ATP-dependent Chromatin Remodeling Factors Research Articles

Genetic Identification of a Network of Factors that Functionally Interact with the Nucleosome Remodeling ATPase ISWI

Nucleosome remodeling and covalent modifications of histones play fundamental roles in chromatin structure and function. However, much remains to be learned about how the action of ATP-dependent chromatin remodeling factors and histone-modifying enzymes is coordinated to modulate chromatin organization and transcription. The evolutionarily conserved ATP-dependent chromatin-remodeling factor ISWI plays essential roles in chromosome organization, DNA replication, and transcription regulation. To gain insight into regulation and mechanism of action of ISWI, we conducted an unbiased genetic screen to identify factors with which it interacts in vivo. We found that ISWI interacts with a network of factors that escaped detection in previous biochemical analyses, including the Sin3A gene. The Sin3A protein and the histone deacetylase Rpd3 are part of a conserved histone deacetylase complex involved in transcriptional repression. ISWI and the Sin3A/Rpd3 complex co-localize at specific chromosome domains. Loss of ISWI activity causes a reduction in the binding of the Sin3A/Rpd3 complex to chromatin. Biochemical analysis showed that the ISWI physically interacts with the histone deacetylase activity of the Sin3A/Rpd3 complex. Consistent with these findings, the acetylation of histone H4 is altered when ISWI activity is perturbed in vivo. These findings suggest that ISWI associates with the Sin3A/Rpd3 complex to support its function in vivo.

The Chromatin Remodelling Factor dATRX Is Involved in Heterochromatin Formation

Despite extensive study of heterochromatin, relatively little is known about the mechanisms by which such a structure forms. We show that the Drosophila homologue of the human α-thalassemia and mental retardation X-linked protein (dATRX), is important in the formation or maintenance of heterochromatin through modification of position effect variegation. We further show that there are two isoforms of the dATRX protein, the longer of which interacts directly with heterochromatin protein 1 (dHP-1) through a CxVxL motif both in vitro and in vivo. These two proteins co-localise at heterochromatin in a manner dependent on this motif. Consistent with this observation, the long isoform of the dATRX protein localises primarily to the heterochromatin at the chromocentre on salivary gland polytene chromosomes, whereas the short isoform binds to many sites along the chromosome arms. We suggest that the establishment of a regular nucleosomal organisation may be common to heterochromatin and transcriptionally repressed chromatin in other locations, and may require the action of ATP dependent chromatin remodelling factors.

ATP-dependent Chromatin Remodeling Factors Regulate Nuclear and Epigenetic Maturation of Bovine Oocytes.

Chromatin remodeling involves in dynamic transition of chromatin structure and includes alterations for the DNA methylation, histone modification, histone composition and chromatin conformation through the action of ATP-dependent chromatin remodeling enzymes. During oocyte maturation, transition of chromatin to chromosome occurs via a series of processes including germinal vesicle (GV), germinal vesicle breakdown (GVBD), metaphase I and metaphase II. However, dynamics of chromatin remodeling factors in the progress is unclear. This study was performed to understand how ATP-dependent chromatin remodeling factors (ACRFs) act during the oocyte maturation. To inhibit the activity of ACRFs, oocytes were first treated with 20 U/ml apyrase, an enzyme for ATP hydrolysis. Oocytes that were obtained at 1 h, 9 h, 24 h and 36 h after maturation, respectively, were immunostained with various antibodies specific for ACRFs and epigenetic markers such as Brg-1, BAF-170, Mi-2, hSNF2H, 5-MeC, AcH3K9, AcH4K5, mono-, di- and tri-methyl H3K9. After apyrase treatment, the localization and the distribution of ACRFs such as Brg-1, BAF-170, Mi-2 and hSNF2H showed normal patterns in chromatin or metaphase chromosomes of maturing oocytes, but the timing of their chromatin remodeling was retarded. In contrast to normal oocytes, Mi-2 didn't disappear at 1 h after maturation in the nucleus of apyrase-treated oocytes. These results demonstrate that suppression of the activity of ACRFs give rise to delayed chromatin remodeling in the nuclear maturation. The distribution patterns of epigenetic markers, including DNA methylation of 5-MeC, histone acetylation of H3K9 and H4K5, and histone mono-, di-, tri-methylation of H3K9, were temporally consistent with the timing of chromatin remodeling in apyrase-treated oocytes. Thus, nuclear maturation of bovine oocytes was delayed by inhibition of ACRFs. Developmental competence of apyrase-treated oocytes fertilized in vitro was significantly decreased compared with that of normal oocytes. Our findings suggest that ACRFs control timely nuclear maturation by chromatin remodeling, thereby leading to oocyte maturation and early embryonic development.

