicarbonate and formic acid were obtained from Millipore Sigma. Protease inhibitors 4-(2-aminoethyl)-benzenesulfonyl fluoride hydrochloride (AEBSF) and pepstatin were obtatined from Santa Cruz, bestatin from Alfa Aesar and leupeptin from EMD Millipore. Trypsin and GluC proteases were obtained from Promega. Chymotrypsin protease was obtained from Pierce Thermo. LysC was obtained from Wako Pure Chemical Industries.Cell culture and protein isolation. HEK293T cells were cultured in DMEM supplemented with 10% (v/v) fetal bovine serum, penicillin and streptomycin. HEK293T cells (50 million) were sedimented by centrifugation at 500 g and lysed in 500 µl 6M guanidine hydrochloride in 100 mM ammonium bicarbonate buffer, pH 8. The lysate was sonicated (E210 adaptive focused acoustic sonicator, Covaris) for 5 minutes at 4°C and homogenized by passing through a 27G needle. The lysate was then clarified by centrifugation at 18,000 g for 10 min at 4°C. Protein concentration of clarified lysates was determined using the bicinchoninic acid (BCA) assay, according to manufacturer's instructions (Thermo Scientific).Preparation of cross-linked bovine serum albumin and peptide purification. 50 µg of BSA was solubilized in 50 µl HEPES buffer (20 mM HE...

show abstract

Section: Analysis Of the Cross-linked Chromatin Fraction Identified 1mentioning

confidence: 64%

Optimized cross-linking mass spectrometry for in situ interaction proteomics

Ser¹,

Cifani²,

Kentsis³

2018

Preprint

View full text Add to dashboard Cite

show abstract

“…They have been considered to be the functional homologues of histones in bacteria. The interactions between the DNA architectural proteins are central to eukaryotic chromatin dynamics and therefore gene expression (Smerdon and Isenberg, 1976;Yu and Spring, 1977;Kohlstaedt and Cole, 1994;Trieschmann et al, 1998;Cato et al, 2008;Fonin et al, 2010;Vogler et al, 2010;Watson et al, 2014;Postnikov and Bustin, 2016). Such interactions, if any exist in bacteria, have not been addressed previously.…”

Section: Discussionmentioning

confidence: 99%

“…Like histones, the NAPs not only condense the chromosome, but they also play a key role in global transcription regulation (Dillon and Dorman, 2010;Browning et al, 2010). While histones are known to interact with each other to form nucleosomes and with non-histone proteins to fine-tune chromatin structure and gene expression (Smerdon and Isenberg, 1976;Yu and Spring, 1977;Kohlstaedt and Cole, 1994;Trieschmann et al, 1998;Cato et al, 2008;Fonin et al, 2010;Vogler et al, 2010;Watson et al, 2014;Postnikov and Bustin, 2016), interactions between bacterial NAPs has not been reported. In the present study, we looked for possible interactions between NAPs, with particular focus on HU.…”

Section: Introductionmentioning

confidence: 99%

Physical and functional interaction between nucleoid‐associated proteins HU and Lsr2 of Mycobacterium tuberculosis: altered DNA binding and gene regulation

Datta¹,

Jha²,

Ahmed³

et al. 2019

Molecular Microbiology

View full text Add to dashboard Cite

Summary Nucleoid‐associated proteins (NAPs) in bacteria contribute to key activities such as DNA compaction, chromosome organization and regulation of gene expression. HU and Lsr2 are two principal NAPs in Mycobacterium tuberculosis (Mtb). HU is essential for Mtb survival and is one of the most abundant NAPs. It differs from other eubacterial HU proteins in having a long, flexible lysine‐ and arginine‐rich carboxy‐terminal domain. Lsr2 of Mtb is the functional analogue of the bacterial NAP commonly called H‐NS. Lsr2 binds to and regulates expression of A/T‐rich portions of the otherwise G/C‐rich mycobacterial chromosome. Here, we demonstrate that HU and Lsr2 interact to form a complex. The interaction occurs primarily through the flexible carboxy‐terminal domain of HU and the acidic amino‐terminal domain of Lsr2. The resulting complex, upon binding to DNA, forms thick nucleoprotein rods, in contrast to the DNA bridging seen with Lsr2 and the DNA compaction seen with HU. Furthermore, transcription assays indicate that the HU‐Lsr2 complex is a regulator of gene expression. This physical and functional interaction between two NAPs, which has not been reported previously, is likely to be important for DNA organization and gene expression in Mtb and perhaps other bacterial species.

show abstract

“…A variation of the template obstruction model — involving competitive binding — was postulated for the interplay between linker histones and high-mobility group (HMG) proteins 125 , highly abundant, ubiquitous chromatin components that affect chromatin condensation and enhance DNA access for regulatory factors. Each distinct HMG family member associates with a separate set of chromatin binding sites, and it was proposed that H1 is able to compete with all of the HMG proteins, thereby regulating global chromosome organization (FIG.…”

Section: Molecular Mechanisms Of Actionmentioning

confidence: 99%

Emerging roles of linker histones in regulating chromatin structure and function

Fyodorov

Zhou

Skoultchi

et al. 2017

Nat Rev Mol Cell Biol

395

383

View full text Add to dashboard Cite

Together with core histones, which make up the nucleosome, the linker histone (H1) is one of the five main histone protein families present in chromatin in eukaryotic cells. H1 binds to the nucleosome to form the next structural unit of metazoan chromatin, the chromatosome, which may help chromatin to fold into higher-order structures. Despite their important roles in regulating the structure and function of chromatin, linker histones have not been studied as extensively as core histones. Nevertheless, substantial progress has been made recently. The first near-atomic resolution crystal structure of a chromatosome core particle and an 11 Å resolution cryo-electron microscopy-derived structure of the 30 nm nucleosome array have been determined, revealing unprecedented details about how linker histones interact with the nucleosome and organize higher-order chromatin structures. Moreover, several new functions of linker histones have been discovered, including their roles in epigenetic regulation and the regulation of DNA replication, DNA repair and genome stability. Studies of the molecular mechanisms of H1 action in these processes suggest a new paradigm for linker histone function beyond its architectural roles in chromatin.

show abstract

Functional interplay between histone H1 and HMG proteins in chromatin

Cited by 62 publications

References 83 publications

Optimized cross-linking mass spectrometry for in situ interaction proteomics

Optimized cross-linking mass spectrometry for in situ interaction proteomics

Physical and functional interaction between nucleoid‐associated proteins HU and Lsr2 of Mycobacterium tuberculosis: altered DNA binding and gene regulation

Emerging roles of linker histones in regulating chromatin structure and function

Contact Info

Product

Resources

About