ATP-dependent Chromatin Remodeling Enzymes and their Various Roles in Cell Cycle Control

The modification of chromatin structure by various mechanisms has emerged as a key regulatory component of nuclear programs. Cell cycle progression and exit are affected by the integrity of chromatin architecture as well as by regulatory cues that chromatin structure imposes on the expression of cell cycle genes. ATP-dependent chromatin remodeling factors use the energy derived from ATP-hydrolysis to modulate histone-DNA contacts. These molecular machines play important roles in all aspects of chromosome biology and are thus intimately linked to cell cycle control. Regulation of complex activity by various signaling pathways has been a rising theme in recent years. Moreover, some chromatin remodeling factors have been characterized as potent tumor suppressor proteins. Thus, to understand the functions and activities of ATP-utilizing chromatin remodeling factors is an important goal towards their use as potential targets in cancer therapy.

Distinct Chromatin Modulators Regulate the Formation of Accessible and Repressive Chromatin at the Fission Yeast Recombination Hotspotade6-M26

Histone acetyltransferases (HATs) and ATP-dependent chromatin remodeling factors (ADCRs) regulate transcription and recombination via alteration of local chromatin configuration. The ade6-M26 allele of Schizosaccharomyces pombe creates a meiotic recombination hotspot that requires a cAMP-responsive element (CRE)-like sequence M26, the Atf1/Pcr1 heterodimeric ATF/CREB transcription factor, the Gcn5 HAT, and the Snf22 SWI2/SNF2 family ADCR. Chromatin alteration occurs meiotically around M26, leading to the activation of meiotic recombination. We newly report the roles of other chromatin remodeling factors that function positively and negatively in chromatin alteration at M26: two CHD-1 family ADCRs (Hrp1 and Hrp3), a Spt-Ada-Gcn5 acetyltransferase component (Ada2), and a member of Moz-Ybf2/Sas3-Sas2-Tip60 family (Mst2). Ada2, Mst2, and Hrp3 are required for the full activation of chromatin changes around M26 and meiotic recombination. Acetylation of histone H3 around M26 is remarkably reduced in gcn5Delta, ada2Delta and snf22Delta, suggesting cooperative functions of these HAT complexes and Snf22. Conversely, Hrp1, another CHD-1 family ADCR, maintains repressive chromatin configuration at ade6-M26. Interestingly, transcriptional initiation site is shifted to a site around M26 from the original initiation sites, in couple with the histone acetylation and meiotic chromatin alteration induced around 3' region of M26, suggesting a collaboration between these chromatin modulators and the transcriptional machinery to form accessible chromatin. These HATs and ADCRs are also required for the regulation of transcription and chromatin structure around M26 in response to osmotic stress. Thus, we propose that multiple chromatin modulators regulate chromatin structure reversibly and participate in the regulation of both meiotic recombination and stress-induced transcription around CRE-like sequences.

ISWI Regulates Higher-Order Chromatin Structure and Histone H1 Assembly In Vivo

Imitation SWI (ISWI) and other ATP-dependent chromatin-remodeling factors play key roles in transcription and other processes by altering the structure and positioning of nucleosomes. Recent studies have also implicated ISWI in the regulation of higher-order chromatin structure, but its role in this process remains poorly understood. To clarify the role of ISWI in vivo, we examined defects in chromosome structure and gene expression resulting from the loss of Iswi function in Drosophila. Consistent with a broad role in transcriptional regulation, the expression of a large number of genes is altered in Iswi mutant larvae. The expression of a dominant-negative form of ISWI leads to dramatic alterations in higher-order chromatin structure, including the apparent decondensation of both mitotic and polytene chromosomes. The loss of ISWI function does not cause obvious defects in nucleosome assembly, but results in a significant reduction in the level of histone H1 associated with chromatin in vivo. These findings suggest that ISWI plays a global role in chromatin compaction in vivo by promoting the association of the linker histone H1 with chromatin.

RSC Functions as an Early Double-Strand-Break Sensor in the Cell's Response to DNA Damage

The detection of a DNA double-strand break (DSB) is necessary to initiate DSB repair. Several proteins, including the MRX/N complex, Tel1/ATM (ataxia telangiectasia mutated), and Mec1/ATR (ATM and Rad3 related), have been proposed as sensors of DNA damage, yet how they recognize the breaks is poorly understood. DSBs occur in the context of chromatin, implicating factors capable of altering local and/or global chromatin structure in the cellular response to DNA damage, including DSB sensing. Emerging evidence indicates that ATP-dependent chromatin-remodeling complexes function in DNA repair. Here we describe an important and novel early role for the RSC ATP-dependent chromatin remodeler linked to DSB sensing in the cell's DNA-damage response. RSC is required for full levels of H2A phosphorylation because it facilitates the recruitment of Tel1/ATM and Mec1/ATR to the break site. Consistent with these results, we also show that Rsc2 is needed for efficient activation of the Rad53-dependent checkpoint, as well as for Cohesin's association with the break site. Finally, Rsc2 is needed for the DNA-damage-induced changes in nucleosome structure surrounding the DSB site. Together, these new findings functionally link RSC to DSB sensing, highlighting the importance of ATP-dependent chromatin-remodeling factors in the cell's early response to DNA damage.

Brg1 chromatin remodeling factor is involved in cell growth arrest, apoptosis and senescence of rat mesenchymal stem cells

Self-renewal, proliferation and differentiation properties of stem cells are controlled by key transcription factors. However, their activity is modulated by chromatin remodeling factors that operate at the highest hierarchical level. Studies on these factors can be especially important to dissect molecular pathways governing the biology of stem cells. SWI/SNF complexes are adenosine triphosphate (ATP)-dependent chromatin remodeling enzymes that have been shown to be required for cell cycle control, apoptosis and cell differentiation in several biological systems. The aim of our research was to investigate the role of these complexes in the biology of mesenchymal stem cells (MSCs). To this end, in MSCs we caused a forced expression of the ATPase subunit of SWI/SNF (Brg1 - also known as Smarca4) by adenoviral transduction. Forced Brg1 expression induced a significant cell cycle arrest of MSCs in culture. This was associated with a huge increase in apoptosis that reached a peak 3 days after transduction. In addition, we observed signs of senescence in cells having ectopic Brg1 expression. At the molecular level these phenomena were associated with activation of Rb- and p53-related pathways. Inhibition of either p53 or Rb with E1A mutated proteins allowed us to hypothesize that both Rb and p53 are indispensable for Brg1-induced senescence, whereas only p53 seems to play a role in triggering programmed cell death. We also looked at the effects of forced Brg1 expression on canonical MSC differentiation in adipocytes, chondrocytes and osteocytes. Brg1 did not induce cell differentiation per se; however, this protein could contribute, at least in part, to the adipocyte differentiation process. In conclusion, our results suggest that whereas some ATP-dependent chromatin remodeling factors, such as ISWI complexes, promote stem cell self-renewal and conservation of an uncommitted state, others cause an escape from 'stemness' and induction of differentiation along with senescence and cell death phenomena.

Isolation of a novel complex of the SWI/SNF family from Schizosaccharomyces pombe and its effects on in vitro transcription in nucleosome arrays

The family of ATP-dependent chromatin-remodeling factors plays a central role in eukaryotic transcriptional regulation. These complexes can alter the structure of chromatin by mechanisms that involve nucleosome sliding, dissociation, or replacement over a specific promoter. The SWI/SNF chromatin-remodeling complex is required for transcriptional activation or repression in a subset of genes. In the present study we have isolated the spSWI/SNF complex from Schizosaccharomyces pombe, which has at least seven subunits among them spSwi1-like and the catalytic subunit spBrg1. These subunits are homologues to Swi1 and Swi2/Snf2, respectively in Sacharomyces cerevisiae. Moreover, we have demonstrated that spSWI/SNF is able to promote in vitro transcription by RNA polymerase II (RNAPII) in a reconstituted system. In our transcription assays with cellular extracts of Sc. pombe we did not observe inhibition when alpha-Swi1 antibodies were utilized, indicating that other chromatin-remodeling complexes may allow transcription in Sc. pombe.

Molecular Implications of Evolutionary Differences in CHD Double Chromodomains

Double chromodomains occur in CHD proteins, which are ATP-dependent chromatin remodeling factors implicated in RNA polymerase II transcription regulation. Biochemical studies suggest important differences in the histone H3 tail binding of different CHD chromodomains. In human and Drosophila, CHD1 double chromodomains bind lysine 4-methylated histone H3 tail, which is a hallmark of transcriptionally active chromatin in all eukaryotes. Here, we present the crystal structure of the yeast CHD1 double chromodomains, and pinpoint their differences with that of the human CHD1 double chromodomains. The most conserved residues in these double chromodomains are the two chromoboxes that orient adjacently. Only a subset of CHD chromoboxes can form an aromatic cage for methyllysine binding, and methyllysine binding requires correctly oriented inserts. These factors preclude yeast CHD1 double chromodomains from interacting with the histone H3 tail. Despite great sequence similarity between the human CHD1 and CHD2 chromodomains, variation within an insert likely prevents CHD2 double chromodomains from binding lysine 4-methylated histone H3 tail as efficiently as in CHD1. By using the available structural and biochemical data we highlight the evolutionary specialization of CHD double chromodomains, and provide insights about their targeting capacities.

ATP-dependent chromatin remodeling factors and DNA damage repair

The organization of eukaryotic DNA into chromatin poses a barrier to all processes that require access of enzymes and regulatory factors to their sites of action. While the majority of studies in this area have concentrated on the role of chromatin in the regulation of transcription, there has been a recent emphasis on the relationship of chromatin to DNA damage repair. In this review, we focus on the role of chromatin in nucleotide excision repair (NER) and double-strand break (DSB) repair. NER and DSB repair use very different enzymatic machineries, and these two modes of DNA damage repair are also differentially affected by chromatin. Only a small number of nucleosomes are likely to be involved in NER, while a more extensive region of chromatin is involved in DSB repair. However, a key feature of both NER and DSB repair pathways is the participation of ATP-dependent chromatin remodeling factors at various points in the repair process. We discuss recent data that have identified roles for SWI/SNF-related chromatin remodeling factors in the two repair pathways.

The regulation of ATP-dependent nucleosome remodelling factors

The plasticity of chromatin is governed by multi-subunit protein complexes that enzymatically regulate chromosomal structure and activity. Such complexes include ATP-dependent chromatin remodelling factors that are involved in many fundamental processes such as transcription, DNA repair, replication and chromosome structure maintenance. Because ATP-dependent chromatin remodelling factors play important roles, it is not surprising to find that their functions are regulated in a plethora of ways, including post-translational modifications of their subunits and subunit composition changes. The activity of these enzymes is modulated by many factors, including linker histones, histone variants, histone chaperones, non-histone chromatin constituents such as HMG-proteins and secondary messengers, such as inositolpolyphosphates. Additionally, specific histone modifications and interaction with site-specific transcriptional regulators direct the targeting of these activities. Understanding the network of mechanisms that control ATP-dependent chromatin remodelling will constitute an important challenge towards our understanding of chromatin dynamics.

Structural Polymorphism of Chromodomains in Chd1

Chromodomain from heterochromatin protein 1 and polycomb protein is known to be a lysine-methylated histone H3 tail-binding module. Chromo-helicase/ATPase DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin remodeling factor, containing two tandem chromodomains. In human CHD1, both chromodomains are essential for specific binding to a K4 methylated histone H3 (H3 MeK4) peptide and are found to bind cooperatively in the crystal structure. For the budding yeast homologue, Chd1, the second but not the first chromodomain was once reported to bind to an H3 MeK4 peptide. Here, we reveal that neither the second chromodomain nor a region containing tandem chromodomains from yeast Chd1 bind to any lysine-methylated or arginine-methylated histone peptides that we examined. In addition, we examined the structures of the chromodomains from Chd1 by NMR. Although the tertiary structure of the region containing tandem chromodomains could not be obtained, the secondary structure deduced from NMR is well conserved in the tertiary structures of the corresponding first and second chromodomains determined individually by NMR. Both chromodomains of Chd1 demonstrate a structure similar to that of the corresponding part of CHD1, consisting of a three-stranded β-sheet followed by a C-terminal α-helix. However, an additional helix between the first and second β-strands, which is found in both of the first chromodomains of Chd1 and CHD1, is positioned in an entirely different manner in Chd1 and CHD1. In human CHD1 this helix forms the peptide-binding site. The amino acid sequences of the chromodomains could be well aligned on the basis of these structures. The alignment showed that yeast Chd1 lacks several key functional residues, which are responsible for specific binding to a methylated lysine residue in other chromodomains. Chd1 is likely to have no binding affinity for any H3 MeK peptide, as found in other chromodomain proteins.

The Histone Variant Macro-H2A Preferentially Forms “Hybrid Nucleosomes”

The histone domain of macro-H2A, which constitutes the N-terminal one third of this histone variant, is only 64% identical to major H2A. We have shown previously that the main structural differences in a nucleosome in which both H2A moieties have been replaced by macro-H2A reside in the only point of contact between the two histone dimers, the L1-L1 interface of macro-H2A. Here we show that the L1 loop of macro-H2A is responsible for the increased salt-dependent stability of the histone octamer, with implications for the nucleosome assembly pathway. It is unknown whether only one or both of the H2A-H2B dimers within a nucleosome are replaced with H2A variant containing nucleosomes in vivo. We demonstrate that macro-H2A preferentially forms hybrid nucleosomes containing one chain each of major H2A and macro-HA in vitro. The 2.9-A crystal structure of such a hybrid nucleosome shows significant structural differences in the L1-L1 interface when comparing with homotypic major H2A- and macro-H2A-containing nucleosomes. Both homotypic and hybrid macro-nucleosome core particles (NCPs) are resistant to chaperone-assisted H2A-H2B dimer exchange. Together, our findings suggest that the histone domain of macro-H2A modifies the dynamic properties of the nucleosome. We propose that the possibility of forming hybrid macro-NCP adds yet another level of complexity to variant nucleosome structure and function.

Molecular Genetic Analysis of an SNF2 / brahma -Related Gene in Tetrahymena thermophila Suggests Roles in Growth and Nuclear Development

We used a reverse genetic approach to identify three members of the SNF2 superfamily of chromatin remodeling genes in the ciliated protozoan Tetrahymena thermophila in order to investigate possible functions of ATP-dependent chromatin remodeling factors in growth and nuclear development. Comparative sequence analysis of the gene product of the Tetrahymena brahma-related gene (TtBRG1) indicates it is a member of the SNF2/BRM subgroup of the SNF2 superfamily. Northern analysis suggests that TtBRG1 has roles in growth and nuclear development in Tetrahymena. Indirect immunofluorescence analysis during nuclear development indicates that TtBrg1p localizes to both the parental and developing macronucleus of Tetrahymena during the time period corresponding to genome rearrangements. We generated germ line knockout heterokaryons for TtBRG1 and demonstrated that expression of the gene is required to complete nuclear development of Tetrahymena. In addition, the formation of distinct Pdd1p-containing structures is disturbed during the late stages of conjugation in TtBRG1 germ line knockout heterokaryons. We discuss these results in light of possible roles of SNF2-related proteins in growth and nuclear development of Tetrahymena.

Brg1 is required for murine neural stem cell maintenance and gliogenesis

Epigenetic alterations in cell-type-specific gene expression control the transition of neural stem cells (NSCs) from predominantly neurogenic to predominantly gliogenic phases of differentiation, but how this switch occurs is unclear. Here, we show that brahma-related gene 1 (Brg1), an ATP-dependent chromatin remodeling factor, is required for the repression of neuronal commitment and the maintenance of NSCs in a state that permits them to respond to gliogenic signals. Loss of Brg1 in NSCs in conditional brg1 mutant mice results in precocious neuronal differentiation, such that cells in the ventricular zone differentiate into post-mitotic neurons before the onset of gliogenesis. As a result, there is a dramatic failure of astrocyte and oligodendrocyte differentiation in these animals. The ablation of brg1 in gliogenic progenitors in vitro also prevents growth-factor-induced astrocyte differentiation. Furthermore, proteins implicated in the maintenance of stem cells, including Sox1, Pax6 and Musashi-1, are dramatically reduced in the ventricular zones of brg1 mutant mice. We conclude that Brg1 is required to repress neuronal differentiation in NSCs as a means of permitting glial cell differentiation in response to gliogenic signals, suggesting that Brg1 regulates the switch from neurogenesis to gliogenesis.

Forced Unraveling of Nucleosomes Assembled on Heterogeneous DNA Using Core Histones, NAP-1, and ACF

Periodic arrays of nucleosomes were assembled on heterogeneous DNA using core histones, the histone chaperone NAP-1, and ATP-dependent chromatin assembly and remodeling factor (ACF). The mechanical properties of these complexes were interrogated by stretching them with optical tweezers. Abrupt events releasing approximately 55-95 base-pairs of DNA, attributable to the non-equilibrium unraveling of individual nucleosomes, were frequently observed. This finding is comparable with a previous observation of 72-80 bp unraveling events for nucleosomes assembled by salt dialysis on a repeating sea urchin 5 S RNA positioning element, but the unraveling force varied over a wider range ( approximately 5-65 pN, with the majority of events at lower force). Because ACF assembles nucleosomes uniformly on heterogeneous DNA sequences, as in native chromatin, we attribute this variation to a dependence of the unraveling force on the DNA sequence within individual nucleosomes. The mean force increased from 24 pN to 31 pN as NaCl was decreased from 100 mM to 5 mM. Spontaneous DNA re-wrapping events were occasionally observed in real time during force relaxation. The observed wide variations in the dynamic force needed to unravel individual nucleosomes and the occurrences of sudden DNA re-wrapping events may have an important regulatory influence on DNA-directed nuclear processes, such as the binding of transcription factors and the movement of polymerase complexes on chromatin.

Linker histone variants control chromatin dynamics during early embryogenesis

Complex transitions in chromatin structure produce changes in genome function during development in metazoa. Linker histones, the last component of nucleosomes to be assembled into chromatin, comprise considerably divergent subtypes as compared with core histones. In all metazoa studied, their composition changes dramatically during early embryogenesis concomitant with zygotic gene activation, leading to distinct functional changes that are still poorly understood. Here, we show that early embryonic linker histone B4, which is maternally expressed, is functionally different from somatic histone H1 in influencing chromatin structure and dynamics. We developed a chromatin assembly system with nucleosome assembly protein-1 as a linker histone chaperone. This assay system revealed that maternal histone B4 allows chromatin to be remodeled by ATP-dependent chromatin remodeling factor, whereas somatic histone H1 prevents this remodeling. Structural analysis shows that histone B4 does not significantly restrict the accessibility of linker DNA. These findings define the functional significance of developmental changes in linker histone variants. We propose a model that holds that maternally expressed linker histones are key molecules specifying nuclear dynamics with respect to embryonic totipotency.

Cell cycle regulation of chromatin at an origin of DNA replication

Selection and licensing of mammalian DNA replication origins may be regulated by epigenetic changes in chromatin structure. The Epstein-Barr virus (EBV) origin of plasmid replication (OriP) uses the cellular licensing machinery to regulate replication during latent infection of human cells. We found that the minimal replicator sequence of OriP, referred to as the dyad symmetry (DS), is flanked by nucleosomes. These nucleosomes were subject to cell cycle-dependent chromatin remodeling and histone modifications. Restriction enzyme accessibility assay indicated that the DS-bounded nucleosomes were remodeled in late G1. Remarkably, histone H3 acetylation of DS-bounded nucleosomes decreased during late G1, coinciding with nucleosome remodeling and MCM3 loading, and preceding the onset of DNA replication. The ATP-dependent chromatin-remodeling factor SNF2h was also recruited to DS in late G1, and formed a stable complex with HDAC2 at DS. siRNA depletion of SNF2h reduced G1-specific nucleosome remodeling, histone deacetylation, and MCM3 loading at DS. We conclude that an SNF2h-HDAC1/2 complex coordinates G1-specific chromatin remodeling and histone deacetylation with the DNA replication initiation process at OriP.

TheDrosophilatrithorax group protein Kismet facilitates an early step in transcriptional elongation by RNA Polymerase II

The Drosophila trithorax group gene kismet (kis) was identified in a screen for extragenic suppressors of Polycomb (Pc) and subsequently shown to play important roles in both segmentation and the determination of body segment identities. One of the two major proteins encoded by kis (KIS-L) is related to members of the SWI2/SNF2 and CHD families of ATP-dependent chromatin-remodeling factors. To clarify the role of KIS-L in gene expression, we examined its distribution on larval salivary gland polytene chromosomes. KIS-L is associated with virtually all sites of transcriptionally active chromatin in a pattern that largely overlaps that of RNA Polymerase II (Pol II). The levels of elongating Pol II and the elongation factors SPT6 and CHD1 are dramatically reduced on polytene chromosomes from kis mutant larvae. By contrast, the loss of KIS-L function does not affect the binding of PC to chromatin or the recruitment of Pol II to promoters. These data suggest that KIS-L facilitates an early step in transcriptional elongation by Pol II.